Mi-Young Park

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD+ cofactor.

The ethanologenic bacterium Zymomonas mobilis ZM4 is of special interest because it has a high ethanol yield. This is made possible by the two alcohol dehydrogenases (ADHs) present in Z. mobilis ZM4 (zmADHs), which shift the equilibrium of the reaction toward the synthesis of ethanol. They are metal-dependent enzymes: zinc for zmADH1 and iron for zmADH2. However, zmADH2 is inactivated by oxygen, thus implicating zmADH2 as the component of the cytosolic respiratory system in Z. mobilis. Here, we show crystal structures of zmADH2 in the form of an apo-enzyme and an NAD+–cofactor complex. The overall folding of the monomeric structure is very similar to those of other functionally related ADHs with structural variations around the probable substrate and NAD+ cofactor binding region. A dimeric structure is formed by the limited interactions between the two subunits with the bound NAD+ at the cleft formed along the domain interface. The catalytic iron ion binds near to the nicotinamide ring of NAD+, which is likely to restrict and locate the ethanol to the active site together with the oxidized Cys residue and several nonpolar bulky residues. The structures of the zmADH2 from the proficient ethanologenic bacterium Z. mobilis, with and without NAD+ cofactor, and modeling ethanol in the active site imply that there is a typical metal-dependent catalytic mechanism.

MPIRace-check: detection of message races in MPI programs

Message races, which can cause nondeterministic executions of a parallel program, should be detected for debugging because nondeterminism makes debugging parallel programs a difficult task. Even though there are some tools to detect message races in MPI programs, they do not provide practical information to locate and debug message races in MPI programs. In this paper, we present an on-the-fly detection tool, which is MPIRace-Check, for debugging MPI programs written in C language. MPIRace-Check detects and reports all race conditions in all processes by checking the concurrency of the communication between processes. Also it reports the message races with some practical information such as the line number of a source code, the processes number, and the channel information which are involved in the races. By providing those information, it lets programmers distinguish of unintended races among the reported races, and lets the programmers know directly where the races occur in a huge source code. In the experiment we will show that MPIRace-Check detects the races using some testing programs as well as the tool is efficient.

Ethyl Pyruvate Has Anti-Inflammatory and Delayed Myocardial Protective Effects after Regional Ischemia/Reperfusion Injury

Purpose Ethyl pyruvate has anti-inflammatory properties and protects organs from ischemia/reperfusion (I/R)-induced tissue injury. The aim of this study was to determine whether ethyl pyruvate decreases the inflammatory response after regional I/R injury and whether ethyl pyruvate protects against delayed regional I/R injury in an in vivo rat heart model after a 24 hours reperfusion. Materials and Methods Rats were randomized to receive lactated Ringers solution or ethyl pyruvate dissolved in Ringers solution, which was given by intraperitoneal injection 1 hour prior to ischemia. Rats were subjected to 30 min of ischemia followed by reperfusion of the left coronary artery territory. After a 2 hours reperfusion, nuclear factor κB, myocardial myeloperoxidase activity, and inflammatory cytokine levels were determined. After the 24 hours reperfusion, the hemodynamic function and myocardial infarct size were evaluated. Results At 2 hours after I/R injury, ethyl pyruvate attenuated I/R-induced nuclear factor κB translocation and reduced myeloperoxidase activity in myocardium. The plasma circulating levels of inflammatory cytokines decreased significantly in the ethyl pyruvate-treated group. At 24 hours after I/R injury, ethyl pyruvate significantly improved cardiac function and reduced infarct size after regional I/R injury. Conclusion Ethyl pyruvate has the ability to inhibit neutrophil activation, inflammatory cytokine release, and nuclear factor κB translocation. Ethyl pyruvate is associated with a delayed myocardial protective effect after regional I/R injury in an in vivo rat heart model.

A Comparison of Scalable Labeling Schemes for Detecting Races in OpenMP Programs

Detecting races is important for debugging shared-memory parallel programs, because the races result in unintended nondeterministic executions of the program. On-the-fly technique to detect races uses a scalable labeling scheme which generates concurrency information of parallel threads without any globally-shared data structure. Two efficient schemes of scalable labeling, BD Labeling and NR Labeling, show the similar complexities in space and time, but their actual efficiencies have been compared empirically in no literature to the best of our knowledge. In this paper, we empirically compare these two labeling schemes by monitoring a set of OpenMP kernel programs with nested parallelism. The empirical results show that NR Labeling is more efficient than BD Labeling by at least 1.5 times in generating the thread labels, and by at least 3.5 times in using the labels to detect races in the kernel programs.

