A sampling optimization analysis of soil‐bugs diversity (Crustacea,Isopoda, Oniscidea)

Biological diversity analysis is among the most informative approaches to describe communities and regional species compositions. Soil ecosystems include large numbers of invertebrates, among which soil bugs (Crustacea, Isopoda, Oniscidea) play significant ecological roles. The aim of this study was to provide advices to optimize the sampling effort, to efficiently monitor the diversity of this taxon, to analyze its seasonal patterns of species composition, and ultimately to understand better the coexistence of so many species over a relatively small area. Terrestrial isopods were collected at the Natural Reserve “Saline di Trapani e Paceco” (Italy), using pitfall traps monthly monitored over 2 years. We analyzed parameters of α‐ and β‐diversity and calculated a number of indexes and measures to disentangle diversity patterns. We also used various approaches to analyze changes in biodiversity over time, such as distributions of species abundances and accumulation and rarefaction curves. As concerns species richness and total abundance of individuals, spring resulted the best season to monitor Isopoda, to reduce sampling efforts, and to save resources without losing information, while in both years abundances were maximum between summer and autumn. This suggests that evaluations of β‐diversity are maximized if samples are first collected during the spring and then between summer and autumn. Sampling during these coupled seasons allows to collect a number of species close to the γ‐diversity (24 species) of the area. Finally, our results show that seasonal shifts in community composition (i.e., dynamic fluctuations in species abundances during the four seasons) may minimize competitive interactions, contribute to stabilize total abundances, and allow the coexistence of phylogenetically close species within the ecosystem.     

The need for richness‐independent measures of turnover when delineating biogeographical regions

Delineating biogeographical regions is one of the primary steps when analysing biogeographical patterns. In their proposed quantitative framework, Kreft & Jetz (2010, Journal of Biogeography, 37 , 2029–2053) recommended the use of the β_sim index to delineate biogeographical regions because this turnover measure is weakly affected by differences in species richness between localities. A recent study by Carvalho et al. (2012, Global Ecology and Biogeography, 21 , 760–771) critiziced the use of β_sim in ecological and biogeographical studies, and proposed the β_‐3 index. Here we used simple numerical examples and an empirical case study (European freshwater fishes) to highlight potential pitfalls associated with the use of β_‐3 for bioregionalization. We show that β_‐3 is not a richness‐independent measure of species turnover. We also show that this index violates the ‘complementarity’ property, namely that localities without species in common have the largest dissimilarity, which is an essential prerequisite for beta diversity studies.     

Redesigning the type II' β‐turn in green fluorescent protein to type I': Implications for folding kinetics and stability

Both Type I' and Type II' β‐turns have the same sense of the β‐turn twist that is compatible with the β‐sheet twist. They occur predominantly in two residue β‐hairpins, but the occurrence of Type I' β‐turns is two times higher than Type II' β‐turns. This suggests that Type I' β‐turns may be more stable than Type II' β‐turns, and Type I' β‐turn sequence and structure can be more favorable for protein folding than Type II' β‐turns. Here, we redesigned the native Type II' β‐turn in GFP to Type I' β‐turn, and investigated its effect on protein folding and stability. The Type I' β‐turns were designed based on the statistical analysis of residues in natural Type I' β‐turns. The substitution of the native “GD” sequence of i+1 and i+2 residues with Type I' preferred “(N/D)G” sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β‐turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β‐turns in natural β‐hairpins can be further optimized by converting the sequence to Type I'. Proteins 2014; 82:2812–2822. © 2014 Wiley Periodicals, Inc.     

An approach based on the total‐species accumulation curve and higher taxon richness to estimate realistic upper limits in regional species richness

Most of accumulation curves tend to underestimate species richness, as they do not consider spatial heterogeneity in species distribution, or are structured to provide lower bound estimates and limited extrapolations. The total‐species (T–S) curve allows extrapolations over large areas while taking into account spatial heterogeneity, making this estimator more prone to attempt upper bound estimates of regional species richness. However, the T–S curve may overestimate species richness due to (1) the mismatch among the spatial units used in the accumulation model and the actual units of variation in β‐diversity across the region, (2) small‐scale patchiness, and/or (3) patterns of rarity of species. We propose a new framework allowing the T–S curve to limit overestimation and give an application to a large dataset of marine mollusks spanning over 11 km² of subtidal bottom (W Mediterranean). As accumulation patterns are closely related across the taxonomic hierarchy up to family level, improvements of the T–S curve leading to more realistic estimates of family richness, that is, not exceeding the maximum number of known families potentially present in the area, can be considered as conducive to more realistic estimates of species richness. Results on real data showed that improvements of the T–S curve to accounts for true variations in β‐diversity within the sampled areas, small‐scale patchiness, and rarity of families led to the most plausible richness when all aspects were considered in the model. Data on simulated communities indicated that in the presence of high heterogeneity, and when the proportion of rare species was not excessive (>2/3), the procedure led to almost unbiased estimates. Our findings highlighted the central role of variations in β‐diversity within the region when attempting to estimate species richness, providing a general framework exploiting the properties of the T–S curve and known family richness to estimate plausible upper bounds in γ‐diversity.     

