Contrasting patterns in elevational diversity between microorganisms and macroorganisms

Aim Data and analyses of elevational gradients in diversity have been central to the development and evaluation of a range of general theories of biodiversity. Elevational diversity patterns have, however, been severely understudied for microbes, which often represent decomposer subsystems. Consequently, generalities in the patterns of elevational diversity across different trophic levels remain poorly understood. Our aim was to examine elevational gradients in the diversity of macroinvertebrates, diatoms and bacteria along a stony stream that covered a large elevational gradient. Location Laojun Mountain, Yunnan province, China. Methods The sampling scheme included 26 sites spaced at elevational intervals of 89 m from 1820 to 4050 m elevation along a stony stream. Macroinvertebrate and diatom richness were determined based on the morphology of the specimens. Taxonomic richness for bacteria was quantified using a molecular fingerprinting method. Over 50 environmental variables were measured at each site to quantify environmental variables that could correlate with the patterns of diversity. We used eigenvector‐based spatial filters with multiple regressions to account for spatial autocorrelation. Results The bacterial richness followed an unexpected monotonic increase with elevation. Diatoms decreased monotonically, and macroinvertebrate richness showed a clear unimodal pattern with elevation. The unimodal richness pattern for macroinvertebrates was best explained by the mid‐domain effect (r² = 0.72). The diatom richness was best explained by the variation in nutrient supply, and the increase in bacterial richness with elevation may be related to an increased carbon supply. Main conclusions We found contrasting patterns in elevational diversity among the three studied multi‐trophic groups comprising unicellular and multicellular aquatic taxa. We also found that there may be fundamental differences in the mechanisms underlying these species diversity patterns.     

Consequences of herbivory in the mountain birch (Betula pubescens ssp tortuosa): importance of the functional organization of the tree

Summary Three types of experiments indicate that the functional organization of the mountain birch may influence the ways in which the tree responds to simulated or natural herbivory. The first experiment showed that herbivory to both short and long shoot leaves affects plant development but, because growth largely proceeds by resources of the previous year, is manifested only in the year following the damage. The second experiment showed that even partial damage to a single long shoot leaf caused the axillary bud of that leaf to produce a shorter shoot the next year. Therefore, the value of a leaf depends also on the organ which it is subtending. In the third experiment we manipulated the apical dominance of shoots in ramets and caused improvement to leaf quality in extant shoots. Ramets within a tree responded individually, probably mediated by disturbance of the hormonal control because removal of apical buds elicited the response although removal of the same number of basal buds did not. Induced amelioration is a different response to induced resistance. The two responses are triggered by different cues and may occur in the same plant. By altering hormonal balance of shoots it is potentially possible for herbivores to induce amelioration of food quality. The ways in which herbivory is simulated may explain variability of results obtained when herbivory-induced responses in plants have been studied.     

A proline-rich chitinase from Beta vulgaris

A gene (Chl) encoding a novel type of chitinase was isolated from Beta vulgaris. The Ch1 protein consists of an N-terminal hydrophobic prepeptide of 25 amino acids followed by a hevein-like domain of 22 amino acid residues, an unusually long proline-rich domain of 131 amino acid residues with 90 prolines, and finally a catalytic domain of 261 amino acid residues. Proteins with similar proline-rich domains are present in some other plants. The Chl gene shows a transient expression in response to fungal infection.     

Sonication: A new method for gene transfer to plants

Sonication is a novel method for gene transfer into plant protoplasts and intact plant cells. The mode of action of ultrasound and its chemical, biochemical and physiological effects are reviewed. The state of the art of acoustic transformation is presented and possible mechanisms are discussed.     

Affinity prefractionation for MS‐based plasma proteomics

The plasma proteome has proven to be one of the most challenging proteomes to profile using currently available proteomics technologies. A plethora of methodologies have been used to profile human plasma in order to discover potential biomarkers for disease and for therapy optimization. Affinity‐based prefractionation coupled to MS has been shown to be one of the most successful ways to dig deeper into the plasma proteome. Depletion of high abundant plasma proteins is becoming an initial method of choice in any plasma profiling project. However, several other affinity‐based enrichment methods have been published in recent years. Here we review both protein and peptide affinity prefractionation methods coupled with MS‐based proteomics. Analysis of the proportion of cellular and extracellular annotated proteins of publicly available MS plasma proteomics data is performed to estimate the analytical depth of various prefractionation methods.     

