The biochemical origin of pentenol emissions from wounded leaves

Large releases of 1-penten-3-ol (pentenol) and 1-penten-3-one (pentenone) were recently observed from a variety of leaves subjected to freeze-thaw damage in the presence of oxygen. In order to understand the biochemical origins of these volatiles, soybean leaf extracts were used to determine if the formation of pentenol and pentenone can be explained by known O(2)-dependent lipoxygenase (LOX) reactions. Enzymatic formation of these C5 volatiles was found to be dependent on alpha-linolenic acid or the 13(S)-hydroperoxide of alpha-linolenic acid [13(S)-HPOT] and blocked by LOX inhibitors. Five soybean leaf LOX isozyme genes (VLXA, VLXB, VLXC, VLXD, and VLXE) were then expressed in Escherichia coli and used in in vitro incubations with 13(S)-HPOT to test for volatile formation. Each of the LOX isozymes catalyzed the formation of low levels of pentenol, but not pentenone. It therefore seems likely that the C5,13-cleavage activity of LOX is the direct source of abundant pentenol and the indirect source of pentenone observed upon leaf wounding.     

The disappearance of dry matter,nitrogen and amino acids in the gastrointestinal tract from Calliandra leaves

The total tract disappearance of dry matter (DM), nitrogen and amino acids in different Calliandra leaves harvested from Kenya and Zimbabwe were measured using the mobile bag technique. In the mobile bag measurements, disappearance was measured in the rumen in sacco, by pepsin–HCl hydrolysis in vitro and in the intestine. The hydrolysis in the pepsin–HCl solution was designed to mimic digestion in the abomasum. The total tract disappearance of DM, nitrogen, and amino acids were generally low. The highest total apparent DM, nitrogen and total amino acid disappearance obtained were 425 (g/kg), 458 (g/kg total nitrogen), and 593 (g/kg amino acid), respectively. There were differences between the leaves in the disappearance of DM, nitrogen and amino acids, and in the proportion of nutrients lost in the rumen, after pepsin–HCl hydrolysis and in the intestine. More DM, nitrogen, and amino acids in the leaves from Kenya disappeared in the intestine in comparison to the disappearance in leaves from Zimbabwe. The reasons for the differences between the nutritive values of the leaves is unclear but appears to be strongly influenced by the stage of growth and conditions in which the plants were grown.     

CD247 can bind SHC1, no matter if CD247 is phosphorylated

On T cell receptor (TCR) stimulation, src homology 2 domain‐containing transforming protein C1 (SHC1) had been found to bind the tyrosine‐phosphorylated CD247 chain of the receptor via its src homology 2 (SH2) domain, delivering signals that control T cell development and activation. However, how the phosphorylation of CD247 led to the instant binding has not been characterized clearly. To study the binding process in detail, we simulated and compared the interaction processes of the SH2 domain with CD247 and phosphorylated CD247, respectively. Unexpectedly, the simulation revealed that SHC1 can also bind the nonphosphorylated CD247 peptide, which was further validated to be a weak binding by affinity pull‐down experiment. The molecular dynamics (MD) simulation also revealed that the CD247 peptide formed a folding conformation with its Leu209 inserted into the hydrophobic binding pocket in SHC1. And on phosphorylation, it was the electrostatic attraction between the CD247 Tyr(P)206 and the SHC1 Tyr(P)‐binding pocket that destroyed the folding conformation of the nonphosphorylated CD247 and, aided by the electrostatic attraction between SHC1 and the Asp203 of CD247, led to the extended conformation of the phosphorylated CD247 binding to SHC1 strongly. The results suggest that nonphosphorylated CD247 can recruit SHC1 in advance to prepare for the instant needs for SHC1 on TCR stimulation. In view of the ubiquity of phosphorylation in protein interaction regulation, we think this study also exemplified the usefulness of MD in more interactome research involving phosphorylation. Copyright © 2009 John Wiley & Sons, Ltd.     

