A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases

Calcium-dependent protein kinases (CDPKs) are a novel class of signaling molecules that have been broadly implicated in relaying specific calcium-mediated responses to biotic and abiotic stress as well as developmental cues in both plants and protists. Calcium-dependent autophosphorylation has been observed in almost all CDPKs examined, but a physiological role for autophosphorylation has not been demonstrated. To date, only a handful of autophosphorylation sites have been mapped to specific residues within CDPK amino acid sequences. In an attempt to gain further insight into this phenomenon, we have mapped autophosphorylation sites and compared these phosphorylation patterns among multiple CDPK isoforms. From eight CDPKs and two CDPK-related kinases from Arabidopsis thaliana and Plasmodium falciparum, 31 new autophosphorylation sites were characterized, which in addition to the previously described sites, allowed the identification of five conserved loci. Of the 35 total sites analyzed approximately one-half were observed in the N-terminal variable domain. Homology models were generated for the protein kinase and calmodulin-like domains, each containing two of the five conserved sites, to allow intelligent speculation regarding subsequent lines of investigation.     

GMDD: a database of GMO detection methods

Background  

Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed.     

Extinction risk and diversification are linked in a plant biodiversity hotspot

It is widely recognized that we are entering an extinction event on a scale approaching the mass extinctions seen in the fossil record. Present-day rates of extinction are estimated to be several orders of magnitude greater than background rates and are projected to increase further if current trends continue. In vertebrates, species traits, such as body size, fecundity, and geographic range, are important predictors of vulnerability. Although plants are the basis for life on Earth, our knowledge of plant extinctions and vulnerabilities is lagging. Here, we disentangle the underlying drivers of extinction risk in plants, focusing on the Cape of South Africa, a global biodiversity hotspot. By comparing Red List data for the British and South African floras, we demonstrate that the taxonomic distribution of extinction risk differs significantly between regions, inconsistent with a simple, trait-based model of extinction. Using a comprehensive phylogenetic tree for the Cape, we reveal a phylogenetic signal in the distribution of plant extinction risks but show that the most threatened species cluster within short branches at the tips of the phylogeny--opposite to trends in mammals. From analyzing the distribution of threatened species across 11 exemplar clades, we suggest that mode of speciation best explains the unusual phylogenetic structure of extinction risks in plants of the Cape. Our results demonstrate that explanations for elevated extinction risk in plants of the Cape flora differ dramatically from those recognized for vertebrates. In the Cape, extinction risk is higher for young and fast-evolving plant lineages and cannot be explained by correlations with simple biological traits. Critically, we find that the most vulnerable plant species are nonetheless marching towards extinction at a more rapid pace but, surprisingly, independently from anthropogenic effects. Our results have important implications for conservation priorities and cast doubts on the utility of current Red List criteria for plants in regions such as the Cape, where speciation has been rapid, if our aim is to maximize the preservation of the tree-of-life.     

Components and Controls of Water Flux in an Old-growth Douglas-fir–Western Hemlock Ecosystem

We report measurements of rates of sap flow in dominant trees, changes in soil moisture, and evaporation from coarse woody debris in an old-growth Douglas-fir–western hemlock ecosystem at Wind River, Washington, USA, during dry periods in summer. The measurements are compared with eddy-covariance measurements of water-vapor fluxes above the forest (E_e) and at the forest floor (E_u) to examine the components of ecosystem water loss and the factors controlling them. Daily values of E_u were about 10% of E_e. Evaporation from coarse woody debris was only about 2% of E_e. Transpiration (E_t), estimated by scaling sap-flow measurements accounted for about 70% of (E_e– E_u); transpiration from subdominant trees may account for the remainder. The daily total change in soil moisture (E_s) in the top 30 cm was larger than the net change, probably because of hydraulic redistribution of soil water by roots. Observed differences between E_s and E_e were probably because roots also extract water from greater depth, and/or because the measuring systems sample at different spatial scales. The ratio of E_t to E_s decreased with decreasing soil water content, suggesting that partitioning in water use between understory and overstory changed during the season. The rate of soil drying exceeded E_e early in the day, probably because water vapor was being stored in canopy air space and condensed or adsorbed on tree stems, lichens, and mosses. The daily variation of E_e with vapor-pressure deficit showed strong hysteresis, most likely associated with transpiration of water stored in tree stems and branches.     

