Food encounter rate of simulated termite tunnels in heterogeneous landscapes

The aim of this study was to explore how a heterogeneous landscape affects food encounter rate in the Formosan subterranean termite, Coptotermes formosanus Shiraki. To do this, a lattice model was formulated to simulate the tunneling structure of the termite. The model made use of minimized local rules derived from empirical data. In addition, a landscape structure was generated on a lattice space by using a neutral landscape model. Each lattice cell has a value h, representing spatially distributed property of the landscape (e.g., temperature or moisture). The heterogeneity of the landscape was characterized by a parameter, H controlling aggregation of lattice cells with higher values of h. Higher H values correspond to higher aggregation levels. The effect of the landscape heterogeneity on the encounter rate was clear in the presence of higher food density than in lower density. The effect was also enhanced by the increase of the number of primary tunnels.     

Operon prediction in Pyrococcus furiosus

Identification of operons in the hyperthermophilic archaeon Pyrococcus furiosus represents an important step to understanding the regulatory mechanisms that enable the organism to adapt and thrive in extreme environments. We have predicted operons in P.furiosus by combining the results from three existing algorithms using a neural network (NN). These algorithms use intergenic distances, phylogenetic profiles, functional categories and gene-order conservation in their operon prediction. Our method takes as inputs the confidence scores of the three programs, and outputs a prediction of whether adjacent genes on the same strand belong to the same operon. In addition, we have applied Gene Ontology (GO) and KEGG pathway information to improve the accuracy of our algorithm. The parameters of this NN predictor are trained on a subset of all experimentally verified operon gene pairs of Bacillus subtilis. It subsequently achieved 86.5% prediction accuracy when applied to a subset of gene pairs for Escherichia coli, which is substantially better than any of the three prediction programs. Using this new algorithm, we predicted 470 operons in the P.furiosus genome. Of these, 349 were validated using DNA microarray data.     

Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit

The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τ_C16), and domains shortened at the C-terminus by 11 and 18 residues, respectively. The only interacting residues were found in the C-terminal 30-residue segment of τ, most of which is structurally disordered in free τ_C16. Since the N- and C-termini of the structured core of τ_C16 are located close to each other, this limits the possible distance between α and the pentameric δτ₂γδ′ clamp–loader complex and, hence, between the two α subunits involved in leading- and lagging-strand DNA synthesis. Analysis of an N-terminally extended construct (τ_C22) showed that τ_C14 presents the only part of Domains IVa and V of τ which comprises a globular fold in the absence of other interaction partners.     

The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τ_C16. We show that the extreme C-terminal region of τ_C16 constitutes the site of interaction with α. The τ_C16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τ_C16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (K_D) of the α−τ_C16 complex to be ~260pM. Competition with immobilized τ_C16 by τ_C16 derivatives for binding to α gave values of K_D of 7μM for the α−τ_C16Δ7 complex. Low-level expression of the genes encoding τ_C16 and τ_C167, but not τ_C16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τ_C16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τ_C24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τ_C16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.     

Heat shock augments myosin phosphatase target-subunit phosphorylation

Our previous study demonstrated that heat shock augmented vascular contraction. In the present study, we hypothesized that heat shock augments myosin phosphatase target-subunit (MYPT1) phosphorylation resulting in augmented vascular contraction. Endothelium-denuded rat aortic rings were mounted in organ baths, exposed to heat shock (42 degrees C for 45 min), and subjected to contraction 4 h after the heat shock followed by Western blot analysis for MLC(20) (the 20 kDa light chains of myosin II) or MYPT1. The contractile responses in both control and heat shock-treated aorta were inhibited by Y27632, an inhibitor of Rho-kinase. The level of the MLC(20) and MYPT1(Thr855) phosphorylation in response to KCl was higher in heat shock-treated aorta than that in timed-control. The increased MYPT1(Thr855) phosphorylation was inhibited by Y27632 (1.0 microM) in parallel with inhibition of MLC(20) phosphorylation and vascular contraction. These results indicate that heat shock augments MYPT1 phosphorylation resulting in augmented vascular contraction.     

