Outer membrane proteins can be simply identified using secondary structure element alignment

<p>Abstract</p> <p>Background</p> <p>Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery.</p> <p>Results</p> <p>Based on the observation that almost all OMPs consist of antiparallel β-strands in a barrel shape and that their secondary structure arrangements differ from those of other types of proteins, we propose a simple method called SSEA-OMP to identify OMPs using secondary structure element alignment. Through intensive benchmark experiments, the proposed SSEA-OMP method is better than some well-established OMP detection methods.</p> <p>Conclusions</p> <p>The major advantage of SSEA-OMP is its good prediction performance considering its simplicity. The web server implements the method is freely accessible at <url>http://protein.cau.edu.cn/SSEA-OMP/index.html</url>.</p

An Evacuation Model for Passenger Ships That Includes the Influence of Obstacles in Cabins

Passenger behavior and ship environment are the key factors affecting evacuation efficiency. However, current studies ignore the interior layout of passenger ship cabins and treat the cabins as empty rooms. To investigate the influence of obstacles (e.g., tables and stools) on cabin evacuation, we propose an agent-based social force model for advanced evacuation analysis of passenger ships; this model uses a goal-driven submodel to determine a plan and an extended social force submodel to govern the movement of passengers. The extended social force submodel considers the interaction forces between the passengers, crew, and obstacles and minimises the range of these forces to improve computational efficiency. We drew the following conclusions based on a series of evacuation simulations conducted in this study: (1) the proposed model endows the passenger with the behaviors of bypassing and crossing obstacles, (2) funnel-shaped exits from cabins can improve evacuation efficiency, and (3) as the exit angle increases, the evacuation time also increases. These findings offer ship designers some insight towards increasing the safety of large passenger ships

Standard metabolic rate predicts growth trajectory of juvenile Chinese crucian carp (Carassius auratus) under changing food availability

Phenotypic traits vary greatly within populations and can have a significant influence on aspects of performance. The present study aimed to investigate the effects of individual variation in standard metabolic rate (SMR) on growth rate and tolerance to food-deprivation in juvenile crucian carp (Carassius auratus) under varying levels of food availability. To address this issue, 19 high and 16 low SMR (individuals were randomly assigned to a satiation diet for 3 weeks, whereas another 20 high and 16 low SMR individuals were assigned to a restricted diet (approximately 50% of satiation) for the same period. Then, all fish were completely food-deprived for another 3 weeks. High SMR individuals showed a higher growth rate when fed to satiation, but this advantage of SMR did not exist in food-restricted fish. This result was related to improved feeding efficiency with decreased food intake in low SMR individuals, due to their low food processing capacity and maintenance costs. High SMR individuals experienced more mass loss during food-deprivation as compared to low SMR individuals. Our results here illustrate context-dependent costs and benefits of intraspecific variation in SMR whereby high SMR individuals show increased growth performance under high food availability but had a cost under stressful environments (i.e., food shortage)