Useful Species Richness,Proportion of Exotic Species,and Market Orientation on Amazonian Dark Earths and Oxisols<Superscript>1</Superscript>

Useful Species Richness, Proportion of Exotic Species, and Market Orientation on Amazonian Dark Earths and Oxisols Anthropogenic soils of Amazonia, known as Amazonian Dark Earths (ADE), are environments with elevated soil fertility that can produce crops that otherwise yield poorly on the leached and highly acidic Oxisols that dominate much of the basin. While ADE sites near urban centers often attract commercial horticultural production of nutrient–demanding exotics, these soils are also considered possibly unique reservoirs of endemic agrobiodiversity because of their relationship to pre–Columbian indigenous occupation. Through botanical surveys and interviews with smallholder farmers, this study compared useful species richness, proportion of exotic species, and market orientation of farms situated on ADE and non–anthropogenic Oxisols in the municipality of Borba in Central Brazilian Amazonia. Species richness was similar on Amazonian Dark Earth and Oxisol farms (19.6 spp vs. 18.3 spp); however, ADE farms showed significantly higher proportions of exotic species (39% vs. 26%; p = 0.025). Furthermore, ADE farms in Borba demonstrated significantly higher market orientation (61.0% vs. 47.3%; p = 0.028), likely a result of the advantage of Amazonian Dark Earths for production of crops that are nutrient–demanding or pH–sensitive crops that have higher values in the nearby regional market of Manaus.     

Parasite-mediated intraguild predation as one of the drivers of co-existence and exclusion among invasive and native amphipods (Crustacea)

Parasitism is emerging as one of the forces determining the outcome of biological invasions. Using field survey and laboratory experiments, we investigate parasitism as one of the factors mediating the interactions among invasive and native amphipods. An extensive survey (100 sites) of a small British island, revealed the native Gammarus duebeni celticus to be parasitised by the muscle wasting microsporidian Pleistophora mulleri and the acanthocephalan duck parasite Polymorphus minutus, the introduced European Gammarus pulex only by P. minutus and the North American Crangonyx pseudogracilis by neither. While Gammarus spp. were widespread in rivers (one or both species present in 64% of sites), C. pseudogracilis had a restricted distribution (7% of sites) and always co-occurred with Gammarus spp. In contrast, Gammarus spp. were absent from all pond/reservoir sites, with C. pseudogracilis present in over 90%. While the negative association of C. pseudogracilis with Gammarus spp. undoubtedly results from factors such as physico-chemical tolerance and predation as C. pseudogracilis can be heavily predated by Gammarus spp., it was notable that C. pseudogracilis co-occurred with Gammarus spp. more frequently when the latter were parasitised. Laboratory experiments clearly showed that predation on C. pseudogracilis was greatly diminished when G. d. celticus was parasitised by P. mulleri and G. pulex by P. minutus. Our study provides evidence that parasitism, by mediating a key interspecific interaction, is one of an array of interacting factors that may have a role in driving patterns of exclusion and co-existence in natives and invaders.     

CDH1 -160C>A gene polymorphism is an ethnicity-dependent risk factor for gastric cancer

The associations between E-cadherin (CDH1) gene polymorphisms and gastric cancer (GC) susceptibility are still controversial. Given this uncertainty, we carried out a meta-analysis of published case-control studies to derive more precise estimations of these relationships. Relevant studies were identified from PubMed and EMBASE up to March 2011. Seventeen studies with 3511 GC cases and 4826 controls were selected. Crude odds ratios (OR) and 95% confidence intervals (CI) were used to investigate the strength of the associations. No associations between CDH1 (+54T>C, -160C>A, -347G>GA, -616G>C, -2076C>T and -3159T>C) gene polymorphisms and GC risk for all genetic models were found. As for CDH1 -160C>A polymorphism, subgroup analyses by country, gender, study design, smoking status, Helicobacter pylori infection, and the Lauren classification of GC did not change the results. When stratified by ethnicity, we found the A allele carriers had a significantly increased risk of GC among Caucasians (AA vs. CA+CC: OR=1.50, 95% CI=1.03-2.19, P=0.03), but not among Asians (AA vs. CA+CC: OR=0.87, 95% CI=0.56-1.37, P=0.56). No publication bias was found in the present study. This meta-analysis suggests that CDH1 -160C>A gene polymorphism may contribute to increased risk of GC among Caucasians.     