Estimating final height from parental heights and sex in Taiwanese

We have developed a simple function for accurately estimating target height for use in evaluating growth and growth-promoting therapies in Taiwanese children. The heights of parents and their adult offspring born in the 1970s were determined in 1229 healthy families who accompanied another family member to our pediatric clinic. We directly measured the heights of the population-based cohort of adult offspring. The heights of their parents were based on self-report. Both the parents and their offspring were healthy. The increases in height between the two generations were 1.49-3.19 cm for boys and 2.03-2.61 cm for girls. These increases lie between those reported for Chinese children in Hong Kong (4.2-4.8 cm) and children in Sweden (0.7-1.0 cm). Final height was underestimated using the corrected midparental height method and was overestimated using the final parental height model developed from Swedish data. We developed a new linear model by fitting our data: boy height = 79.3 + 0.56 (midparental height); girl height = 35.2 + 0.76 (midparental height). The intercept and slope of the model are similar to those reported for Swedish girls but not to those reported for Swedish boys. Use of the new equations derived from our data may increase the accuracy of estimates of target height in Taiwanese children. The intermediate position of our fairly representative Taiwanese sample in both final height and generational increases in final height may reflect an intermediate stage between the Swedes and Hong Kong Chinese in the secular trend of heights.     

Phylogenetic origin of <Emphasis Type="Italic">Salmo trutta</Emphasis> L 1758 from Sicily,based on mitochondrial and nuclear DNA analyses

The phylogenetic status of brown trout Salmo trutta L 1758 in Sicily is uncertain as some reports describe these trout as S. macrostigma or S. cettii on one hand while other, contradictory reports imply a hatchery origin on the other. In order to clarify this situation, we performed sequence analysis of the mtDNA control region and restriction fragment analysis of the nuclear lactate dehydrogenase (LDH-C1*) gene. A single mitochondrial haplotype (At-s6) found previously in brown trout in Morocco, and two alleles at LDH-C1* (the ancestral*100, at a high frequency, and *90) were revealed. Our results suggest that Sicilian brown trout are native and that they probably colonized Sicily from west to east in an expansion, from the Atlantic Ocean basin, along the North-West African coast. Handling editor: C. Sturmbauer     

Evaluation of biogenic and anthropogenic inputs of aliphatic hydrocarbons to Lake Taihu sediments using biomarkers

Surficial sediments from 13 sites throughout Lake Taihu, one of the largest urbanized freshwater lake systems in China, were analyzed for biomarkers (e.g., n-alkanes and hopanes) to track the origin of organic inputs (biogenic or anthropogenic), and, thus, to identify any ‘hot spots’ of hydrocarbon contamination. A distinct spatial distribution of aliphatic hydrocarbons in sediments was observed in Lake Taihu. At the northern tip of the lake (i.e., Meiliang and Wuli Bays), the highest mean aliphatic hydrocarbon concentration, with a significant contribution of an unresolved complex mixture (UCM), was found, indicating possible anthropogenic petroleum contamination (mainly from untreated and partially treated industrial and domestic sewage from Wuxi, Changzhou and other cities). This was supported by the n-alkane indices (e.g., small Carbon Preference Index and odd-to-even values) and a high degree of maturity of the hopane biomarkers. However, hydrocarbons from East Taihu were mainly biogenic, with the lowest mean concentrations, negligible or no contribution of UCM, abundance of vascular plant C₂₃–C₃₃ n-alkanes with a high odd-to-even predominance, and the presence of biogenic hopanes (e.g., 17β(H), 21β(H)-hopanes and hopenes). In the other areas of the lake, however, the predominance of biogenic in combination with petrogenic hydrocarbons was indicated by the biomarkers.