A method for analysing spatial scales of variation in composition of assemblages

In several areas of research on ecological assemblages, it is useful to be able to analyse patterns of spatial variation at various scales. Multivariate analyses of dissimilarity or similarity in assemblages of species are limited by problems of non-independence caused by repeated use of the sample-units. Where rank-order procedures are used, no comparative quantitative measurements of dissimilarity at different scales are produced. An alternative method is described that uses the sample's average assemblage (or centroid). These estimates are themselves averaged to give centroids for larger spatial scales. Dissimilarities from the centroids at each scale are then calculated using independent replicates for each scale from those in each sample. The dissimilarity measures can then be examined by analysis of variance to detect spatial scales of differences for each sample at every level of a hierarchy of scales. The method is illustrated using data from mangrove forests and rocky shores, involving up to 97 taxonomic groups (species, other taxa). Differences among assemblages at the scales of sites (tens of meters apart) or locations at shores (hundreds of meters apart) were identified. Consequences of different numbers of replicates are discussed, with some potential problems (and their solutions) in application. Received: 14 November 1997 / Accepted: 14 September 1998     

Prey preferences of six species of Carabidae (Coleoptera) and one Lycosidae (Araneae) commonly found in UK arable crop fields

Abstract: Laboratory experiments were used to determine the feeding preferences of six carabid beetles and one lycosid spider on aphid and collembolan prey. The first investigation used only five species of carabid Pterostichus melanarius Illiger, Pterostichus madidus F., Harpalus rufipes DeGeer, Nebria brevicollis F. and Carabus violaceus L., which had been caught most commonly in pitfall traps in the headland region of arable crop fields. When offered Brevicoryne brassicae L., Sitobion avenae F., Metopolophium dirhodum Walker and Rhopalosiphum padi L. as prey items, the species consistently consumed in high numbers was M. dirhodum . In subsequent experiments four carabids Pterostichus cupreus L., P. melanarius, P. madidus. H. rufipes and a lycosid spider Trochosa ruricola DeGeer whose distribution was shown by pitfall trapping to extend throughout the arable crop, were the chosen predators. These predators were offered a choice between M. dirhodum and entomobryid collembolans (a recognised alternative prey item) to gauge their preference between the two prey types. Both male and female P. cupreus and P. melanarius showed a significant preference for the aphid prey, while there was no significant preference displayed by the other species. The effect of temperature on the voracity of these five predators fed on M. dirhodum was investigated. There were significant differences in the number of aphids consumed by the species and sexes at the different temperatures. Regression analysis on the mean numbers of aphids eaten by each sex of the five predators, showed that in the majority of cases there was a significant increase in predation with increasing temperature. In considering the dietary preferences illustrated by these experiments, it appeared that P. cupreus and P. melanarius offered the greatest potential in controlling aphids on arable crops.     

Metabolic perturbations of postnatal growth restriction and hyperoxia-induced pulmonary hypertension in a bronchopulmonary dysplasia model

Introduction

Neonatal pulmonary hypertension (PH) is a common manifestation of bronchopulmonary dysplasia (BPD) and contributes to increased morbidity and mortality of preterm birth. Postnatal growth restriction (PNGR) and hyperoxia are independent contributors to PH development, as indicated by our previous work in a rat model of BPD.

Objective

To explore the metabolic consequences of induction of PH with hyperoxia and PNGR in a rat model of BPD.

Methods

Sprague–Dawley rat pups (n?=?4/group) underwent three modes of PH induction: (1) growth restriction-induced by larger litter size; (2) hyperoxia-induced by 75% oxygen exposure; (3) combined growth restriction and hyperoxia. Primary metabolism, complex lipids, biogenic amines, and lipid mediators were characterized in plasma and lung tissue using GC- and LC-MS technologies.

Results

Specific to hyperoxic induction, pulmonary metabolomics suggested increased reactive oxygen species (ROS) generation as indicated by: (1) increased indicators of β-oxidation and mitochondrial respiration; (2) changes in ROS-sensitive pathway activity and metabolites including the polyol pathway and xanthine oxidase pathways, and reduced glutathione; (3) decreased plasmalogens. Unlike the lung, circulating metabolite changes were induction mode-specific or additive in the combined modes (e.g. 1) growth-restriction reduced phosphatidylcholine; (2) hyperoxia increased oxylipins and trimethylamine-N-oxide (TMAO); (3) additive effects on 3-hydroxybutyric acid and arginine.

Conclusion

The present study highlights the variety of metabolic changes that occur due to PNGR- and hyperoxia-induced PH, identifying numerous metabolites and pathways influenced by treatment-specific or combined effects. The rat model used in this study presents a robust means of uncovering the mechanisms that contribute to the pathology of PH.

     

DNA barcoding of South Africa’s ornamental freshwater fish – are the names reliable?

Trade in freshwater ornamental fish in South Africa is currently regulated by a ‘blacklist’ to prevent potentially invasive taxa from establishing in the country. Because its effective implementation requires accurate identification, the aim of the present study was to test whether DNA barcoding is a useful tool to identify freshwater fishes in the South African pet trade. A total of 351 aquarium fish specimens, representing 185 traded taxa, were sequenced for the mitochondrial COI barcoding marker in 2011 and 2012. Lake Malawi cichlids were treated as a single group due to a lack of resolution in their COI marker, resulting in a data set of 137 successfully sequenced taxa. The Barcode Of Life Database (BOLD) and GenBank were used for taxonomic assignment comparisons. The genetic identification matched the scientific name inferred from the trade name for 60 taxa (43.8%) using BOLD, and for 67 taxa (48.9%) using GenBank. A genetic ID could not be assigned in 47 (34.3%) cases using BOLD and in 37 cases (27%) using GenBank. Whereas DNA barcoding can be a useful tool to help identify imported freshwater fishes, it requires further development of publicly available databases to become a reliable means of identification.     

The p75 neurotrophin receptor

The pan neurotrophin receptor (p75(NTR)) is best known for mediating neural cell death during development as well as in the adult following injury, the latter making it a target for the treatment of neurodegenerative disease. Although p75(NTR) has been studied for over 30 years, a number of recent discoveries have changed our understanding of its regulation. Here we provide a brief overview of the p75(NTR) protein, its post-translational modifications, and the phenotype of p75(NTR)-deficient mice as a starting point for researchers unfamiliar with this complex receptor. The accepted mechanisms underlying the ability of p75(NTR) to regulate cell death as well as a number of other neural functions, most notably neuronal differentiation, neurite outgrowth and synaptic plasticity, are also summarised.