On the origin of tropospheric ozone and NOx over the tropical South Pacific

The budgets of ozone and nitrogen oxides (NOx = NO + NO2) in the tropical South Pacific troposphere are analyzed by photochemical point modeling of aircraft observations at 0-12 km altitude from the Pacific Exploratory Mission-Tropics A campaign flown in September-October 1996. The model reproduces the observed NO2/NO concentration ratio to within 30% and has similar success in simulating observed concentrations of peroxides (H2O2, CH3OOH), lending confidence in its use to investigate ozone chemistry. It is found that chemical production of ozone balances only half of chemical loss in the tropospheric column over the tropical South Pacific. The net loss is 1.8 x 1011 molecules cm-2 s-1. The missing source of ozone is matched by westerly transport of continental pollution into the region. Independent analysis of the regional ozone budget with a global three-dimensional model corroborates the results from the point model and reveals the importance of biomass burning emissions in South America and Africa for the ozone budget over the tropical South Pacific. In this model, biomass burning increases average ozone concentrations by 7-8 ppbv throughout the troposphere. The NOx responsible for ozone production within the South Pacific troposphere below 4 km can be largely explained by decomposition of peroxyacetylnitrate (PAN) transported into the region with biomass burning pollution at higher altitudes. Copyright 1999 by the American Geophysical Union

An assessment of western North Pacific ozone photochemistry based on springtime observations from NASA's PEM-West B (1994) and TRACE-P (2001) field studies

The current study provides a comparison of the photochemical environments for two NASA field studies focused on the western North Pacific (PEM-West-B (PWB) and TRACE-P (TP)). These two studies were separated in calendar time by approximately 7 years. Both studies were carried out under springtime conditions, with PWB being launched in 1994 and TP being deployed in 2001 (i.e., 23 February - 15 March 1994 and 10 March-15 April 2001, respectively). Because of the 7-year time separation, these two studies presented a unique scientific opportunity to assess whether evidence could be found to support the Department of Energy\u27s projections in 1997 that increases in anthropogenic emissions from East Asia could reach 5%/yr. Such projections would lead one to the conclusion that a significant shift in the atmospheric photochemical properties of the western North Pacific would occur. To the contrary, the findings from this study support the most recent emission inventory data [Streets et al., 2003] in that they show no significant systematic trend involving increases in any O3 precursor species and no evidence for a significant shift in the level of photochemical activity over the western North Pacific. This conclusion was reached in spite of there being real differences in the concentration levels of some species as well as differences in photochemical activity between PWB and TP. However, nearly all of these differences were shown to be a result of a near 3-week shift in TP\u27s sampling window relative to PWB, thus placing it later in the spring season. The photochemical enhancements seen during TP were most noticeable for latitudes in the range of 25-45°N. Most important among these were increases in J(O1D), OH, and HO2 and values for photochemical ozone formation and destruction, all of which were typically two times larger than those calculated for PWB. A comparison of these airborne results with ozonesonde data from four Japanese stations provided further evidence showing that the 3-week shift in the respective sampling windows of PWB and TP was a likely cause for the differences seen in O3 levels and in photochemical activity between the two airborne studies. Copyright 2003 by the American Geophysical Union

Denitrification and nitrous oxide emissions from riparian forests soils exposed to prolonged nitrogen runoff

Compared to upland forests, riparian forest soils have greater potential to remove nitrate (NO3) from agricultural run-off through denitrification. It is unclear, however, whether prolonged exposure of riparian soils to nitrogen (N) loading will affect the rate of denitrification and its end products. This research assesses the rate of denitrification and nitrous oxide (N2O) emissions from riparian forest soils exposed to prolonged nutrient run-off from plant nurseries and compares these to similar forest soils not exposed to nutrient run-off. Nursery run-off also contains high levels of phosphate (PO4). Since there are conflicting reports on the impact of PO4 on the activity of denitrifying microbes, the impact of PO4 on such activity was also investigated. Bulk and intact soil cores were collected from N-exposed and non-exposed forests to determine denitrification and N2O emission rates, whereas denitrification potential was determined using soil slurries. Compared to the non-amended treatment, denitrification rate increased 2.7- and 3.4-fold when soil cores collected from both N-exposed and non-exposed sites were amended with 30 and 60 μg NO3-N g-1 soil, respectively. Net N2O emissions were 1.5 and 1.7 times higher from the N-exposed sites compared to the non-exposed sites at 30 and 60 μg NO3-N g-1 soil amendment rates, respectively. Similarly, denitrification potential increased 17 times in response to addition of 15 μg NO3-N g-1 in soil slurries. The addition of PO4 (5 μg PO4–P g-1) to soil slurries and intact cores did not affect denitrification rates. These observations suggest that prolonged N loading did not affect the denitrification potential of the riparian forest soils; however, it did result in higher N2O emissions compared to emission rates from non-exposed forests

