Removal of NOx and NOy in Asian outflow plumes: Aircraft measurements over the western Pacific in Januray 2002

The Pacific Exploration of Asian Continental Emission Phase A (PEACE-A) aircraft measurement campaign was conducted over the western Pacific in January 2002. Correlations of carbon monoxide (CO) with carbon dioxide (CO2) and back trajectories are used to identify plumes strongly affected by Asian continental emissions. ΔCO/ΔCO2 ratios (i.e., linear regression slopes of CO-CO2) in the plumes generally fall within the variability range of the CO/CO2 emission ratios estimated from an emission inventory for east Asia, demonstrating the consistency between the aircraft measurements and the emission characterization. Removal rates of reactive nitrogen (NOx and NOy) for the study region (altitude <4 km, 124°-140°E, 25°-45°N) are estimated using the correlation with CO2, the photochemical age of the plumes, and the NOx/ CO2 emission ratio derived from the emission inventory. The plume age is estimated from the rates of hydrocarbon decay and hydroxyl radical (OH) concentration calculated using a constrained photochemical box model. The average lifetime of NOx is estimated to be 1.2 ± 0.4 days. Possible processes controlling the NOx lifetime are discussed in conjunction with results from earlier studies. The average lifetime of NOy is estimated to be 1.7 ± 0.5 days, which is comparable to the NOy lifetime of 1.7-1.8 days that has been previously reported for outflow from the United States. This similarity suggests the importance of chemical processing near the source regions in determining the NOy abundance. Copyright 2004 by the American Geophysical Union

Mechanism of Chemical Activation of Nrf2

NF-E2 related factor-2 (Nrf2) promotes the transcription of many cytoprotective genes and is a major drug target for prevention of cancer and other diseases. Indeed, the cancer-preventive activities of several well-known chemical agents were shown to depend on Nrf2 activation. It is well known that chemopreventive Nrf2 activators stabilize Nrf2 by blocking its ubiquitination, but previous studies have indicated that this process occurs exclusively in the cytoplasm. Kelch-like ECH-associated protein 1 (Keap1) binds to Nrf2 and orchestrates Nrf2 ubiquitination, and it has been a widely-held view that inhibition of Nrf2 ubiquitination by chemopreventive agents results from the dissociation of Nrf2 from its repressor Keap1. Here, we show that while the activation of Nrf2 by prototypical chemical activators, including 5,6-dihydrocyclopenta-1,2-dithiole-3-thione (CPDT) and sulforaphane (SF), results solely from inhibition of its ubiquitination, such inhibition occurs predominantly in the nucleus. Moreover, the Nrf2 activators promote Nrf2 association with Keap1, rather than disassociation, which appears to result from inhibition of Nrf2 phosphorylation at Ser40. Available evidence suggests the Nrf2 activators may block Nrf2 ubiquitination by altering Keap1 conformation via reaction with the thiols of specific Keap1 cysteines. We further show that while the inhibitory effects of CPDT and SF on Nrf2 ubiquitination depend entirely on Keap1, Nrf2 is also degraded by a Keap1-independent mechanism. These findings provide significant new insight about Nrf2 activation and suggest that exogenous chemical activators of Nrf2 enter the nucleus to exert most of their inhibitory impact on Nrf2 ubiquitination and degradation

Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling

The Notch signaling pathway controls numerous cell fate decisions during development and adulthood through diverse mechanisms. Thus, whereas it functions as an oscillator during somitogenesis, it can mediate an all-or-none cell fate switch to influence pattern formation in various tissues during development. Furthermore, while in some contexts continuous Notch signaling is required, in others a transient Notch signal is sufficient to influence cell fate decisions. However, the signaling mechanisms that underlie these diverse behaviors in different cellular contexts have not been understood. Notch1 along with two downstream transcription factors hes1 and RBP-Jk forms an intricate network of positive and negative feedback loops, and we have implemented a systems biology approach to computationally study this gene regulation network. Our results indicate that the system exhibits bistability and is capable of switching states at a critical level of Notch signaling initiated by its ligand Delta in a particular range of parameter values. In this mode, transient activation of Delta is also capable of inducing prolonged high expression of Hes1, mimicking the “ON” state depending on the intensity and duration of the signal. Furthermore, this system is highly sensitive to certain model parameters and can transition from functioning as a bistable switch to an oscillator by tuning a single parameter value. This parameter, the transcriptional repression constant of hes1, can thus qualitatively govern the behavior of the signaling network. In addition, we find that the system is able to dampen and reduce the effects of biological noise that arise from stochastic effects in gene expression for systems that respond quickly to Notch signaling

The influence of up-wave barge motion on the water resonance at a narrow gap between two rectangular barges under waves in the sea

A three-dimensional time-domain potential flow model is developed and applied to simulate the wave resonance in a gap between two side-by-side rectangular barges. A fourth-order predict-correct method is implemented to update free surface boundary conditions. The response of an up-wave barge is predicted by solving the motion equation with the Newmark-β method. Following the validation of the developed numerical model for wave radiation and diffraction around two side-by-side barges, the influence of up-wave barge motion on the gap surfaceresonance is investigated in two different locations of the up-wave barge relative to the back-wave barge at various frequencies. The results reveal that the freely floating up-wave barge significantly influences the resonance frequency and the resonance wave amplitude. Simultaneously, the up-wave barge located in the middle of the back-wave barge leads to a reduction in the resonance wave amplitude and motion response when compared with other configurations

The human chromokinesin Kid is a plus end-directed microtubule-based motor

Kid is a kinesin-like DNA-binding protein known to be involved in chromosome movement during mitosis, although its actual motor function has not been demonstrated. Here, we describe the initial characterization of Kid as a microtubule-based motor using optical trapping microscopy. A bacterially expressed fusion protein consisting of a truncated Kid fragment (amino acids 1–388 or 1–439) is indeed an active microtubule motor with an average speed of ∼160 nm/s, and the polarity of movement is plus end directed. We could not detect processive movement of either monomeric Kid or dimerizing chimeric Kid; however, low levels of processivity (a few steps) cannot be detected with our method. These results are consistent with Kid having a role in chromosome congression in vivo, where it would be responsible for the polar ejection forces acting on the chromosome arms

Dual Regulation of the Transcriptional Activity of Nrf1 by β-TrCP- and Hrd1-Dependent Degradation Mechanisms ▿

A growing body of evidence suggests that Nrf1 is an inducible transcription factor that maintains cellular homeostasis. Under physiological conditions, Nrf1 is targeted to the endoplasmic reticulum (ER), implying that it translocates into the nucleus in response to an activating signal. However, the molecular mechanisms by which the function of Nrf1 is modulated remain poorly understood. Here, we report that two distinct degradation mechanisms regulate Nrf1 activity and the expression of its target genes. In the nucleus, β-TrCP, an adaptor for the SCF (Skp1-Cul1-F-box protein) ubiquitin ligase, promotes the degradation of Nrf1 by catalyzing its polyubiquitination. This activity requires a DSGLS motif on Nrf1, which is similar to the canonical β-TrCP recognition motif. The short interfering RNA (siRNA)-mediated silencing of β-TrCP markedly augments the expression of Nrf1 target genes, such as the proteasome subunit PSMC4, indicating that β-TrCP represses Nrf1 activation. Meanwhile, in the cytoplasm, Nrf1 is degraded and suppressed by the ER-associated degradation (ERAD) ubiquitin ligase Hrd1 and valosin-containing protein (VCP) under normal conditions. We identified a cytoplasmic degradation motif on Nrf1 between the NHB1 and NHB2 domains that exhibited species conservation. Thus, these results clearly suggest that both β-TrCP- and Hrd1-dependent degradation mechanisms regulate the transcriptional activity of Nrf1 to maintain cellular homeostasis