Human salivary gland branching morphogenesis: morphological localization of claudins and its parallel relation with developmental stages revealed by expression of cytoskeleton and secretion markers

Development of salivary glands is a highly complex and dynamic process termed branching morphogenesis, where branched structures differentiate into mature glands. Tight junctions (TJ) are thought to play critical roles in physiological functions of tubular organs, contributing to cell polarity and preventing lateral movement of membrane proteins. Evidence demonstrated that claudins are directly involved in TJ formation and function. Using immunohistochemistry and immunofluorescence we have mapped the distribution of claudins-1, 2, 3, 4, 5, 7 and 11 and compared it with the expression of differentiation markers in human salivary glands obtained from foetuses ranging from weeks 4 to 24 of gestation. Expression of all claudins, except claudin-2 was detected in the various phases of human salivary gland development, up to fully mature salivary gland. The expression of all claudins increased according to the progression of salivary gland maturation evidenced by the classical markers-cytokeratin 14, cytokeratin low molecular weight, smooth muscle actin and human secretory component. Tight junction proteins-claudins appear to be important in the final shape and physiological functions of human salivary glands and are parallel related with markers of salivary gland differentiation.     

Biased competition through variations in amplitude of <Emphasis Type="Italic">γ</Emphasis>-oscillations

Experiments in visual cortex have shown that the firing rate of a neuron in response to the simultaneous presentation of a preferred and non-preferred stimulus within the receptive field is intermediate between that for the two stimuli alone (stimulus competition). Attention directed to one of the stimuli drives the response towards the response induced by the attended stimulus alone (selective attention). This study shows that a simple feedforward model with fixed synaptic conductance values can reproduce these two phenomena using synchronization in the gamma-frequency range to increase the effective synaptic gain for the responses to the attended stimulus. The performance of the model is robust to changes in the parameter values. The model predicts that the phase locking between presynaptic input and output spikes increases with attention.     

NS-kNN: a modified <Emphasis Type="Italic">k</Emphasis>-nearest neighbors approach for imputing metabolomics data

Introduction

A common problem in metabolomics data analysis is the existence of a substantial number of missing values, which can complicate, bias, or even prevent certain downstream analyses. One of the most widely-used solutions to this problem is imputation of missing values using a k-nearest neighbors (kNN) algorithm to estimate missing metabolite abundances. kNN implicitly assumes that missing values are uniformly distributed at random in the dataset, but this is typically not true in metabolomics, where many values are missing because they are below the limit of detection of the analytical instrumentation.

Objectives

Here, we explore the impact of nonuniformly distributed missing values (missing not at random, or MNAR) on imputation performance. We present a new model for generating synthetic missing data and a new algorithm, No-Skip kNN (NS-kNN), that accounts for MNAR values to provide more accurate imputations.

Methods

We compare the imputation errors of the original kNN algorithm using two distance metrics, NS-kNN, and a recently developed algorithm KNN-TN, when applied to multiple experimental datasets with different types and levels of missing data.

Results

Our results show that NS-kNN typically outperforms kNN when at least 20–30% of missing values in a dataset are MNAR. NS-kNN also has lower imputation errors than KNN-TN on realistic datasets when at least 50% of missing values are MNAR.

Conclusion

Accounting for the nonuniform distribution of missing values in metabolomics data can significantly improve the results of imputation algorithms. The NS-kNN method imputes missing metabolomics data more accurately than existing kNN-based approaches when used on realistic datasets.

     

In Vitro Studies on the Putative Function of N-acetylaspartate as an Osmoregulator

Efflux and tissue content of N-acetylaspartate (NAA) and amino acids were evaluated from cultured and acutely prepared hippocampal slices in response to changes in osmolarity. The osmoregulator taurine, but not NAA, was lost from both types of slices after moderate reductions in extracellular osmolarity (−60 mOsm) for 10–48 h. Hypoosmotic shock (−166 mOsm) for 5 min resulted in unselective efflux of several amino acids from acutely prepared slices. Notably, the efflux of taurine, but not NAA, was prominent also after the shock. Efflux of NAA was markedly enhanced by NMDA and high K⁺, in particular after the stimulation period. The high K⁺-mediated efflux was decreased by high extracellular osmolarity and a NMDA-receptor antagonist. The results indicate that NAA efflux can be induced by a sudden non-physiological decrease in extracellular osmolarity but not by prolonged more moderate changes in osmolarity. The mechanisms behind the efflux of NAA by high K⁺ are complex and may involve both swelling and activation of NMDA-receptors.     