Crystal structure of Cmr5 from Pyrococcus furiosus and its functional implications

pfCmr5 and pfCmr4 bind by ion exchange chromatography (View interaction)

Magnetic Turbulence Associated with Magnetic Dipolarizations in the Near-Tail of the Earth's Magnetosphere: Test of Anisotropy

In this paper, the anisotropic nature of the magnetic turbulence associated with magnetic dipolarizations in the Earth’s plasma sheet is examined. Specifically, we determine the power spectral indices for the perpendicular and parallel com ponents of the fluctuating magnetic field with respect to the background magnetic field, and compare them in order to identify possible anisotropic features. For this study, we identify a total of 47 dipolarization events in February 2008 using the magnetic field data observed by the THEMIS A, D and E satellites when they are situated near the neutral sheet in the near-Earth tail. For the identified events, we estimate the spectral indices for the frequency range from 1.3 mHz to 42 mHz. The results show that the degree of anisotropy, as defined by the ratio of the spectral index of the perpendicular components to that of the parallel component, can range from ~0.2 to ~2.6, and there are more events associated with the ratio greater than unity (i.e., the perpendicular index being greater than the parallel index) than those which are anisotropic in the opposite sense. This implies that the dipolarization-associated turbulence of the magnetic field is often anisotropic, to some non-negligible degree. We then discuss how this result differs from what the theory of homogeneous, anisotropic, magnetohydrodynamic turbulence would predict.

Heavy-Ion radiation characteristics of DDR2 synchronous dynamic random access memory fabricated in 56 nm technology

Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara 229-8510, JapanWe developed a mass-memory chip by staking 1 Gbit double data rate 2 (DDR2) synchronous dynamic random access memory (SDRAM) memory core up to 4 Gbit storage for future satellite missions which require large storage for data collected during the mission execution. To investigate the resistance of the chip to the space radiation environment, we have performed heavy-ion-driven single event experiments using Heavy Ion Medical Accelerator in Chiba medium energy beam line. The radiation characteristics are presented for the DDR2 SDRAM (K4T1G164QE) fabricated in 56 nm technology. The statistical analyses and comparisons of the characteristics of chips fabricated with previous technologies are presented. The cross-section values for various single event categories were derived up to ~80 MeVcm

Visualization of Affect-Relations of Message Races for Debugging MPI Programs

Detecting unaffected races is important for debugging MPI parallel programs, because unaffected races can cause the occurrence of affected races which do not need to be debugged. However, the previous techniques can not discern unaffected races from affected races so that programmers will be easily overwhelmed by the vast information of race detection. In this paper, we present a new visualization which lets programmers know which race is affected or not. For this, our technique checks whether any message racing toward a race is affected or not based on happen- before relation, and also checks which process influences a race during an execution. After the execution, it visualizes the affect-relations of the detected races. Therefore, our visualization helps for programmers to effectively distinguish unaffected races from affected races, and to debug MPI parallel programs.

Visualization of Message Races in MPI Parallel Programs

As parallel programs become larger and more complex, it is harder to understand and debug parallel programs. If those programs have race conditions, intended or otherwise, it is more difficult to understand and debug. Visualization is widely accepted as a powerful technique to understand and manage the complexity of parallel programs as well as to detect race conditions. This paper presents a new visualization tool for debugging race conditions in message-passing programs. Our visualization aims to provide effective and useful visualization for programmers to understand complex phenomena such as the interaction of concurrent processes, to handle enormous visual information, and to debug message races in MPI parallel programs.

An asymmetric dimeric structure of TrmJ tRNA methyltransferase from Zymomonas mobilis with a flexible C-terminal dimer

The tRNA methyltransferase J (TrmJ) and D (TrmD) catalyze the transferring reaction of a methyl group to the tRNA anticodon loop. They commonly have the N-terminal domain (NTD) and the C-terminal domain (CTD). Whereas two monomeric CTDs symmetrically interact with a dimeric NTD in TrmD, a CTD dimer has exhibited an asymmetric interaction with the NTD dimer in the presence of a product. The elucidated apo-structure of the full-length TrmJ from Zymomonas mobilis ZM4 shows a dimeric CTD that asymmetrically interacts with the NTD dimer, thereby distributing non-symmetrical potential charge on the both side of the protein surface. Comparison with the product-bound structures reveals a local re-orientation of the two arginine-containing loop at the active site, which interacts with the product. Further, the CTD dimers have diverse orientations compared to the NTD dimers, suggesting their flexibility. These data indicate that an asymmetric interaction between the NTD dimer and the CTD dimer is a common structural feature among TrmJ proteins, regardless of the presence of a substrate or a product.