Structural Aspects and Prediction of Calmodulin-Binding Proteins

Calmodulin (CaM) is an important intracellular protein that binds Ca²⁺ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM’s ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca²⁺ concentration through interactions with CaM.     

Accurate ensemble pruning with PL-bagging

Ensemble pruning deals with the selection of base learners prior to combination in order to improve prediction accuracy and efficiency. In the ensemble literature, it has been pointed out that in order for an ensemble classifier to achieve higher prediction accuracy, it is critical for the ensemble classifier to consist of accurate classifiers which at the same time diverse as much as possible. In this paper, a novel ensemble pruning method, called PL-bagging, is proposed. In order to attain the balance between diversity and accuracy of base learners, PL-bagging employs positive Lasso to assign weights to base learners in the combination step. Simulation studies and theoretical investigation showed that PL-bagging filters out redundant base learners while it assigns higher weights to more accurate base learners. Such improved weighting scheme of PL-bagging further results in higher classification accuracy and the improvement becomes even more significant as the ensemble size increases. The performance of PL-bagging was compared with state-of-the-art ensemble pruning methods for aggregation of bootstrapped base learners using 22 real and 4 synthetic datasets. The results indicate that PL-bagging significantly outperforms state-of-the-art ensemble pruning methods such as Boosting-based pruning and Trimmed bagging.     

Pheromone Disruption of Argentine Ant Trail Integrity

Disruption of Argentine ant trail following and reduced ability to forage (measured by bait location success) was achieved after presentation of an oversupply of trail pheromone, (Z)-9-hexadecenal. Experiments tested single pheromone point sources and dispersion of a formulation in small field plots. Ant walking behavior was recorded and digitized by using video tracking, before and after presentation of trail pheromone. Ants showed changes in three parameters within seconds of treatment: (1) Ants on trails normally showed a unimodal frequency distribution of walking track angles, but this pattern disappeared after presentation of the trail pheromone; (2) ants showed initial high trail integrity on a range of untreated substrates from painted walls to wooden or concrete floors, but this was significantly reduced following presentation of a point source of pheromone; (3) the number of ants in the pheromone-treated area increased over time, as recruitment apparently exceeded departures. To test trail disruption in small outdoor plots, the trail pheromone was formulated with carnuba wax-coated quartz laboratory sand (1 g quartz sand/0.2 g wax/1 mg pheromone). The pheromone formulation, with a half-life of 30 h, was applied by rotary spreader at four rates (0, 2.5, 7.5, and 25 mg pheromone/m²) to 1- and 4-m² plots in Volcanoes National Park, Hawaii. Ant counts at bait cards in treated plots were significantly reduced compared to controls on the day of treatment, and there was a significant reduction in ant foraging for 2 days. These results show that trail pheromone disruption of Argentine ants is possible, but a much more durable formulation is needed before nest-level impacts can be expected. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Modeling alternative zoning strategies in forest management

To satisfy public demands for environmental values, forest companies are facing the prospect of a reduction in wood supply and increases in costs. Some Canadian provincial governments have proposed intensifying silviculture in special zones dedicated to timber production as the means for pushing out the forest possibility frontiers. In this paper, we compare the traditional two‐zone land allocation framework which includes ecological reserves and integrated forest management zones with the triad — a three‐zone scheme which adds a zone dedicated to intensive timber production. We compare the solutions of the mixed‐integer linear programs formulated under both land‐allocation frameworks. We explore through sensitivity analysis the conditions under which the triad regime can offset the impact on timber production from increased environmental demands. We show that under the realistic conditions characteristic to Coastal British Columbia, higher environmental demands may be satisfied under the triad regime without increasing the financial burdens on the industry or reducing its wood supply. This occurs, however, only if regulatory constraints in timber production zone are flexible.     

Harvesting small trees and forest residues

Eight countries collaborated and shared technical information on the harvesting of small trees and forest residues in a three year program. Proceedings and reports from workshops and reviews are summarized in a review of activities and harvesting systems of the participating countries. Four databases were developed for harvesting and transportation of these materials.     

