Synthesis,receptor binding studies,optical spectroscopic and in silico structural characterization of morphiceptin analogs with cis‐4‐amino‐L‐proline residues

Three novel morphiceptin analogs, in which Pro in position 2 and/or 4 was replaced by cis‐4‐aminoproline connected with the preceding amino acid through the primary amino group, were synthesized. The opioid receptor affinities, functional assay results, enzymatic degradation studies and experimental and in silico structural analysis of such analogs are presented. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Factors affecting population regulation of a colonial vulture

Two hypotheses have been proposed to link population regulation to density‐dependent changes in demographical parameters: the habitat heterogeneity hypothesis (HHH) states that, as population density rises, an increasing proportion of individuals are forced to occupy low‐quality territories, which provokes a decline in average per‐capita survival and/or productivity although some individuals show no decline in fecundity; and the individual adjustment hypothesis (IAH), which suggests that increased densities lead to reductions in survival and/or fecundity by enhancing agonistic interactions, which affect all individuals to a similar extent. However, density‐dependent effects can be affected by density‐independent factors (DIF), such as weather. We test the effects of density dependence on annual reproductive success in Griffon Vultures Gyps fulvus at four spatial scales, nest‐site, cliff, colony and metacolony, in northern Spain from 2008 to 2015. Our results showed most support for the HHH at all scales. At the colony and cliff scale, IAH and DIF had similar importance, whereas there was little evidence of IAH at the metacolony and the nest scale. The best protected eyries (caves, potholes and sheltered ledges) produced the most fledglings and were used preferentially, whereas low‐quality eyries (exposed ledges or open crevices) were used only when the number of breeders increased. The significant interaction between breeding failure and density found for the more exposed eyries suggests that at higher densities, breeding pairs are forced to use poorer nesting areas, and the negative effect of density at the cliff scale could be due to the combined effect of a higher proportion of pairs using low‐quality eyries and the negative effect of rainfall.     

Optimization of free ammonia concentration for nitrite accumulation in shortcut biological nitrogen removal process

A shortcut biological nitrogen removal (SBNR) utilizes the concept of a direct conversion of ammonium to nitrite and then to nitrogen gas. A successful SBNR requires accumulation of nitrite in the system and inhibition of the activity of nitrite oxidizers. A high concentration of free ammonia (FA) inhibits nitrite oxidizers, but unfortunately decreases the ammonium removal rate as well. Therefore, the optimal range of FA concentration is necessary not only to stabilize nitrite accumulation but also to achieve maximum ammonium removal. In order to derive such optimal FA concentrations, the specific substrate utilization rates of ammonium and nitrite oxidizers were measured. The optimal FA concentration range appeared to be 5–10 mg/L for the adapted sludge. The simulated results from the modified inhibition model expressed by FA and ammonium/nitrite concentrations were shown very similar to the experimental results.     

Animal movements in fire‐prone landscapes

Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire‐prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer‐term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire‐prone ecosystems.     

Combinatory responses of proinflamamtory cytokines on nitric oxide-mediated function in mouse calvarial osteoblasts

Combinatory responses of proinflamamtory cytokines have been examined on the nitric oxide-mediated function in cultured mouse calvarial osteoblasts. Interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) induced iNOS gene expression and NO production, although these actions were inhibited by L-NG-monomethylarginine (L-NMMA) and decreased alkaline phosphatase (ALPase) activity. Furthermore, NO donors, sodium nitroprusside (SNP) and NONOate dose-dependently elevated ALPase activity. In contrast, transforming-growth factor-β (TGF-β) decreased NO production stimulated by IL-1β, TNF-α and interferon-γ (IFN-γ). iNOS was expressed by mouse calvarial osteoblast cells after stimulation with IL-1β, TNF-α, and IFN-γ. Incubation of mouse calvarial osteoblast cells with the cytokines inhibited growth and ALPase activity. However, TGF-β-treatment abolished these effects of IL-1β, TNF-α and IFN-γ on growth inhibition and stimulation of ALPase in mouse calvarial osteoblast cells. In contrast, IL-1β, TNF-α, and IFN-γ exerted growth-inhibiting effects on mouse calvarial osteoblast cells which were partly NO-dependent. The results suggest that NO may act predominantly as a modulator of cytokine-induced effects on mouse calvarial osteoblast cells and TGF-β is a negative regulator of the NO production stimulated by IL-1β, TNF-α and IFN-γ.     

