Disentangling the relative importance of climate,size and competition on tree growth in Iberian forests: implications for forest management under global change

Most large‐scale multispecies studies of tree growth have been conducted in tropical and cool temperate forests, whereas Mediterranean water‐limited ecosystems have received much less attention. This limits our understanding of how growth of coexisting tree species varies along environmental gradients in these forests, and the implications for species interactions and community assembly under current and future climatic conditions. Here, we quantify the absolute effect and relative importance of climate, tree size and competition as determinants of tree growth patterns in Iberian forests, and explore interspecific differences in the two components of competitive ability (competitive response and effect) along climatic and size gradients. Spatially explicit neighborhood models were developed to predict tree growth for the 15 most abundant Iberian tree species using permanent‐plot data from the Spanish Second and Third National Forest Inventory (IFN). Our neighborhood analyses showed a climatic and size effect on tree growth, but also revealed that competition from neighbors has a comparatively much larger impact on growth in Iberian forests. Moreover, the sensitivity to competition (i.e. competitive response) of target trees varied markedly along climatic gradients causing significant rank reversals in species performance, particularly under xeric conditions. We also found compelling evidence for strong species‐specific competitive effects in these forests. Altogether, these results constitute critical new information which not only furthers our understanding of important theoretical questions about the assembly of Mediterranean forests, but will also be of help in developing new guidelines for adapting forests in this climatic boundary to global change. If we consider the climatic gradients of this study as a surrogate for future climatic conditions, then we should expect absolute growth rates to decrease and sensitivity to competition to increase in most forests of the Iberian Peninsula (in all but the northern Atlantic forests), making these management considerations even more important in the future.     

Molecular basis of toxicity of Clostridium perfringens epsilon toxin

Clostridium perfringens ε-toxin is produced by toxinotypes B and D strains. The toxin is the aetiological agent of dysentery in newborn lambs but is also associated with enteritis and enterotoxaemia in goats, calves and foals. It is considered to be a potential biowarfare or bioterrorism agent by the US Government Centers for Disease Control and Prevention. The relatively inactive 32.9 kDa prototoxin is converted to active mature toxin by proteolytic cleavage, either by digestive proteases of the host, such as trypsin and chymotrypsin, or by C. perfringens λ-protease. In vivo, the toxin appears to target the brain and kidneys, but relatively few cell lines are susceptible to the toxin, and most work has been carried out using Madin-Darby canine kidney (MDCK) cells. The binding of ε-toxin to MDCK cells and rat synaptosomal membranes is associated with the formation of a stable, high molecular weight complex. The crystal structure of ε-toxin reveals similarity to aerolysin from Aeromonas hydrophila, parasporin-2 from Bacillus thuringiensis and a lectin from Laetiporus sulphureus. Like these toxins, ε-toxin appears to form heptameric pores in target cell membranes. The exquisite specificity of the toxin for specific cell types suggests that it binds to a receptor found only on these cells.     

Beta1 integrins regulate mammary gland proliferation and maintain the integrity of mammary alveoli

Integrin-extracellular matrix interactions play important roles in the coordinated integration of external and internal cues that are essential for proper development. To study the role of beta1 integrin in the mammary gland, Itgbeta1(flox/flox) mice were crossed with WAPiCre transgenic mice, which led to specific ablation of beta1 integrin in luminal alveolar epithelial cells. In the beta1 integrin mutant mammary gland, individual alveoli were disorganized resulting from alterations in cell-basement membrane associations. Activity of focal adhesion kinase (FAK) was also decreased in mutant mammary glands. Luminal cell proliferation was strongly inhibited in beta1 integrin mutant glands, which correlated with a specific increase of p21 Cip1 expression. In a p21 Cip1 null background, there was a partial rescue of BrdU incorporation, providing in vivo evidence linking p21 Cip1 to the proliferative defect observed in beta1 integrin mutant glands. A connection between p21 Cip1 and beta1 integrin as well as FAK was also established in primary mammary cells. These results point to the essential role of beta1 integrin signaling in mammary epithelial cell proliferation.     

Elf5 is essential for early embryogenesis and mammary gland development during pregnancy and lactation

Elf5 is an epithelial-specific ETS factor. Embryos with a null mutation in the Elf5 gene died before embryonic day 7.5, indicating that Elf5 is essential during mouse embryogenesis. Elf5 is also required for proliferation and differentiation of mouse mammary alveolar epithelial cells during pregnancy and lactation. The loss of one functional allele led to complete developmental arrest of the mammary gland in pregnant Elf5 heterozygous mice. A quantitative mRNA expression study and Western blot analysis revealed that decreased expression of Elf5 correlated with the downregulation of milk proteins in Elf5(+/-) mammary glands. Mammary gland transplants into Rag(-/-) mice demonstrated that Elf5(+/-) mammary alveolar buds failed to develop in an Elf5(+/+) mammary fat pad during pregnancy, demonstrating an epithelial cell autonomous defect. Elf5 expression was reduced in Prolactin receptor (Prlr) heterozygous mammary glands, which phenocopy Elf5(+/-) glands, suggesting that Elf5 and Prlr are in the same pathway. Our data demonstrate that Elf5 is essential for developmental processes in the embryo and in the mammary gland during pregnancy.     

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data

SUMMARY: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation. AVAILABILITY: CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).     

DRUIDS--detection of regions with unexpected internal deviation from stationarity

Most methods for inferring phylogenies from sequence data assume that patterns of substitution have been stationary over time. Changes in evolutionary constraint can result in nonstationary substitution patterns that are phylogenetically misleading unless modeled appropriately. Here we present a multiple-alignment-based method to identify regions that are likely to contain misleading phylogenetic signals due to changes in evolutionary constraints. The method uses a moving window approach to identify regions with a statistically significant deviation from stationarity in the physicochemical properties of amino acids among taxa. The protocol has been implemented in the software package DRUIDS (Detecting Regions of Unexpected Internal Deviation from Stationarity), available from the first author upon request.     

Mammalian electron transferring flavoprotein.flavoprotein dehydrogenase complexes observed by microelectrospray ionization-mass spectrometry and surface plasmon resonance

Microelectrospray ionization-mass spectrometry was used to directly observe electron transferring flavoprotein.flavoprotein dehydrogenase interactions. When electron transferring flavoprotein and porcine dimethylglycine dehydrogenase or sarcosine dehydrogenase were incubated together in the absence of substrate, a relative molecular mass corresponding to the flavoprotein.electron transferring flavoprotein complex was observed, providing the first direct observation of these mammalian complexes. When an acyl-CoA dehydrogenase family member, human short chain acyl-CoA dehydrogenase, was incubated with dimethylglycine dehydrogenase and electron transferring flavoprotein, the microelectrospray ionization-mass spectrometry signal for the dimethylglycine dehydrogenase.electron transferring flavoprotein complex decreased, indicating that the acyl-CoA dehydrogenases have the ability to compete with the dimethylglycine dehydrogenase/sarcosine dehydrogenase family for access to electron transferring flavoprotein. Surface plasmon resonance solution competition experiments revealed affinity constants of 2.0 and 5.0 microm for the dimethylglycine dehydrogenase-electron transferring flavoprotein and short chain acyl-CoA dehydrogenase-electron transferring flavoprotein interactions, respectively, suggesting the same or closely overlapping binding motif(s) on electron transferring flavoprotein for dehydrogenase interaction.