Characterization of Upstream Sequences of the <Emphasis Type=Italic>LOJ</Emphasis> Gene Leads to Identification of a Novel Enhancer Element Conferring Lateral Organ Junction-Specific Expression in <Emphasis Type=Italic>Arabidopsis thaliana</Emphasis>

Isolation and characterization of promoters are important in understanding gene regulation and genetic engineering of crop plants. Earlier, a pentatricopeptide repeat protein (PPR) encoding gene (At2g39230), designated as Lateral Organ Junction (LOJ) gene, was identified through T-DNA promoter trapping in Arabidopsis thaliana. The upstream sequence of the LOJ gene conferred on the reporter gene a novel LOJ-specific expression. The present study was aimed at identifying and characterizing the cis-regulatory motifs responsible for tissue-specific expression in the −673 and +90 bases upstream of the LOJ gene recognized as LOJ promoter. In silico analysis of the LOJ promoter revealed the presence of a few relevant regulatory motifs and a unique feature like AT-rich inverted repeat. Deletion analysis of the LOJ promoter confirmed the presence of an enhancer-like element in the distal region (−673/−214), which stimulates a minimal promoter-like sequence in the −424/−214 region in a position and orientation autonomous manner. The −136/+90 region of the LOJ promoter was efficient in driving reporter gene expression in tissues like developing anthers and seeds of Arabidopsis. A positive regulation for the seed- and anther-specific expression module was contemplated within the 5′ untranslated region of the LOJ gene. However, this function was repressed in the native context by the lateral organ junction-specific expression. The present study has led to the identification of a novel lateral organ junction-specific element and an enhancer sequence in Arabidopsis with potential applications in plant genetic engineering.     

Germination responses of three grassland species differ between native and invasive origins

The germination stage is critical in plant life-history and is also a key process during the expansion of species’ ranges into new environments. In this study we investigated the germination patterns of three plant species (Achillea millefolium, Hieracium pilosella and Hypericum perforatum) that are invasive to New Zealand (NZ) and native to Central Europe. We asked whether the species show differences in germination temperature requirements, germination speed and maximum germination rates, and thus, whether they display evidence of adaptation to different conditions in the invasive range. Seeds from three populations per species and region were subjected to three different temperature regimes to compare germination rates among origins and across temperature conditions. For Achillea millefolium and Hypericum perforatum, germination rates were significantly higher for invasive NZ provenances than for native German ones. Seeds from invasive populations of all three species displayed increased maximum germination at medium temperature conditions when compared to native populations, which indicates altered germination strategies in the invaded range. Changes in temporal development patterns were most conspicuous for invasive Hieracium pilosella and Hypericum perforatum populations. These findings imply that adaptation in germination patterns towards different climatic conditions in invasive populations has occurred. Our study emphasises the importance of the germination stage during plant invasion and its role in explaining range expansion of these species.     

A landscape of shifting-mosaic steady state in Lassen Volcanic National Park,California

It is generally perceived that landscape patterns or textures in a given protected area are spatially stationary. The findings of this study suggest that this common perception is only partially correct. Over the course of 52 years, equilibrium in landscape shifting was detected using digital data for the Lassen Volcanic National Park (USA). Vertical aerial photographs taken of the park in 1941 were geo-referenced with the digital orthophoto quarter quadrangle (DOQQ) images of the same area from 1993 to identify landscape compositions and to measure change. Spatial analysis was used to observe pattern changes over time. The results suggested that landscape development maintained equilibrium while patches were in various stages of a successional sequence. The total area of each landscape component held steady, although over time patches throughout the landscape changed—a shifting-mosaic steady state (SMSS). These findings reflect the limitations of contemporary environmental conservation theory. They also suggest the importance of considering landscape change in policies that currently govern park planning and management.