Cell death induced by vincristine in the intestinal crypts of mice and in a human Burkitt's lymphoma cell line

Abstract. Although vincristine is widely used clinically in the treatment of some human cancers, its mechanism of action has not been clearly established. In this study, the patterns of cell death induced y vincristine in the intestinal crypts of mice and in a human Burkitt's lymphoma cell line were investigated by light and electron microscopy. Vincristine was found to enhance apoptosis of interphase cells in both systems and also to cause the arrest of cells in mitosis, the latter effect being ore pronounced in the intestinal crypts. Arrested mitotic cells went on to die by a process that had a number of features in common with apoptosis. These include compaction of chromatin (following coalescence of chromosomes), condensation of the cytoplasm, initial preservation of organelle integrity, and eventually the fragmentation of the cell into a number of membrane-enclosed bodies which are morphologically similar to conventional apoptotic bodies. The results suggest that the cytocidal effect of vincristine is not solely dependent on metaphase arrest but is a cumulative one, resulting both from apoptosis of interphase cells and the 'apoptotic-like' death of cells arrested in metaphase.     

Evaluation of broiler litter with reference to the microbial composition as assessed by using 16S rRNA and functional gene markers

Very little is known about the microbial composition of animal bedding wastes, including poultry litter, and what is known has been deduced from standard culture methods, by which some fastidious organisms that exist in the environment may not be detected. We evaluated the bacterial composition of poultry litter by using a combination of culture and molecular detection. Total aerobic bacteria in poultry litter were detected by culture at 10(9) CFU/g of material. Enteric bacteria such as Enterococcus spp. and coliforms composed 0.1 and 0.01%, respectively, of the total aerobic cultivatable bacteria in poultry litter; no Salmonella strains were detected by culture. In order to characterize the most abundant bacterial groups, we sequenced 16S ribosomal DNA (rDNA) genes amplified by PCR with microbial community DNA isolated from poultry litter as the template. From the 16S rDNA library, 31 genera were identified. Twelve families or groups were identified with lactobacilli and Salinococcus spp. forming the most abundant groups. In fact, 82% of the total sequences were identified as gram-positive bacteria with 62% of total belonging to low G+C gram-positive groups. In addition to detection of 16S rDNA sequences associated with the expected fecal bacteria present in manure, we detected many bacterial sequences for organisms, such as Globicatella sulfidofaciens, Corynebacterium ammoniagenes, Corynebacterium urealyticum, Clostridium aminovalericum, Arthrobacter sp., and Denitrobacter permanens, that may be involved in the degradation of wood and cycling of nitrogen and sulfur. Several sequences were identified in the library for bacteria associated with disease in humans and poultry such as clostridia, staphylococci, and Bordetella spp. However, specific PCR targeting other human and veterinary pathogens did not detect the presence of Salmonella, pathogenic Escherichia coli, Campylobacter spp., Yersinia spp., Listeria spp., or toxigenic staphylococci. PCR and DNA hybridization revealed the presence of class 1 integrons with gene cassettes that specify resistance to aminoglycosides and chloramphenicol. Only from understanding the microbial community of animal wastes such as poultry litter can we manage animal disease and limit the impact of animal waste on the environment and human and animal health.     

Extended lifetime of reagentless detector for multiple inhibitors of acetylcholinesterase

Competitive inhibitors of acetylcholinesterase (AChE) are detected using an evanescent wave technique to monitor changes in the absorbance spectrum of an AChE-monosulfonate tetraphenyl porphyrin (TPPS(1)) complex immobilized on the surface of a glass slide. In this technique, porphyrin is displaced from the AChE active site by the inhibitor. The loss in absorbance intensity of the characteristic absorbance peak for the AChE-TPPS(1) complex at 446 nm is linearly dependent on the log of the inhibitor concentration. This technique yields detection limits at 3:1 S/N of 37 ppt for eserine, 50 ppt for galanthamine, 100 ppt for scopolamine, 250 ppt for tetracaine, 45 ppt for diazinon, and 83 ppb for Triton X-100. When stored under vacuum, the enzymatic lifetime of the immobilized AChE surface is greater than 73 days while the responsive lifetime of the immobilized AChE-TPPS(1) surface is currently 49 days.