Ensemble structural analyses depict the regulatory mechanism of non-phosphorylated human MAP2K4

Mitogen-activated protein kinase kinase 4 (MAP2K4) plays a critical role in regulating the stress-activated protein kinase signaling cascade. A small angle X-ray scattering experiment, a powerful technique for analyzing a solution structure cleared from the structural artifacts due to crystal packing, provided the ensemble structures of human non-phosphorylated MAP2K4 in three states involving the apo form, the binary complex with an ATP analogue, and the ternary complex with the ATP analogue and substrate peptide. These ensemble structures provided more detailed mechanisms for regulating MAP2K4 in addition to those delineated only by the crystal structures in three states.     

Distribution analysis of Leptoglossus occidentalis Heidemann (Heteroptera: Coreidae) in South Korea using climate and host plant ensemble maps

Leptoglossus occidentalis Heidemann (Heteroptera: Coreidae) is a notorious pest that causes irreversible damage to coniferous forests in South Korea. However, an effective control strategy is still under development. In this study, we used CLIMEX to analyze the potential distribution of L. occidentalis in relation to climate and host plants in South Korea for the identification of effective control spots. The climate needs of L. occidentalis under current and future climate conditions were analyzed and projected on a map along with the distribution of coniferous forests. The CLIMEX model projected that the area of L. occidentalis distribution would decrease slightly in 2060 compared with that at present. However, it was projected that occurrence in mountainous regions would be sustained, suggesting continued damage to coniferous forests in South Korea.     

Dynamic Diet Planner: A Personal Diet Recommender System Based on Daily Activity and Physical Condition

Background and ObjectivesAt the beginning of human civilization, human being needs to undergo immense physical labor to survive. During those days high-calorie diet was essential. However, the evolution of technology has changed the scenario and much lesser amount of physical labor is required to survive in modern hi-tech days, requiring less amount of calorie. The excess calorie gets deposited in the body in the form of white fat. As a consequence, obesity appears as an epidemic all over the world. Long term obesity causes many diseases like heart attack, stroke, diabetes, and many other ailments. It is tough for people, who honestly want to check their obesity by controlling food habits, to continue a static diet chart with fixed restricted foods for a long time. Most of the time, people give up such restrictions on food. It will be very useful if a system exists, that will generate a dynamic diet chart based on calorie spend by the body.MethodsThis research describes a system that will generate a dynamic diet chart based on calorie spend by the body and other data like user's BMI, food preferences, etc. In this system, user can tailor his/her diet chart by changing daily physical activities (activities that burn calories). The main contributions of the proposed system are as follows:

• •A dedicated hardware system to quantify physical labor during walking and running throughout the day from feet pressure changes along with walk cycle detection.
• •The proposed hardware system can distinguish between walk and run.
• •A dynamic diet chart preparation system, where the user has the provision to plan his/her diet chart with food affinity.

The entire work is divided into two modules; the first one focuses on the hardware design to detect and quantify physical activities during “walking” and “running”. These data are used in the second part. The second part contains calorie calculation along with the preparation of a dynamic diet chart with food affinity. In the hardware design, an Application Specific Integrated Circuit (ASIC) is proposed to measure the physical activity during “walking” and “running”.ResultAt the time of hardware logic synthesis, VHDL and FPGA are used. Experimental results show that the proposed hardware provides more accurate results than a pedometer. There is no standard metric to measure the performance of the dynamic diet chart generation system. Competency of the dietitian at the time of setting the parameters, honesty of the users at the time of the interactive session, etc. are the main factors that influence heavily the performance of the dynamic diet chart preparation system. The advantage of dynamic diet chart is that users can modify the diet menu as per their wish, and the system generates a diet chart in such a way that calorie intake (through food items) is maintained properly. In addition to this, the user can plan his future meals.DiscussionThis work is an interdisciplinary work. It is a blending of electronics (FSM), design, and computation for decision making; the computation portion includes software engineering, soft computing, etc. Future plan of this work is to integrate this system with “Cloud” to provide different data analysis related services, like region-wise food habit pattern prediction, health-related statistics, etc.     

SMET: Systematic multiple enzyme targeting – a method to rationally design optimal strains for target chemical overproduction

Identifying multiple enzyme targets for metabolic engineering is very critical for redirecting cellular metabolism to achieve desirable phenotypes, e.g., overproduction of a target chemical. The challenge is to determine which enzymes and how much of these enzymes should be manipulated by adding, deleting, under-, and/or over-expressing associated genes. In this study, we report the development of a systematic multiple enzyme targeting method (SMET), to rationally design optimal strains for target chemical overproduction. The SMET method combines both elementary mode analysis and ensemble metabolic modeling to derive SMET metrics including l-values and c-values that can identify rate-limiting reaction steps and suggest which enzymes and how much of these enzymes to manipulate to enhance product yields, titers, and productivities. We illustrated, tested, and validated the SMET method by analyzing two networks, a simple network for concept demonstration and an Escherichia coli metabolic network for aromatic amino acid overproduction. The SMET method could systematically predict simultaneous multiple enzyme targets and their optimized expression levels, consistent with experimental data from the literature, without performing an iterative sequence of single-enzyme perturbation. The SMET method was much more efficient and effective than single-enzyme perturbation in terms of computation time and finding improved solutions.     

Lysine acetylation sites prediction using an ensemble of support vector machine classifiers

Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/.