Interactive roles of core clock components and histone methyltransferases in circadian chromatin regulation in Arabidopsis

The importance of circadian clock function has been demonstrated in almost all organisms examined to date. Despite divergences in oscillator components, a chromatin-dependent mechanism of clock gene regulation appears to be common in the circadian system among different organisms. Previous studies have shown that rhythmic expression of core clock components correlates with circadian oscillations of active chromatin markers at the promoters. In this study, we investigate the time-dependent pattern of activating chromatin marks H3K4me3 and H3K9ac on a genomic scale to identify genes with a circadian chromatin profile in Arabidopsis. We found that about one fourth of loci with H3K4me3 occupancy or H3K9ac occupancy showed a rhythmic chromatin oscillation. We further identified that the H3K4me3 methyltransferases Arabidopsis Thaliana Trithorax Protein 1 (ATX1) and the Arabidopsis ASH1 HOMOLOG 2 (ASHH2) are subjected to clock control. In addition, ASHH2 was shown to be a novel regulator of core clock genes. Our findings propose a functional link between core clock regulators and temporal modification of activating chromatin marks in plant.Cellular and Molecular Biolog

Solving Bluetooth deficiencies through publish and subscribe systems

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (p. 85-87).Research in pervasive computing aims to fully integrate computing devices into our everyday environments in a seamless and efficient manner. Wireless technology such as Bluetooth takes us a step closer by replacing traditional cable connections with a more searnless communication transport, adding mobility and more human-centric computation. However, if we are to fully integrate this technology, we must first address some of its shortcomings, particularly those with respect to areas with a high density of Bluetooth devices. Four of these shortcomings: susceptibility to anonymous attacks, poor power management, synchrony requirement, and lack of friendships stem from the tight coupling of device interactions during the discovery protocol. One solution to this problem uses the advantages of publish and subscribe systems to decouple this interaction between smart mobile devices. Available devices can announce their availability to a central controller while devices interested in finding others can announce their interests. When a match occurs, the controller notifies both parties and provides information on how they can form a direct connection. This solution preserves the functionality of the Bluetooth connection protocol while circumventing the four shortcomings. The assumptions it makes are reasonable when placed in a the context of personal computing environment. Future considerations include optimizations that utilize caching, improvements on performance, increases in system capacity, and solutions for including dumb devices.by Jessica Yu-Tien Huang.M.Eng

Real value prediction of protein solvent accessibility using enhanced PSSM features

<p>Abstract</p> <p>Background</p> <p>Prediction of protein solvent accessibility, also called accessible surface area (ASA) prediction, is an important step for tertiary structure prediction directly from one-dimensional sequences. Traditionally, predicting solvent accessibility is regarded as either a two- (exposed or buried) or three-state (exposed, intermediate or buried) classification problem. However, the states of solvent accessibility are not well-defined in real protein structures. Thus, a number of methods have been developed to directly predict the real value ASA based on evolutionary information such as position specific scoring matrix (PSSM).</p> <p>Results</p> <p>This study enhances the PSSM-based features for real value ASA prediction by considering the physicochemical properties and solvent propensities of amino acid types. We propose a systematic method for identifying residue groups with respect to protein solvent accessibility. The amino acid columns in the PSSM profile that belong to a certain residue group are merged to generate novel features. Finally, support vector regression (SVR) is adopted to construct a real value ASA predictor. Experimental results demonstrate that the features produced by the proposed selection process are informative for ASA prediction.</p> <p>Conclusion</p> <p>Experimental results based on a widely used benchmark reveal that the proposed method performs best among several of existing packages for performing ASA prediction. Furthermore, the feature selection mechanism incorporated in this study can be applied to other regression problems using the PSSM. The program and data are available from the authors upon request.</p

Impact analysis of model combined by hand-arm and golf club when striking ball

Golf is an extremely popular activity that over 60 million of people enjoy playing it. Overuse injuries associated with the back, neck, wrist, shoulder, elbow, knee, etc., are common for both professional and amateur player due to golf swing. A lot of researchers investigate the mechanical behavior of golf club or biological response of human body individually. But there is little study on the dynamic interaction between the hand-arm and golf club mashie (HAGCM) when striking ball. Solidworks package is used to draw the 3D geometric model of a left hand-arm contacted at the grip of the golf club. Then the 3D biomechanical model is imported into ANSYS software for transient (impact) analysis. Due to complicated geometry of the sharp edge at the club head and the hand-arm, the tetrahedral element is applied for all components of HAGCM to save computer resource during ANSYS process. Finite element convergence test is obtained before any further analysis. In order to simulate the ball-striking, the hitting surface of the club head is subjected to the impact force of 22 N within 0.01 seconds. All the deformations, principle and shear stresses of the time response found in the vibrating golf head, shaft, grip and hand are compared with each other. Normal and eccentric impact analyses for HAGCM are examined as well. The angular velocity found in eccentric impact is much higher than that in normal impact, and it will cause the muscle to exert more power to hold the golf club

