Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to ellucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63164/1/153623102321112746.pd

Left atrial appendage occlusion with the AMPLATZER Amulet device: Periprocedural and early clinical/echocardiographic data from a global prospective observational study

AIMS: The global, prospective AMPLATZER Amulet observational study documents real-world periprocedural, transoesophageal echocardiographic (TEE) and clinical outcomes from left atrial appendage occlusion (LAAO) using the AMPLATZER Amulet device. The aim of this report is to describe the periprocedural and early clinical/TEE results from this study. METHODS AND RESULTS: This multicentre prospective real-world registry included 1,088 patients (75\ub18.5 years, 64.5% male, CHA2DS2-VASc: 4.2\ub11.6, HAS-BLED: 3.3\ub11.1) with non-valvular atrial fibrillation; 82.8% of patients were considered to have an absolute or relative contraindication to long-term anticoagulation and 72.4% had had a previous major bleeding. Periprocedural results, clinical outcomes up to the first three months and the available TEE results from the first scheduled follow-up (one to three months post implant) are reported. Successful device implantation was achieved in 99.0% of patients. During the procedure and index hospitalisation, major adverse events occurred in 3.2% of patients. Patients were discharged on a single antiplatelet agent (23.0%), dual antiplatelets (54.3%) or an oral anticoagulant (18.9%). TEE follow-up 67\ub123 days post procedure in 673 patients showed adequate (<3 mm jet) occlusion of the appendage in 98.2% of patients and device thrombus in 10 patients (1.5%), as evaluated by core laboratory analysis. CONCLUSIONS: This large real-world prospective registry of catheter-based LAAO using the AMPLATZER Amulet device reports a high implant success rate and a low periprocedural complication rate in a population with a high risk of stroke and bleeding. Transoesophageal echo data confirm good closure rates during follow-up and low rates of device-associated thrombus

Comparison of linear and nonlinear shallow wave water equations applied to tsunami waves over the China Sea

This paper discusses the applications of linear and nonlinear shallow water wave equations in practical tsunami simulations. We verify which hydrodynamic theory would be most appropriate for different ocean depths. The linear and nonlinear shallow water wave equations in describing tsunami wave propagation are compared for the China Sea. There is a critical zone between 400 and 500 m depth for employing linear and nonlinear models. Furthermore, the bottom frictional term exerts a noticeable influence on the propagation of the nonlinear waves in shallow water. We also apply different models based on these characteristics for forecasting potential seismogenic tsunamis along the Chinese coast. Our results indicate that tsunami waves can be modeled with linear theory with enough accuracy in South China Sea, but the nonlinear terms should not be neglected in the eastern China Sea region