Selection for complex traits leaves little or no classic signatures of selection

Background

Selection signatures aim to identify genomic regions underlying recent adaptations in populations. However, the effects of selection in the genome are difficult to distinguish from random processes, such as genetic drift. Often associations between selection signatures and selected variants for complex traits is assumed even though this is rarely (if ever) tested. In this paper, we use 8 breeds of domestic cattle under strong artificial selection to investigate if selection signatures are co-located in genomic regions which are likely to be under selection.

Results

Our approaches to identify selection signatures (haplotype heterozygosity, integrated haplotype score and F_ST) identified strong and recent selection near many loci with mutations affecting simple traits under strong selection, such as coat colour. However, there was little evidence for a genome-wide association between strong selection signatures and regions affecting complex traits under selection, such as milk yield in dairy cattle. Even identifying selection signatures near some major loci was hindered by factors including allelic heterogeneity, selection for ancestral alleles and interactions with nearby selected loci.

Conclusions

Selection signatures detect loci with large effects under strong selection. However, the methodology is often assumed to also detect loci affecting complex traits where the selection pressure at an individual locus is weak. We present empirical evidence to suggests little discernible ‘selection signature’ for complex traits in the genome of dairy cattle despite very strong and recent artificial selection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-246) contains supplementary material, which is available to authorized users.     

Urea hydrogen peroxide reduces the numbers of lactobacilli, nourishes yeast, and leaves no residues in the ethanol fermentation

Urea hydrogen peroxide (UHP) at a concentration of 30 to 32 mmol/liter reduced the numbers of five Lactobacillus spp. (Lactobacillus plantarum, L. paracasei, Lactobacillus sp. strain 3, L. rhamnosus, and L. fermentum) from approximately 10(7) to approximately 10(2) CFU/ml in a 2-h preincubation at 30 degrees C of normal-gravity wheat mash at approximately 21 g of dissolved solids per ml containing normal levels of suspended grain particles. Fermentation was completed 36 h after inoculation of Saccharomyces cerevisiae in the presence of UHP, even when wheat mash was deliberately contaminated (infected) with L. paracasei at approximately 10(7) CFU/ml. There were no significant differences in the maximum ethanol produced between treatments when urea hydrogen peroxide was used to kill the bacteria and controls (in which no bacteria were added). However, the presence of L. paracasei at approximately 10(7) CFU/ml without added agent resulted in a 5.84% reduction in the maximum ethanol produced compared to the control. The bactericidal activity of UHP is greatly affected by the presence of particulate matter. In fact, only 2 mmol of urea hydrogen peroxide per liter was required for disinfection when mashes had little or no particulate matter present. No significant differences were observed in the decomposition of hydrogen peroxide in normal-gravity wheat mash at 30 degrees C whether the bactericidal agent was added as H(2)O(2) or as urea hydrogen peroxide. NADH peroxidase activity (involved in degrading H(2)O(2)) increased significantly (P = 0.05) in the presence of 0.75 mM hydrogen peroxide (sublethal level) in all five strains of lactobacilli tested but did not persist in cells regrown in the absence of H(2)O(2). H(2)O(2)-resistant mutants were not expected or found when lethal levels of H(2)O(2) or UHP were used. Contaminating lactobacilli can be effectively managed by UHP, a compound which when used at ca. 30 mmol/liter happens to provide near-optimum levels of assimilable nitrogen and oxygen that aid in vigorous fermentation performance by yeast.     

Dry matter,energy and nitrogen conversion by Lepidoptera and Hymenoptera larvae fed leaves of black cherry

Summary Dry matter, energy and nitrogen budgets of the form: ingestion=growth+feces+respiration, were determined for larvae of 34 species of Hymenoptera and Lepidoptera collected from and fed leaves of black cherry (Prunus serotina). The mean growth efficiencies based on energy were: gross (100 growth/ingestion)= 17±4, and net (100 growth/(ingestion-feces))=44±8. The mean nitrogen conversion efficiency was 42±10%. Correlation analysis of the relationships among larval factors (larval nitrogen content, energy equivalents, and size), leaf factors (leaf nitrogen, energy, and water content) and larval growth rates or growth efficiencies suggest that the species are temporally adapted, compensating for the limiting effects of decreasing nitrogen and leaf water as leaves mature.     