To Sleep, to Strive, or Both: How Best to Optimize Memory

While numerous studies have shown that a night of sleep profits memory relative to wake, we still have little understanding about what factors mediate this effect of sleep. A clear understanding of the dynamics of this effect of sleep beyond the initial night of sleep is also lacking. Here, we examined the effect of extrinsic rewards on sleep-dependent declarative memory processing across 12 and 24 hr training-retest intervals. Subjects were either paid based on their performance at retest ($1 for each correct answer), or received a flat fee for participation. After a 12 hr interval we observed pronounced benefits of both sleep and reward on memory. Over an extended 24 hr interval we found 1) that an initial night of sleep partially protects memories from subsequent deterioration during wake, and 2) that sleep blocks further deterioration, and may even have a restorative effect on memory, when it follows a full day of wake. Interestingly, the benefit imparted to rewarded (relative to unrewarded) stimuli was equal for sleep and wake subjects, suggesting that the sleeping brain may not differentially process rewarded information, relative to wake. However, looking at the overall impact of sleep relative to reward in this protocol, it was apparent that sleep both imparted a stronger mnemonic boost than reward, and provided a benefit to memory regardless of whether it occurred in the first or the second 12 hrs following task training

ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics

<p>Abstract</p> <p>Background</p> <p>Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or MS^E) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer.</p> <p>Results</p> <p>An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data.</p> <p>Conclusion</p> <p>The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories.</p

The Wolbachia endosymbiont as an anti-filarial nematode target

Human disease caused by parasitic filarial nematodes is a major cause of global morbidity. The parasites are transmitted by arthropod intermediate hosts and are responsible for lymphatic filariasis (elephantiasis) or onchocerciasis (river blindness). Within these filarial parasites are intracellular alpha-proteobacteria, Wolbachia, that were first observed almost 30 years ago. The obligate endosymbiont has been recognized as a target for anti-filarial nematode chemotherapy as evidenced by the loss of worm fertility and viability upon antibiotic treatment in an extensive series of human trials. While current treatments with doxycycline and rifampicin are not practical for widespread use due to the length of required treatments and contraindications, anti-Wolbachia targeting nevertheless appears a promising alternative for filariasis control in situations where current programmatic strategies fail or are unable to be delivered and it provides a superior efficacy for individual therapy. The mechanisms that underlie the symbiotic relationship between Wolbachia and its nematode hosts remain elusive. Comparative genomics, bioinfomatic and experimental analyses have identified a number of potential interactions, which may be drug targets. One candidate is de novo heme biosynthesis, due to its absence in the genome sequence of the host nematode, Brugia malayi, but presence in Wolbachia and its potential roles in worm biology. We describe this and several additional candidate targets, as well as our approaches for understanding the nature of the host-symbiont relationship

Combined effects of precipitation and nitrogen deposition on native and invasive winter annual production in California deserts

Primary production in deserts is limited by soil moisture and N availability, and thus is likely to be influenced by both anthropogenic N deposition and precipitation regimes altered as a consequence of climate change. Invasive annual grasses are particularly responsive to increases in N and water availabilities, which may result in competition with native forb communities. Additionally, conditions favoring increased invasive grass production in arid and semi-arid regions can increase fire risk, negatively impacting woody vegetation that is not adapted to fire. We conducted a seeded garden experiment and a 5-year field fertilization experiment to investigate how winter annual production is altered by increasing N supply under a range of water availabilities. The greatest production of invasive grasses and native forbs in the garden experiment occurred under the highest soil N (inorganic N after fertilization = 2.99 g m−2) and highest watering regime, indicating these species are limited by both water and N. A classification and regression tree (CART) analysis on the multi-year field fertilization study showed that winter annual biomass was primarily limited by November–December precipitation. Biomass exceeded the threshold capable of carrying fire when inorganic soil N availability was at least 3.2 g m−2 in piñon-juniper woodland. Due to water limitation in creosote bush scrub, biomass exceeded the fire threshold only under very wet conditions regardless of soil N status. The CART analyses also revealed that percent cover of invasive grasses and native forbs is primarily dependent on the timing and amount of precipitation and secondarily dependent on soil N and site-specific characteristics. In total, our results indicate that areas of high N deposition will be susceptible to grass invasion, particularly in wet years, potentially reducing native species cover and increasing the risk of fire

Accelerated Evolution of Mitochondrial but Not Nuclear Genomes of Hymenoptera: New Evidence from Crabronid Wasps

Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes