Simulating reactive nitrogen, carbon monoxide, and ozone in California during ARCTAS-CARB 2008 with high wildfire activity

Predictions of O_3, CO, total NO_y and individual NO_y species (NO, NO_2, HNO_3, PAN, alkyl nitrates and aerosol nitrate) from a fine resolution regional air quality modeling system for the South Coast Air Basin (SoCAB) and San Joaquin Valley Air Basin (SJVAB) of California are presented and evaluated for the 2008 ARCTAS-CARB campaign. The measurements of the chemical compounds from the fire plumes during the field campaign allow for the evaluation of the model's ability to simulate fire-influenced air masses as well. In general, the model successfully simulated the broad spatial distribution of chemical compounds in both air basins as well as the variation within the basins. Using inventories that reflect 2008 emissions levels, the model performed well in simulating NO_x (NO + NO_2) in SoCAB. Therefore, the under prediction of O_3 over these areas is more likely caused by uncertainties with the VOC emissions, chemistry, or discrepancies in the meteorology. The model did not capture the relatively high levels of O_3, and some reactive nitrogen species that were measured off shore of the SoCAB, indicating potential missing sources or the transport from on shore to off shore was not successfully captured. In SJVAB, the model had good performance in simulating different chemical compounds in the Fresno and Arvin areas. However, enhanced concentrations of O_3, NO_x, HNO_3 and PAN near dairy farms were significantly underestimated in the model. Negative biases also exist for O_3 and HNO_3 near oil fields, suggesting larger uncertainties associated with these emission sources. While the model simulated the total NO_y mixing ratios reasonably well, the prediction for partitioning between individual compounds showed larger uncertainties in the model simulation. Although the fire emissions inventory was updated to include the latest emissions estimates and speciation profiles, our model shows limited improvement in simulating the enhancement of O_3, CO, and PAN under fire impact as compared to a previous version of the modeling system. Further improvements in simulating fire emissions, especially the timing and the plume injection heights, are desired in order to better simulate the impact of fires

Cloning whole bacterial genomes in yeast

Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation

An extended approach to calculate the ozone relative response factors used in the attainment demonstration for the National Ambient Air Quality Standards

<div><p>With the promulgation of the National Ambient Air Quality Standards (NAAQS or standard) for 8-hr ozone (O₃), the U.S. Environmental Protection Agency (EPA) issued modeling guidance that advocated the use of results from photochemical air quality models in a relative sense. In doing so, the EPA provided guidance on how to calculate relative response factors (RRFs) that can project current design value (DV) mixing ratios into the future for the purpose of determining the attainment status with respect to the O₃ standard. The RRFs recommended by the EPA represent the average response of the photochemical model over a broad range of O₃ mixing ratios above a specified cutoff threshold. However, it is known that O₃ response to emission reductions of limiting precursors (i.e., NO_x and/or VOC) is greater on days with higher O₃ mixing ratios compared to days with lower mixing ratios. In this study, we present a segmented RRF concept termed band-RRF, which takes into account the different model responses at different O₃ mixing ratios. The new band-RRF concept is demonstrated in the San Joaquin Valley (SJV) region of California for the 1-hr and 8-hr O₃ standards. The 1-hr O₃ analysis is relevant to work done in support of the SJV O₃ State Implementation Plan (SIP) submitted to the EPA in 2013. The 8-hr example for the future year of 2019 is presented for illustrative purposes only. Further work will be conducted with attainment deadline of 2032 as part of upcoming SIPs for the 0.075 parts per million (ppm) 8-hr O₃ standard. The applicability of the band-RRF concept to the particulate matter (PM_2.5) standards is also discussed. </p><p></p><p>Implications:</p><p>Results of photochemical models are used in regulatory applications in a relative sense using relative response factors (RRFs), which represent the impacts of emissions reductions over a wide range of ozone (O₃) values. It is possible to extend the concept of RRFs to account for the fact that higher O₃ mixing ratios (both 1-hr and 8-hr) respond more to emissions controls of limiting precursors than do lower O₃ mixing ratios. We demonstrate this extended concept, termed band-RRF, for the 1-hr and 8-hr O₃ National Ambient Air Quality Standard (NAAQS or standard) in the San Joaquin Valley of California. This extension can also be made applicable to the 24-hr PM_2.5 and annual PM_2.5 standards.</p><p></p><p></p></div

Simulating reactive nitrogen, carbon monoxide, and ozone in California during ARCTAS-CARB 2008 with high wildfire activity

Predictions of O3, CO, total NOy and individual NOy species (NO, NO2, HNO3, PAN, alkyl nitrates and aerosol nitrate) from a fine resolution regional air quality modeling system for the South Coast Air Basin (SoCAB) and San Joaquin Valley Air Basin (SJVAB) of California are presented and evaluated for the 2008 ARCTAS-CARB campaign. The measurements of the chemical compounds from the fire plumes during the field campaign allow for the evaluation of the model\u27s ability to simulate fire-influenced air masses as well. In general, the model successfully simulated the broad spatial distribution of chemical compounds in both air basins as well as the variation within the basins. Using inventories that reflect 2008 emissions levels, the model performed well in simulating NOx (NO + NO2) in SoCAB. Therefore, the under prediction of O3 over these areas is more likely caused by uncertainties with the VOC emissions, chemistry, or discrepancies in the meteorology. The model did not capture the relatively high levels of O3, and some reactive nitrogen species that were measured off shore of the SoCAB, indicating potential missing sources or the transport from on shore to off shore was not successfully captured. In SJVAB, the model had good performance in simulating different chemical compounds in the Fresno and Arvin areas. However, enhanced concentrations of O3, NOx, HNO3 and PAN near dairy farms were significantly underestimated in the model. Negative biases also exist for O3 and HNO3 near oil fields, suggesting larger uncertainties associated with these emission sources. While the model simulated the total NOy mixing ratios reasonably well, the prediction for partitioning between individual compounds showed larger uncertainties in the model simulation. Although the fire emissions inventory was updated to include the latest emissions estimates and speciation profiles, our model shows limited improvement in simulating the enhancement of O3, CO, and PAN under fire impact as compared to a previous version of the modeling system. Further improvements in simulating fire emissions, especially the timing and the plume injection heights, are desired in order to better simulate the impact of fires

Selective cleavage of human sex hormone-binding globulin by kallikrein-related peptidases and effects on androgen action in LNCaP prostate cancer cells

Free to read on publisher website Stimulation of the androgen receptor via bioavailable androgens, including testosterone and testosterone metabolites, is a key driver of prostate development and the early stages of prostate cancer. Androgens are hydrophobic and as such require carrier proteins, including sex hormone-binding globulin (SHBG), to enable efficient distribution from sites of biosynthesis to target tissues. The similarly hydrophobic corticosteroids also require a carrier protein whose affinity for steroid is modulated by proteolysis. However, proteolytic mechanisms regulating the SHBG/androgen complex have not been reported. Here, we show that the cancer-associated serine proteases, kallikrein-related peptidase (KLK)4 and KLK14, bind strongly to SHBG in glutathione S-transferase interaction analyses. Further, we demonstrate that active KLK4 and KLK14 cleave human SHBG at unique sites and in an androgen-dependent manner. KLK4 separated androgen-free SHBG into its two laminin G-like (LG) domains that were subsequently proteolytically stable even after prolonged digestion, whereas a catalytically equivalent amount of KLK14 reduced SHBG to small peptide fragments over the same period. Conversely, proteolysis of 5α-dihydrotestosterone (DHT)-bound SHBG was similar for both KLKs and left the steroid binding LG4 domain intact. Characterization of this proteolysis fragment by [(3)H]-labeled DHT binding assays revealed that it retained identical affinity for androgen compared with full-length SHBG (dissociation constant = 1.92 nM). Consistent with this, both full-length SHBG and SHBG-LG4 significantly increased DHT-mediated transcriptional activity of the androgen receptor compared with DHT delivered without carrier protein. Collectively, these data provide the first evidence that SHBG is a target for proteolysis and demonstrate that a stable fragment derived from proteolysis of steroid-bound SHBG retains binding function in vitro

Magnetostratigraphically-calibrated dinoflagellate cyst bioevents for the uppermost Eocene to lowermost Miocene of the western North Atlantic (IODP Expedition 342, Paleogene Newfoundland sediment drifts)

The Oligocene epoch represents a somewhat neglected chapter in paleoclimate and paleoceanographic history, which is at least partially due to the scarcity of complete Oligocene sedimentary archives and poor biostratigraphic age control. Many of the biotic events registered in Oligocene microfossils are strongly diachronous across latitudes as a response to increased global cooling and enhanced meridional temperature gradients. To improve biostratigraphic age control for the Oligocene of the North Atlantic Ocean, we carried out a high-resolution study of dinoflagellate cysts from Integrated Ocean Drilling Program (IODP) Sites U1405, U1406 and U1411 off Newfoundland. Together the sites comprise an apparently complete uppermost Eocene (34.9 Ma) to lowermost Miocene (21.7 Ma) sequence with good magnetostratigraphic age control. This allows us to firmly tie identified dinoflagellate cyst bioevents to the geomagnetic polarity timescale. In the dinoflagellate cyst assemblages studied we have identified and magnetostratigraphically-calibrated ten first and 19 last appearance datums. Our magnetostratigraphically-calibrated dinocyst-based biostratigraphy, which is based on an average sample resolution of a sample every ~ 150 kyrs, will contribute to an improved age framework for future paleoceanographical studies in the higher-latitude North Atlantic