Stochastic Frontier Analysis of Biological Agents (Microbial Inoculants) Input Usage in Apple Production

In this paper, we analyze the impact of the Microbial Inoculants (MI) Technology on apple yields and pesticide application using 2007 farm data. The results show that pesticide usage is not reduced by MI applications. However, there is a significant positive effect on the yields. Apple production efficiency is 37%.Microbial Inoculants, apple production, frontier analysis, damage control, Farm Management, Production Economics, Research and Development/Tech Change/Emerging Technologies, Risk and Uncertainty,

Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell.

A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains. Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell. Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell

Plant-Microbes Interactions in Enhanced Fertilizer-Use Efficiency

The continued use of chemical fertilizers and manures for enhanced soil fertility and crop productivity often results in unexpected harmful environmental effects, including leaching of nitrate into groundwater, surface runoff of phosphorus and nitrogen runoff, and eutrophication of aquatic ecosystems. Integrated nutrient management systems are needed to maintain agricultural productivity and protect the environment. Microbial inoculants are promising components of such management systems. This review is a critical summary of the efforts in using microbial inoculants, including plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi for increasing the use efficiency of fertilizers. Studies with microbial inoculants and nutrients have demonstrated that some inoculants can improve plant uptake of nutrients and thereby increase the use efficiency of applied chemical fertilizers and manures. These proofs of concept studies will serve as the basis for vigorous future research into integrated nutrient management in agriculture

Drawing explicit phylogenetic networks and their integration into SplitsTree

<p>Abstract</p> <p>Background</p> <p>SplitsTree provides a framework for the calculation of phylogenetic trees and networks. It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface.</p> <p>Results</p> <p>In this article, we present solutions to two important problems in the field of phylogenetic networks. The first problem is the visualization of explicit phylogenetic networks. To solve this, we present a modified version of the equal angle algorithm that naturally integrates reticulations into the layout process and thus leads to an appealing visualization of these networks. The second problem is the availability of explicit phylogenetic network methods for the general user. To advance the usage of explicit phylogenetic networks by biologists further, we present an extension to the SplitsTree framework that integrates these networks. By addressing these two problems, SplitsTree is among the first programs that incorporates <it>implicit </it>and <it>explicit </it>network methods together with standard phylogenetic tree methods in a graphical user interface environment.</p> <p>Conclusion</p> <p>In this article, we presented an extension of SplitsTree 4 that incorporates explicit phylogenetic networks. The extension provides a set of core classes to handle explicit phylogenetic networks and a visualization of these networks.</p

Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi

<p>Abstract</p> <p>Background</p> <p>In eukaryotic cells, directional transport between different compartments of the endomembrane system is mediated by vesicles that bud from a donor organelle and then fuse with an acceptor organelle. A family of integral membrane proteins, termed soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins, constitute the key machineries of these different membrane fusion events. Over the past 30 years, the yeast <it>Saccharomyces cerevisiae </it>has served as a powerful model organism for studying the organization of the secretory and endocytic pathways, and a few years ago, its entire set of SNAREs was compiled.</p> <p>Results</p> <p>Here, we make use of the increasing amount of genomic data to investigate the history of the SNARE family during fungi evolution. Moreover, since different SNARE family members are thought to demarcate different organelles and vesicles, this approach allowed us to compare the organization of the endomembrane systems of yeast and animal cells. Our data corroborate the notion that fungi generally encompass a relatively simple set of SNARE proteins, mostly comprising the SNAREs of the proto-eukaryotic cell. However, all fungi contain a novel soluble SNARE protein, Vam7, which carries an N-terminal PX-domain that acts as a phosphoinositide binding module. In addition, the points in fungal evolution, at which lineage-specific duplications and diversifications occurred, could be determined. For instance, the endosomal syntaxins Pep12 and Vam3 arose from a gene duplication that occurred within the Saccharomycotina clade.</p> <p>Conclusion</p> <p>Although the SNARE repertoire of baker's yeast is highly conserved, our analysis reveals that it is more deviated than the ones of basal fungi. This highlights that the trafficking pathways of baker's yeast are not only different to those in animal cells but also are somewhat different to those of many other fungi.</p

A practical guide for the study of human and murine sebaceous glands in situ

The skin of most mammals is characterised by the presence of sebaceous glands (SGs), whose predominant constituent cell population is sebocytes, that is, lipid-producing epithelial cells, which develop from the hair follicle. Besides holocrine sebum production (which contributes 90% of skin surface lipids), multiple additional SG functions have emerged. These range from antimicrobial peptide production and immunomodulation, via lipid and hormone synthesis/metabolism, to the provision of an epithelial progenitor cell reservoir. Therefore, in addition to its involvement in common skin diseases (e.g. acne vulgaris), the unfolding diversity of SG functions, both in skin health and disease, has raised interest in this integral component of the pilosebaceous unit. This practical guide provides an introduction to SG biology and to relevant SG histochemical and immunohistochemical techniques, with emphasis placed on in situ evaluation methods that can be easily employed. We propose a range of simple, established markers, which are particularly instructive when addressing specific SG research questions in the two most commonly investigated species in SG research, humans and mice. To facilitate the development of reproducible analysis techniques for the in situ evaluation of SGs, this methods review concludes by suggesting quantitative (immuno-)histomorphometric methods for standardised SG evaluation

Increased Plant Uptake of Nitrogen from \u3csup\u3e15\u3c/sup\u3eN-depleted Fertilizer Using Plant Growth-Promoting Rhizobacteria

Harmful environmental effects resulting from fertilizer use have spurred research into integrated nutrient management strategies which can include the use of specific microorganisms to enhance nutrient use efficiency by plants. Some strains of plant growth-promoting rhizobacteria (PGPR) have been reported to enhance nutrient uptake by plants, but no studies with PGPR have used 15N isotope techniques to prove that the increased N in plant tissues came from the N applied as fertilizer. The current study was conducted to demonstrate that a model PGPR system can enhance plant uptake of fertilizer N applied to the soil using different rates of 15N-depleted ammonium sulfate. The experiments were conducted in the greenhouse with tomato using a mixture of PGPR strains Bacillus amyloliquefaciens IN937a and Bacillus pumilus T4. Results showed that PGPR together with reduced amounts of fertilizer promoted tomato growth compared to fertilizer without PGPR. In addition, atom% 15N per gram of plant tissue decreased as the amount of fertilizer increased, and PGPR inoculation resulted in a further decrease of the atom% 15N values. The atom% 15N abundance in plants that received 80% fertilizer plus PGPR was 0.1146, which was significantly lower than 0.1441 for plants that received 80% fertilizer without PGPR and statistically equivalent to 0.1184 for plants that received 100% fertilizer without PGPR. The results demonstrate that increased plant uptake of N applied in fertilizer could be achieved with PGPR as indicated by the differences in 15N uptake. Strains of PGPR that lead to increased nutrient uptake by plants should be evaluated further as components in integrated nutrient management systems