Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.     

Preparative Syntheses of Guanylate-Rich Oligonucleotides Using the Phosphotriester Method in Solution

Abstract

The guanylate-rich fragments: 150 mg d(G₄T₄), 180 mg d(T₄G₄), 350 mg d(T₄G₄T₄), 30 mg d(G₄T₄G₄), 85 mg d(T₄G₄T₄G₄)were synthesized using the triester method. By enzymatic ligation of aliquots the 36mer d(G₄T₄G₄T₄G₄T₄G₄T₄G₄) is obtained.     

Design and dosimetric analysis of a 385 MHz TETRA head exposure system for use in human provocation studies

A new head exposure system for double‐blind provocation studies investigating possible effects of terrestrial trunked radio (TETRA)‐like exposure (385 MHz) on central nervous processes was developed and dosimetrically analyzed. The exposure system allows localized exposure in the temporal brain, similar to the case of operating a TETRA handset at the ear. The system and antenna concept enables exposure during wake and sleep states while an electroencephalogram (EEG) is recorded. The dosimetric assessment and uncertainty analysis yield high efficiency of 14 W/kg per Watt of accepted antenna input power due to an optimized antenna directly worn on the subject's head. Beside sham exposure, high and low exposure at 6 and 1.5 W/kg (in terms of maxSAR10g in the head) were implemented. Double‐blind control and monitoring of exposure is enabled by easy‐to‐use control software. Exposure uncertainty was rigorously evaluated using finite‐difference time‐domain (FDTD)‐based computations, taking into account anatomical differences of the head, the physiological range of the dielectric tissue properties including effects of sweating on the antenna, possible influences of the EEG electrodes and cables, variations in antenna input reflection coefficients, and effects on the specific absorption rate (SAR) distribution due to unavoidable small variations in the antenna position. This analysis yielded a reasonable uncertainty of <±45% (max to min ratio of 4.2 dB) in terms of maxSAR10g in the head and a variability of <±60% (max to min ratio of 6 dB) in terms of mass‐averaged SAR in different brain regions, as demonstrated by a brain region‐specific absorption analysis. Bioelectromagnetics 33:594–603, 2012. © 2012 Wiley Periodicals, Inc.     

Glucagon-like peptide 1: evolution of an incretin into a treatment for diabetes

Glucagon-like peptide 1 (GLP-1) is a product of proglucagon that is secreted by specialized intestinal endocrine cells after meals. GLP-1 is insulinotropic and plays a role in the incretin effect, the augmented insulin response observed when glucose is absorbed through the gut. GLP-1 also appears to regulate a number of processes that reduce fluctuations in blood glucose, such as gastric emptying, glucagon secretion, food intake, and possibly glucose production and glucose uptake. These effects, in addition to the stimulation of insulin secretion, suggest a broad role for GLP-1 as a mediator of postprandial glucose homeostasis. Consistent with this role, the most prominent effect of experimental blockade of GLP-1 signaling is an increase in blood glucose. Recent data also suggest that GLP-1 is involved in the regulation of beta-cell mass. Whereas other insulinotropic gastrointestinal hormones are relatively ineffective in stimulating insulin secretion in persons with type 2 diabetes, GLP-1 retains this action and is very effective in lowering blood glucose levels in these patients. There are currently a number of products in development that utilize the GLP-1-signaling system as a mechanism for the treatment of diabetes. These compounds, GLP-1 receptor agonists and agents that retard the metabolism of native GLP-1, have shown promising results in clinical trials. The application of GLP-1 to clinical use fulfills a long-standing interest in adapting endogenous insulinotropic hormones to the treatment of diabetes.     

Thermal tolerance in widespread and tropical Drosophila species: does phenotypic plasticity increase with latitude?

