A conceptual framework for comparing species assemblages in native and exotic habitats

Exotic (nonnative) species are known to have a wide variety of impacts on native biota. One potential set of impacts that have been poorly studied are the effects of replacing native habitat-providing species with exotic ones, e.g. when native trees that compose a woodland are replaced by an exotic tree plantation. Here we develop a graphical model that can be used to explore how multiple taxonomic components (such as birds, mammals and plants) respond to such changes. We suggest that four categorical responses are possible, with respect to changes in species richness (or other quantitative measures) of taxonomic groups within species assemblages. First, that each taxonomic group compared between habitats will be relatively unchanged, e.g. have equivalent values of species richness. Second, that a decrease (for example in species richness) of one group will be compensated for by an increase (in species richness) of another group. Third, that one or more groups will decrease without any compensated increases in other groups. Fourth, that one or more groups will increase without any compensated decreases in other groups. We provide empirical support for 3 of these 4 responses, with respect to measures of species richness, with much evidence for equivalency between habitats. These types of comparisons should provide a valuable tool for evaluating 1) the efficacy of environmental mitigation efforts that artificially create or restore habitats and 2) the types of changes that have occurred over time or across space as native habitat-producing species are replaced by exotic ones. Finally, this conceptual framework should help to broaden the range of possible changes considered by ecologists who study the impacts of exotic species.     

DNA binding induces active site conformational change in the human TREX2 3′-exonuclease

The TREX enzymes process DNA as the major 3′→5′ exonuclease activity in mammalian cells. TREX2 and TREX1 are members of the DnaQ family of exonucleases and utilize a two metal ion catalytic mechanism of hydrolysis. The structure of the dimeric TREX2 enzyme in complex with single-stranded DNA has revealed binding properties that are distinct from the TREX1 protein. The TREX2 protein undergoes a conformational change in the active site upon DNA binding including ordering of active site residues and a shift of an active site helix. Surprisingly, even when a single monomer binds DNA, both monomers in the dimer undergo the structural rearrangement. From this we have proposed a model for DNA binding and 3′ hydrolysis for the TREX2 dimer. The structure also shows how TREX proteins potentially interact with double-stranded DNA and suggest features that might be involved in strand denaturation to provide a single-stranded substrate for the active site.     

Activity of redox-regulatory systems in the tumor and surrounding tissues in various histological types of tumors

According to modern concepts, a malignant tumor is a complex dynamic system possessing numerous links with both the immediate environment and remote non-malignant tissues and organs. Changes in their redox balance can result in disruption of the normal tissue control. The aim of our study was to compare activity of enzymes influencing the redox state in the tumor tissue, peritumoral area, and nonmalignant tissues (taken by resection line) at various histological tumor variants. We found similar close level of reduced glutathione in the tissues of gastric adenocarcinoma and vulvar squamous cell carcinoma; however, dynamics of this parameter in the tumor surrounding tissues was different. In contrast to gastric adenocarcinoma, vulvar squamous cell carcinoma was characterized by a significant increase in glutathione content in the tumor tissue and increased activity of all investigated enzymes of the glutathione system in the tumor tissue and its peritumoral area as compared with the surrounding non-malignant tissue. These results underlie existence of clear differences in the functioning of the redox regulatory systems in the tumor and surrounding tissues of various histological origin and localization; these differences may be possibly attributed to different mechanisms involved in maintenance of the redox balance in the originally non-malignant tissues.     

Multiple-Interval Mapping for Quantitative Trait Loci With a Spike in the Trait Distribution

For phenotypic distributions where many individuals share a common value—such as survival time following a pathogenic infection—a spike occurs at that common value. This spike affects quantitative trait loci (QTL) mapping methodologies and causes standard approaches to perform suboptimally. In this article, we develop a multiple-interval mapping (MIM) procedure based on mixture generalized linear models (GLIMs). An extended Bayesian information criterion (EBIC) is used for model selection. To demonstrate its utility, this new approach is compared to single-QTL models that appropriately handle the phenotypic distribution. The method is applied to data from Listeria infection as well as data from simulation studies. Compared to the single-QTL model, the findings demonstrate that the MIM procedure greatly improves the efficiency in terms of positive selection rate and false discovery rate. The method developed has been implemented using functions in R and is freely available to download and use.     

Amino acid sequence surrounding the lipoic acid cofactor of bovine kidney 2-oxoglutarate dehydrogenase complex

The 2-oxoglutarate dehydrogenase complex was succinylated using 2-oxo[5-14C]glutarate in the presence of N-ethylmaleimide to label the lipoic acid cofactor of the transuccinylase (E2) component. Following peptic digestion, 14C-lipoate-containing peptides were purified and subjected to automated Edman degradation and amino acid analysis. The amino acid sequence surrounding the lipoyllysine residue is reported.     

Early endosteal bone response to incorporated plutonium-238 in mice

Ten Swiss albino ICR SPF female mice 110 days old (weight about 30 g) were exposed for 48 hours to a solution of plutonium-238 nitrate (spec. act. 5 MBq/1 m1, pH 2.7) injected in amounts of 0.01 ml into the popliteal area of the right femur, each thus receiving about 500 kBq per 30 g body weight. Of the injected activity, 50% was retained in the right femur, 2% in the left femur and approximately 2-3% in the excrements collected separately from each animal during the whole exposure period. Ultrastructurally, electron micrographs revealed a variety of changes, including hypertrophy and destruction of endosteal cell organelles (primary damage), deformation and hypertrophy of osteocytes (secondary damage) and the irregularities in the osteocyte self-burial process leading to an abnormal formation of bone tissue structure (tertiary damage). Qualitatively, these changes in the irradiated bone ultrastructure were analogous to those occurring with age. This was confirmed by comparing two groups of control mice 110 and 330 days old. Assessed quantitatively, changes due to irradiation were more pronounced than those associated with aging.