When no catches matter: Coping with zeros in environmental assessments

The environmental legislation of many countries increasingly requires the continuous monitoring of fish assemblages to evaluate the success of river and stream restorations. Predicting species–environment relationships on the basis of monitoring data is central in the evaluation of ecological integrity and planning of rehabilitation strategies. Monitoring data are, however, often plagued by a substantial proportion of zeros (no catch at single sampling points) which are caused by relevant ecological processes, but complicate the use of commonly used statistical methods. This study compares mere count regression models, mixture and hurdle models based on Poisson and negative binomial distribution and logistic regressions with respect to their ability to cope with large zero-inflated data sets obtained by point abundance sampling of young-of-the-year fish from three large German rivers. Only mixture and hurdle models based on negative binomial distribution could satisfactorily be fitted to the zero-inflated and overdispersed count data. The logistic regression models applied to transliterated catch data simplified the computational procedure and yielded qualitative similar results to the count regression models indicating that the use of more complex count data did not generally provide better predictions. Therefore, presence/absence sampling may be a suitable and less costly alternative to abundance surveys for identifying environmental factors which affect the spatial distribution of fish populations at least if information on subtly abundance fluctuations is not needed. Mixture or hurdle models are particularly worth the additional effort if it is reasonable to distinguish between those environmental factors influencing the occurrence probability and others affecting the abundance. All models showed low sensitivity to rare guilds pointing to the need for a further development of statistical models for rare species whose management is a matter of growing environmental concern.     

Intracellular distribution and origin of sterols in Calendula officinalis leaves

In Calendula officinalis leaves 66% of all steryl forms are present in the ‘microsomal fraction’ (IV), 24% in the mitochondrial and Golgi membranes (III), 5% in the ‘chloroplast’ (II), 4% in the ‘cell wall and membrane’ (I) fraction and 1%. in the cytosol. Free sterols, their esters, glycosides and acylated glycosides are present in varying proportions in all cellular subtractions. Mevalonate-[2¹⁴C] labelling of sterols derived from various steryl forms showed that free sterols and all their derivatives, i.e. steryl esters and glucosides, are formed in fraction IV and are then translocated to other organelles. Fraction III is the main site of glycosylation of transported sterols as well as of acylation of steryl glycosides.     

(18)O spatial patterns of vein xylem water,leaf water,and dry matter in cotton leaves

Three leaf water models (two-pool model, Péclet effect, and string-of-lakes) were assessed for their robustness in predicting leaf water enrichment and its spatial heterogeneity. This was achieved by studying the (18)O spatial patterns of vein xylem water, leaf water, and dry matter in cotton (Gossypium hirsutum) leaves grown at different humidities using new experimental approaches. Vein xylem water was collected from intact transpiring cotton leaves by pressurizing the roots in a pressure chamber, whereas the isotopic content of leaf water was determined without extracting it from fresh leaves with the aid of a purpose-designed leaf punch. Our results indicate that veins have a significant degree of lateral exchange with highly enriched leaf water. Vein xylem water is thus slightly, but progressively enriched in the direction of water flow. Leaf water enrichment is dependent on the relative distances from major veins, with water from the marginal and intercostal regions more enriched and that next to veins and near the leaf base more depleted than the Craig-Gordon modeled enrichment of water at the sites of evaporation. The spatial pattern of leaf water enrichment varies with humidity, as expected from the string-of-lakes model. This pattern is also reflected in leaf dry matter. All three models are realistic, but none could fully account for all of the facets of leaf water enrichment. Our findings acknowledge the presence of capacitance in the ground tissues of vein ribs and highlight the essential need to incorporate Péclet effects into the string-of-lakes model when applying it to leaves.