V2PSense: Enabling Cellular-based V2P Collision Warning Service Through Mobile Sensing

The C-V2X (Cellular Vehicle-to-Everything) technology is developing in full swing. One of its mainstream services can be the Vehicle-to-Pedestrian (V2P) service. It can protect pedestrians who are mostly vulnerable on the road. In this work, we seek to enable a V2P service that can identify which pedestrians may be nearby a dangerous driving event and then notify them of warning messages. To enable this V2P service, there are two major challenges. First, a low-latency V2P message transport is required for this infrastructure-based service. Second, the pedestrian’s smartphone requires an energy-efficient outdoor positioning method instead of power-hungry GPS due to its limited battery life. We thus propose a novel solution, V2PSense, which trades off positioning precision for energy savings while achieving low-latency message transport with LTE high-priority bearers. It does a coarse-grained positioning by leveraging intermittent GPS information and mobile sensing data, which includes step count from the pedometer and cellular signal strength changes. Though the V2PSense’s positioning is not as precise as the GPS, it can still ensure that all the pedestrians nearby dangerous spots can be notified. Our results show that it can achieve the average precision ratio 92.6% for estimating where the pedestrian is while saving 20.8% energy, compared with the GPS always-on case.This work was partially supported by the Ministry of Science and Tech-nology, Taiwan, under grant numbers 106-2622-8-009-017 and 106-2218-E-009-018, and by the H2020 collaborative Europe/Taiwan research project 5G-CORAL (grant num. 761586

A study on the flexibility of enzyme active sites

<p>Abstract</p> <p>Background</p> <p>A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted.</p> <p>Results</p> <p>Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites.</p> <p>Conclusions</p> <p>This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites.</p

MicroRNA-146a-5p Mediates High Glucose-Induced Endothelial Inflammation via Targeting Interleukin-1 Receptor-Associated Kinase 1 Expression

Background and Aims: Interleukin-1 receptor-associated kinase-1 (IRAK-1) is critical for mediating toll-like receptor and interleukin-1 receptor signaling. In this study, we have examined whether IRAK-1 expression is altered in high glucose (HG)-stimulated human aortic endothelial cells (HAECs), and whether microRNAs (miRs) target IRAK-1 to regulate HG-induced endothelial inflammation.Methods: HAECs were treated with HG for 24 and 48 h. Real-time PCR, Western blot, monocyte adhesion assay, bioinformatics analysis, TaqMan® arrays, microRNA mimic or inhibitor transfection, luciferase reporter assay and siRNA IRAK-1 transfection were performed. The aortic tissues from db/db type 2 diabetic mice were examined by immunohistochemistry staining.Results: HG time-dependently increased IRAK-1 mRNA and protein levels in HAECs, and was associated with increased VCAM-1/ICAM-1 gene expression and monocyte adhesion. Bioinformatic analysis, TaqMan® arrays, and real-time PCR were used to confirm that miR-146a-5p, miR-339-5p, and miR-874-3p were significantly downregulated in HG-stimulated HAECs, suggesting impaired feedback restraints on HG-induced endothelial inflammation via IRAK-1. However, only miR-146a-5p mimic transfection reduced the HG-induced upregulation of IRAK-1 expression, VCAM-1/ICAM-1 expression, and monocyte adhesion. Additionally, IRAK-1 depletion reduced HG-induced VCAM-1/ICAM-1 gene expression, and monocyte adhesion, indicating that HG-induced endothelial inflammation was mediated partially through IRAK-1. In vivo, intravenous injections of miR-146a-5p mimic prevented endothelial IRAK-1 and ICAM-1 expression in db/db mice.Conclusion: These results suggest that miR-146a-5p is involved in the regulation of HG-induced endothelial inflammation via modulation of IRAK-1; indicating that miR-146a-5p may be a novel target for the treatment of diabetic vascular complications

Xi Jin-Ping's world cup dreams: from a major sports country to a world sports power

Football is among the world’s most popular sports. It is also one which China has sought to develop in the field of global professional sport. Nevertheless, the professionalization of football in China has not to date actually improved China's Olympic achievement in the sport. In stark contrast to the glory of being the country that won most gold medals at the 2008 Olympics, China’s poor football performance has been troublesome for the country’s leader. In 2009, newly elected Xi Jin-Ping made a public statement about promoting elite football and expressed his personal hope that China would be capable of both qualifying for the final stages and winning the FIFA World Cup. With such concern on the part of the state leader, attention turned to football, with many private enterprises beginning to echo government policy by demonstrating a willingness to promote elite football. In addition, to accelerate football development, the Chinese government promised to take action on the separation of government and football associations. Research on this process was based on the theoretical framework of state corporatism derived from the work of Schmitter (1974). Semi-structured interviews were conducted as the method of data collection aimed at helping us understand how Chinese government either integrated or controlled relevant stakeholders such as NGOs and private enterprises, and further, to discuss the interactions between them