Sediment chemistry and nutrient influx in a hydrologically restored bottomland hardwood forest in Midwestern USA

Exchanges of total N and C between a river and its floodplain forest have been enhanced by sedimentation processes during flood pulses at a 5‐ha bottomland hardwood forest located at the Olentangy River Wetland Research Park in central Ohio. In the spring of 2000, the forest was hydrologically restored by notching an artificial levee that had separated the Olentangy River and its floodplain forest for 100 years. One‐hundred flat sediment traps (30 cm × 30 cm) were used to collect sediment samples during spring/summer flooding events from 2003 to 2005. Results showed that sediment deposition is determined by the landscape variability during flooding events, Net sediment deposit in the wettest area averaged 134 ± 12 g‐dry wt m^?2 in 2003, 127 ± 17 g‐dry wt m^?2 in 2004 and 149 ± 23 g‐dry wt m^?2 in 2005. Total N and C sedimentation ranged from 0.49 to 0.92 g‐N m^?2 and 5.2 to 19.9 g‐C m^?2. Fe dominates the sediment chemistry and results show the elemental abundance in the order of Al > Fe > Ca > K > Mg > S > P > Na > Mn > Zn > B > Cu > Mo. A hydrologic pulsing index (HPI) could be used as an indicator for mass changes of energies with hydrologic pulsing events. Restoration of seasonally flooded bottomland forests could stimulate potentially large nutrient and Fe releases, which would eventually lead to an enhanced forest productivity and biodiversity. Copyright © 2007 John Wiley & Sons, Ltd.     

Allelopathic effect of phenolic acids from humic solutions on two spruce mycorrhizal fungi:Cenococcum graniforme andLaccaria laccata

The aim of this investigation was to determine the impact ofp-hydroxyacetophenone,p-hydroxybenzoic acid, catechol, and protocatechuic acid on respiration of two spruce mycorrhizal fungi:Laccaria laccata andCenococcum graniforme. These phenols are produced byVaccinium myrtillus,Athyrium filixfemina, andPicea abies, predominant species of spruce forests in the Alps, and they are also present in humic solutions at 10^–10 M or 10^–5 M. Respiration of the two fungi was inhibited by the four phenolic acids, even at concentrations ranging from 10^–5 M to 10^–7 M. These data show phenolic acids from humic solutions have biological activity at extremely low concentrations, suggesting a contribution ofV. myrtillus, A. filixfemina, andP. abies to allelopathic inhibition of mycorrhizal fungi.     

基于蚁群算法的区域覆盖卫星星座优化设计

首先建立了以区域覆盖性能为目标的卫星星座参数优化模型,通过在连续域定义新的蚂蚁分类与转移策略改进了蚁群算法,使算法能够兼顾多目标优化时目标不兼容的情况,给出了基于该算法实现星座参数优化的框架。优化仿真实验验证了该算法的有效性,可为星座方案决策提供有力的支持。     

The role of forest and bioenergy strategies in the global carbon cycle

Forest and bioenergy strategies offer the prospect of reduced CO₂ emissions to the atmosphere. Such strategies can affect the net flux of carbon to the atmosphere through 4 mechanisms: storage of C in the biosphere; storage of C in forest products; use of biofuels to displace fossil-fuel use; use of wood products which often displaces other products that require more fossil fuel for their production. We use the mathematical model GORCAM (Graz/Oak Ridge Carbon Accounting Model) to examine these mechanisms for 16 land-use scenarios. Over long time intervals the amount of C stored in the biosphere and in forest products reaches a steady state and continuing mitigation of C emissions depends on the extent to which fossil fuel use is displaced by the use of bioenergy and wood products. The relative effectiveness of alternative forest and bioenergy strategies and their impact on net C emissions strongly depend, for example, on the productivity of the site, its current usage, and the efficiency with which the harvest is used. When growth rates are high and harvest is used efficiently, the dominant opportunity for net reduction in C emissions is seen to be fossil-fuel displacement. At the growth rates and efficiencies of harvest utilization adopted in many of our base scenarios, the net C balance at the end of 100 years is very similar whether trees are harvested and used for energy and traditional forest products, or reforestation and forest protection strategies are implemented. The C balance on a plantation system that provides a constant output of biomass products can look different than the balance of a single parcel of land.     

词汇、语法和传情达意--一个湖边餐厅的习作

建筑设计往往是以传达情感为最终目的，因此语言的简单和熟练便显得愈发的重要。这个餐厅的设计尝试以简单的词汇组成直截的语言，力图清晰明确的传递建筑师的情感。