Prostaglandin I2 upregulates the expression of anterior pharynx‐defective‐1α and anterior pharynx‐defective‐1β in amyloid precursor protein/presenilin 1 transgenic mice

Cyclooxygenase‐2 (COX‐2) has been recently identified to be involved in the pathogenesis of Alzheimer's disease (AD). Yet, the role of an important COX‐2 metabolic product, prostaglandin (PG) I₂, in the pathogenesis of AD remains unknown. Using human‐ and mouse‐derived neuronal cells as well as amyloid precursor protein/presenilin 1 (APP/PS1) transgenic mice as model systems, we elucidated the mechanism of anterior pharynx‐defective (APH)‐1α and pharynx‐defective‐1β induction. In particular, we found that PGI₂ production increased during the course of AD development. Then, PGI₂ accumulation in neuronal cells activates PKA/CREB and JNK/c‐Jun signaling pathways by phosphorylation, which results in APH‐1α/1β expression. As PGI₂ is an important metabolic by‐product of COX‐2, its suppression by NS398 treatment decreases the expression of APH‐1α/1β in neuronal cells and APP/PS1 mice. More importantly, β‐amyloid protein (Aβ) oligomers in the cerebrospinal fluid (CSF) of APP/PS1 mice are critical for stimulating the expression of APH‐1α/1β, which was blocked by NS398 incubation. Finally, the induction of APH‐1α/1β was confirmed in the brains of patients with AD. Thus, these findings not only provide novel insights into the mechanism of PGI₂‐induced AD progression but also are instrumental for improving clinical therapies to combat AD.     

Changes in beta diversity and species functional traits differ between saplings and mature trees in an old‐growth forest

Invasion by generalist tree species can cause biotic homogenization, and such community impoverishment is likely more important in rare forest types. We quantified changes in tree diversity within Carolinian (range in Central Hardwood Forest), central (range in Central Hardwood Forest and Northern Hardwood‐Conifer Forest), and northern species [range reached Northern‐Conifer‐Hardwood/closed Boreal (spruce‐Fir) Forest] in an old forest tract in southern Canada at points surveyed 24 years apart. We asked: How did mature tree and sapling composition and abundance change for the three species’ groups? Did those changes lead to biotic homogenization? Can species’ changes be explained by community traits? We tested for differences in temporal and spatial tree β‐diversity, as well as forest composition and structure, using univariate/multivariate analyses and a community trait‐based approach to identify drivers of change. Major increases occurred in abundance for mature Acer rubrum (northern), while other species decreased (Fraxinus americana, Populus grandidentata); declines were found in A. saccharinum (central) and Cornus florida (Carolinian). Species composition of saplings, but not mature trees, changed due to replacement; no evidence for biotic homogenization existed in either cohort. As a group, northern mature tree species increased significantly, while central species decreased; saplings of pooled Carolinian species also declined. Shade tolerance in mature trees increased, reflecting successional changes, while drought tolerance decreased, perhaps due to changing temperatures, altered precipitation or ground water levels. Saplings showed declines in all traits, probably because of compositional change. Our results demonstrated that saplings can more closely reflect change in forest dynamics than mature trees, especially over short time periods. Based on sapling trends, this remnant could ultimately transition to a mesophytic hardwood stand dominated by A. rubrum and other shade‐tolerant species, creating a more homogeneous forest. While encouraging regeneration for Carolinian and central tree species could ensure high levels of diversity are conserved in the future, it is important to balance this with the primary management goal of maintaining the forest''s old‐growth characteristics.     

Optically Active α‐Phenylethylamine as Efficient Organocatalyst in the Solvent‐free Reactions Between 2,3‐Butanedione and Conjugated Nitroolefins

(R)‐(+) and (S)‐(?)‐1‐phenylethylamine have been shown to promote highly diastereoselective and complementary enantioselective formal [3 + 2]carbocyclization reactions between 2,3‐butanedione and conjugated nitroalkenes with formation of enantiomerically rich 2‐hydroxy‐3‐nitrocyclopentanone derivatives. The reactions were carried out both in solvent and under solvent‐free conditions. The absolute configurations of the products were assigned by X‐ray and circular dichroism spectra analyses. Chirality 24:1005–1012, 2012. © 2012 Wiley Periodicals, Inc.     