Bone-induced streak artifact suppression in sparse-view CT image reconstruction

ABSTRACT: BACKGROUND: In sparse-view CT imaging, strong streak artifacts may appear around bony structures and they often compromise the image readability. Compressed sensing (CS) or total variation (TV) minimization-based image reconstruction method has reduced the streak artifacts to a great extent, but, sparse-view CT imaging still suffers from residual streak artifacts. We introduce a new bone-induced streak artifact reduction method in the CS-based image reconstruction. METHODS: We firstly identify the high-intensity bony regions from the image reconstructed by the filtered backprojection (FBP) method, and we calculate the sinogram stemming from the bony regions only. Then, we subtract the calculated sinogram, which stands for the bony regions, from the measured sinogram before performing the CS-based image reconstruction. The image reconstructed from the subtracted sinogram will stand for the soft tissues with little streak artifacts on it. To restore the original image intensity in the bony regions, we add the bony region image, which has been identified from the FBP image, to the soft tissue image to form a combined image. Then, we perform the CS-based image reconstruction again on the measured sinogram using the combined image as the initial condition of the iteration. For experimental validation of the proposed method, we take images of a contrast phantom and a rat using a micro-CT and we evaluate the reconstructed images based on two figures of merit, relative mean square error and total variation caused by the streak artifacts. RESULTS: The images reconstructed by the proposed method have been found to have smaller streak artifacts than the ones reconstructed by the original CS-based method when visually inspected. The quantitative image evaluation studies have also shown that the proposed method outperforms the conventional CS-based method. CONCLUSIONS: The proposed method can effectively suppress streak artifacts stemming from bony structures in sparse-view CT imaging.     

RBRDetector: Improved prediction of binding residues on RNA‐binding protein structures using complementary feature‐ and template‐based strategies

Computational prediction of RNA‐binding residues is helpful in uncovering the mechanisms underlying protein‐RNA interactions. Traditional algorithms individually applied feature‐ or template‐based prediction strategy to recognize these crucial residues, which could restrict their predictive power. To improve RNA‐binding residue prediction, herein we propose the first integrative algorithm termed RBRDetector (RNA‐Binding Residue Detector) by combining these two strategies. We developed a feature‐based approach that is an ensemble learning predictor comprising multiple structure‐based classifiers, in which well‐defined evolutionary and structural features in conjunction with sequential or structural microenvironment were used as the inputs of support vector machines. Meanwhile, we constructed a template‐based predictor to recognize the putative RNA‐binding regions by structurally aligning the query protein to the RNA‐binding proteins with known structures. The final RBRDetector algorithm is an ingenious fusion of our feature‐ and template‐based approaches based on a piecewise function. By validating our predictors with diverse types of structural data, including bound and unbound structures, native and simulated structures, and protein structures binding to different RNA functional groups, we consistently demonstrated that RBRDetector not only had clear advantages over its component methods, but also significantly outperformed the current state‐of‐the‐art algorithms. Nevertheless, the major limitation of our algorithm is that it performed relatively well on DNA‐binding proteins and thus incorrectly predicted the DNA‐binding regions as RNA‐binding interfaces. Finally, we implemented the RBRDetector algorithm as a user‐friendly web server, which is freely accessible at http://ibi.hzau.edu.cn/rbrdetector . Proteins 2014; 82:2455–2471. © 2014 Wiley Periodicals, Inc.