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

ABSTRACT: BACKGROUND: Gene-set enrichment analyses (GEA or GSEA) are commonly used for biological characterization of an experimental gene-set. This is done by finding known functional categories, such as pathways or Gene Ontology terms, that are over-represented in the experimental set; the assessment is based on an overlap statistic. Rich biological information in terms of gene interaction network is now widely available, but this topological information is not used by GEA, so there is a need for methods that exploit this type of information in high-throughput data analysis. RESULTS: We developed a method of network enrichment analysis (NEA) that extends the overlap statistic in GEA to network links between genes in the experimental set and those in the functional categories. For the crucial step in statistical inference, we developed a fast network randomization algorithm in order to obtain the distribution of any network statistic under the null hypothesis of no association between an experimental gene-set and a functional category. We illustrate the NEA method using gene and protein expression data from a lung cancer study. CONCLUSIONS: The results indicate that the NEA method is more powerful than the traditional GEA, primarily because the relationships between gene sets were more strongly captured by network connectivity rather than by simple overlaps.     

A synthesis of methane emissions from 71 northern,temperate, and subtropical wetlands

Wetlands are the largest natural source of atmospheric methane. Here, we assess controls on methane flux using a database of approximately 19 000 instantaneous measurements from 71 wetland sites located across subtropical, temperate, and northern high latitude regions. Our analyses confirm general controls on wetland methane emissions from soil temperature, water table, and vegetation, but also show that these relationships are modified depending on wetland type (bog, fen, or swamp), region (subarctic to temperate), and disturbance. Fen methane flux was more sensitive to vegetation and less sensitive to temperature than bog or swamp fluxes. The optimal water table for methane flux was consistently below the peat surface in bogs, close to the peat surface in poor fens, and above the peat surface in rich fens. However, the largest flux in bogs occurred when dry 30‐day averaged antecedent conditions were followed by wet conditions, while in fens and swamps, the largest flux occurred when both 30‐day averaged antecedent and current conditions were wet. Drained wetlands exhibited distinct characteristics, e.g. the absence of large flux following wet and warm conditions, suggesting that the same functional relationships between methane flux and environmental conditions cannot be used across pristine and disturbed wetlands. Together, our results suggest that water table and temperature are dominant controls on methane flux in pristine bogs and swamps, while other processes, such as vascular transport in pristine fens, have the potential to partially override the effect of these controls in other wetland types. Because wetland types vary in methane emissions and have distinct controls, these ecosystems need to be considered separately to yield reliable estimates of global wetland methane release.     

Adsorption of chitosan on PET films monitored by quartz crystal microbalance

The adsorption behavior of chitosan on poly(ethylene terephthalate) (PET) model film surface was studied using the quartz crystal microbalance (QCM) technique. QCM with a dissipation unit (QCM-D) represents a very sensitive technique for adsorption studies at the solid/liquid interface in situ, with capability of detecting a submonolayer of adsorbate on the quartz crystal surface. Chitosan as well as PET were chosen for this study due to their promising biocompatible properties and numerous possibilities to be used in biomedical applications. As a first step, PET foils were activated by alkaline hydrolysis in order to increase their hydrophilicity. Model thin films were prepared from PET foils by the spin coating technique. The chemical composition of the obtained model PET films was analyzed using X-ray photoelectron spectroscopy (XPS) and their morphology was characterized by atomic force microscopy (AFM). Furthermore, the adsorption behavior of chitosan on these activated PET films and the influence of adsorption parameters (pH, ionic strength and chitosan solution concentration) were investigated in detail. Additionally, the surface chemistry and morphology of the PET films and the chitosan coated PET films were analyzed with XPS and AFM.     

Bile acid receptors as targets for the treatment of dyslipidemia and cardiovascular disease

Dyslipidemia is an important risk factor for cardiovascular disease (CVD) and atherosclerosis. When dyslipidemia coincides with other metabolic disorders such as obesity, hypertension, and glucose intolerance, defined as the metabolic syndrome (MS), individuals present an elevated risk to develop type 2 diabetes (T2D) as well as CVD. Because the MS epidemic represents a growing public health problem worldwide, the development of therapies remains a major challenge. Alterations of bile acid pool regulation in T2D have revealed a link between bile acid and metabolic homeostasis. The bile acid receptors farnesoid X receptor (FXR) and TGR5 both regulate lipid, glucose, and energy metabolism, rendering them potential pharmacological targets for MS therapy. This review discusses the mechanisms of metabolic regulation by FXR and TGR5 and the utility relevance of natural and synthetic modulators of FXR and TGR5 activity, including bile acid sequestrants, in the treatment of the MS.