Wnt signaling loss accelerates the appearance of neuropathological hallmarks of Alzheimer's disease in J20‐APP transgenic and wild‐type mice

Alzheimer's disease (AD ) is a neurodegenerative pathology characterized by aggregates of amyloid‐β (Aβ) and phosphorylated tau protein, synaptic dysfunction, and spatial memory impairment. The Wnt signaling pathway has several key functions in the adult brain and has been associated with AD , mainly as a neuroprotective factor against Aβ toxicity and tau phosphorylation. However, dysfunction of Wnt/β‐catenin signaling might also play a role in the onset and development of the disease. J20 APP swInd transgenic (Tg) mouse model of AD was treated i.p. with various Wnt signaling inhibitors for 10 weeks during pre‐symptomatic stages. Then, cognitive, biochemical and histochemical analyses were performed. Wnt signaling inhibitors induced severe changes in the hippocampus, including alterations in Wnt pathway components and loss of Wnt signaling function, severe cognitive deficits, increased tau phosphorylation and Aβ_1–42 peptide levels, decreased Aβ42/Aβ40 ratio and Aβ_1–42 concentration in the cerebral spinal fluid, and high levels of soluble Aβ species and synaptotoxic oligomers in the hippocampus, together with changes in the amount and size of senile plaques. More important, we also observed severe alterations in treated wild‐type (WT ) mice, including behavioral impairment, tau phosphorylation, increased Aβ_1–42 in the hippocampus, decreased Aβ_1–42 in the cerebral spinal fluid, and hippocampal dysfunction. Wnt inhibition accelerated the development of the pathology in a Tg AD mouse model and contributed to the development of Alzheimer's‐like changes in WT mice. These results indicate that Wnt signaling plays important roles in the structure and function of the adult hippocampus and suggest that inhibition of the Wnt signaling pathway is an important factor in the pathogenesis of AD .

Read the Editorial Highlight for this article on page 356 .

     

Vertical stratification of ichneumonid wasp communities: the effects of forest structure and life‐history traits

Parasitoid wasp communities of the canopy of temperate forests are still largely unexplored. Very little is known about the community composition of parasitoids between canopy and understory and how much of this difference is related to forest structure or parasitoid biological strategies. In this study we investigated upon the difference in the community composition of the parasitic wasps Ichneumonidae between canopy and understory in a lowland temperate forest in northern Italy. We used general linear models to test whether parasitic strategy modifies species vertical stratification and the effect of forest structure. We also tested differences in β‐diversity between canopy and understory traps and over time within single forest layers. We found that stand basal area was positively related to species richness, suggesting that the presence of mature trees can influence local wasp diversity, providing a higher number of microhabitats and hosts. The ichneumonid community of the canopy was different from that of the understory, and the β‐diversity analysis showed higher values for the canopy, due to a higher degree of species turnover between traps. In our analyses, the vertical stratification was different between groups of ichneumonids sharing different parasitic strategies. Idiobiont parasitoids of weakly or deeply concealed hosts were more diverse in the understory than in the canopy while parasitoids of spiders were equally distributed between the two layers. Even though the ichneumonid community was not particularly species‐rich in the canopy of the temperate forests, the extension of sampling to that habitat significantly increased the number of species recorded.     

On‐farm habitat restoration counters biotic homogenization in intensively managed agriculture

To slow the rate of global species loss, it is imperative to understand how to restore and maintain native biodiversity in agricultural landscapes. Currently, agriculture is associated with lower spatial heterogeneity and turnover in community composition (β‐diversity). While some techniques are known to enhance α‐diversity, it is unclear whether habitat restoration can re‐establish β‐diversity. Using a long‐term pollinator dataset, comprising ～9,800 specimens collected from the intensively managed agricultural landscape of the Central Valley of California, we show that on‐farm habitat restoration in the form of native plant ‘hedgerows’, when replicated across a landscape, can boost β‐diversity by approximately 14% relative to unrestored field margins, to levels similar to some natural communities. Hedgerows restore β‐diversity by promoting the assembly of phenotypically diverse communities. Intensively managed agriculture imposes a strong ecological filter that negatively affects several important dimensions of community trait diversity, distribution, and uniqueness. However, by helping to restore phenotypically diverse pollinator communities, small‐scale restorations such as hedgerows provide a valuable tool for conserving biodiversity and promoting ecosystem services.