The distribution of insects can often be related to variation in their response to thermal extremes, which in turn may reflect differences in plastic responses or innate variation in resistance. Species with widespread distributions are expected to have evolved higher levels of plasticity than those from restricted tropical areas. This study compares adult thermal limits across five widespread species and five restricted tropical species of Drosophila from eastern Australia and investigates how these limits are affected by developmental acclimation and hardening after controlling for environmental variation and phylogeny. Irrespective of acclimation, cold resistance was higher in the widespread species. Developmental cold acclimation simulating temperate conditions extended cold limits by 2°-4°C, whereas developmental heat acclimation under simulated tropical conditions increased upper thermal limits by <1°C. The response to adult heat-hardening was weak, whereas widespread species tended to have a larger cold-hardening response that increased cold tolerance by 2°-5°C. These patterns persisted after phylogenetic correction and when flies were reared under high and low constant temperatures. The results do not support the hypothesis that widely distributed species have larger phenotypic plasticity for thermal tolerance limits, and Drosophila species distributions are therefore more closely linked to differences in innate thermal tolerance limits.     

Fertilizer application decreases insect abundance on Plantago lanceolata: a large-scale experiment in three geographic regions

Humans have substantially altered the nitrogen cycle of ecosystems through the application of agricultural fertilizer. Fertilization may not only affect plant species diversity, but also insect dynamics by altering plant nitrogen supplies. We investigated the effect of experimental fertilization on the vegetation, with the ribwort plantain as the focal plant, and on higher trophic levels on differently managed grasslands throughout Germany. Over a period of 2 years, we examined two specialist herbivores and their parasitoid on Plantago lanceolata L., and the composition and structure of the surrounding vegetation. Over 70 sites in three geographic regions, within the large-scale project “German Biodiversity Exploratories”, were included in the study. The model system consisted of the host plant P. lanceolata L., the monophagous weevils Mecinus labilis Herbst and M. pascuorum Gyllenhal, and their parasitoid Mesopolobus incultus Walker. Fertilization decreased plant species richness and host plant abundance, whereas it enhanced the total vegetation growth. The increased size and heigher leaf nitrogen content did not improve herbivore performance. On the contrary, the abundance of the two herbivores was decreased by fertilization. The parasitoid depended on the abundance of one of its hosts, M. pascuorum (positively density-dependent). Reduced herbivore abundance due to fertilization might be explained by a lower abundance of the host plant, a lower stalk number, and by changed patterns of host localization within higher vegetation. Fertilization negatively affected the third trophic level by cascading up via host abundance. The relationships between fertilization, surrounding vegetation and the tritrophic system were measured throughout the three regions and over the 2-year period. Our findings present consequences of intensification for a plant–herbivore–parasitoid system, and may have significant implications for the conservation of multitrophic systems in managed grasslands.     

Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism

A new inhibitor, H-Ala-Ile-pyrrolidin-2-yl boronic acid, was developed as an inhibitor against prolyl tripeptidyl aminopeptidase with a K_i value of 88.1 nM. The structure of the prolyl tripeptidyl aminopeptidase complexed with the inhibitor (enzyme-inhibitor complex) was determined at 2.2 Å resolution. The inhibitor was bound to the active site through a covalent bond between Ser603 and the boron atom of the inhibitor. This structure should closely mimic the structure of the reaction intermediate between the enzyme and substrate. We previously proposed that two glutamate residues, Glu205 and Glu636, are involved in the recognition of substrates. In order to clarify the function of these glutamate residues in substrate recognition, three mutant enzymes, E205A, E205Q, and E636A were generated by site-directed mutagenesis. The E205A mutant was expressed as an inclusion body. The E205Q mutant was expressed in soluble form, but no activity was detected. Here, the structures of the E636A mutant and its complex with the inhibitor were determined. The inhibitor was located at almost the same position as in the wild-type enzyme-inhibitor complex. The amino group of the inhibitor interacted with Glu205 and the main-chain carbonyl group of Gln203. In addition, a water molecule in the place of Glu636 of the wild-type enzyme interacted with the amino group of the inhibitor. This water molecule was located near the position of Glu636 in the wild-type and formed a hydrogen bond with Gln203. The k_cat/K_M values of the E636A mutant toward the two substrates used were smaller than those of the wild-type by two orders of magnitude. The K_i value of our inhibitor for the E636A mutant was 48.8 μM, which was 554-fold higher than that against the wild-type enzyme. Consequently, it was concluded that Glu205 and Glu636 are significant residues for the N-terminal recognition of a substrate.