Wind-induced, cross-frontal exchange on Georges Bank : a mechanism for early summer on-bank biological particle transport

Author Posting. © American Geophysical Union, 2003. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 108, C11 (2003): 8011, doi:10.1029/2002JC001358.Water exchange across the tidal-mixing front on the southern flank of Georges Bank (GB) is examined using a two-dimensional (2D) primitive equation ocean model. The model domain features a cross-frontal transect including a June 1999 hydrographic (CTD)/ADCP study made as part of the U.S. GLOBEC Northwest Atlantic/Georges Bank program. The model was initialized with temperature and salinity fields taken on the 15 June 1999 CTD section and run prognostically with tidal forcing, measured winds, and representative surface heat flux. The results show that fluctuations of wind plus tidal mixing can play the following essential role in the short-term transport of water and particles from the stratified region to the mixed region on GB in early summer, when stratification is just developing with a weak thermocline at a depth of about 10 m. First, a passing weather front drives a wind-induced on-bank Ekman transport of the upper part of the water column at the tidal-mixing front and associated particles in the surface mixed layer. Then, when the wind relaxes or changes direction, the water in the on-bank extension of the front (above the thermocline) mixes quickly through enhanced tidal motion in shallower depths of water. As a result, particles that are advected along the extended front stay in the previously well-mixed region of the bank. Surface heating tends to increase the strength of the thermocline and reduce the thickness of the surface mixed layer. This in turn accelerates the on-bank movement of the front under an easterly wind favorable for Ekman transport and thus enhances the on-bank, cross-frontal transport of particles. Since the wind-induced, cross-frontal on-bank transport of water can occur episodically during passages of meteorological fronts, these could produce a larger net cross-frontal flux than that produced by just tidal forcing on equivalent timescales. Therefore wind-induced processes can be important in the on-bank cross-frontal flux of copepods and other zooplankton species that exhibit shallow maxima in their vertical distributions over the southern flank of GB in early summer.This research was supported by the U.S. GLOBEC Northwest Atlantic/Georges Bank program through NOAA grants NA56RG0487, NA960P003, and NA960P005 to C. Chen, NOAA support to R. Schlitz, G. R. Lough, K. Smith, and J. Manning, and NSF grants OCE 96-32357, OCE 98-06379, and OCE 02-27679 to R. Beardsley

A Gene-Based Association Method for Mapping Traits Using Reference Transcriptome Data

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys the benefits of gene-based approaches such as reduced multiple-testing burden and a principled approach to the design of follow-up experiments. Our results demonstrate that PrediXcan can detect known and new genes associated with disease traits and provide insights into the mechanism of these associations

Global sourcing of low-inorganic arsenic rice grain

Arsenic in rice grain is dominated by two species: the carcinogen inorganic arsenic (the sum of arsenate and arsenite) and dimethylarsinic acid (DMA). Rice is the dominant source of inorganic arsenic into the human diet. As such, there is a need to identify sources of low-inorganic arsenic rice globally. Here we surveyed polished (white) rice across representative regions of rice production globally for arsenic speciation. In total 1180 samples were analysed from 29 distinct sampling zones, across 6 continents. For inorganic arsenic the global x ~ x~ was 66 μg/kg, and for DMA this figure was 21 μg/kg. DMA was more variable, ranging from < 2 to 690 μg/kg, while inorganic arsenic ranged from < 2 to 399 μg/kg. It was found that inorganic arsenic dominated when grain sum of species was < 100 μg/kg, with DMA dominating at higher concentrations. There was considerable regional variance in grain arsenic speciation, particularly in DMA where temperate production regions had higher concentrations. Inorganic arsenic concentrations were relatively consistent across temperate, subtropical and northern hemisphere tropical regions. It was only in southern hemisphere tropical regions, in the eastern hemisphere that low-grain inorganic arsenic is found, namely East Africa (x ~ x~  < 10 μg/kg) and the Southern Indonesian islands (x ~ x~  < 20 μg/kg). Southern hemisphere South American rice was universally high in inorganic arsenic, the reason for which needs further exploration

Ionizing Radiation-Induced Oxidative Stress Alters miRNA Expression

). treatment, and 45 after etoposide treatment. Substantial overlap between the miRNA expression changes between agents was observed suggesting a signature miRNA response to cell stress. Changes in the expression of selected miRNA species varied in response to radiation dose and time. Finally, production of reactive oxygen species (ROS) increased with increasing doses of radiation and pre-treatment with the thiol antioxidant cysteine decreased both ROS production and the miRNA response to radiation., and etoposide. Additionally, pre-treatment with cysteine prevented radiation-induced alterations in miRNA expression which suggests that miRNAs are responsive to oxidative stress. Taken together, these results imply that miRNAs play a role in cellular defense against exogenous stress and are involved in the generalized cellular response to genotoxic oxidative stress

Model simulations of the Bay of Fundy Gyre : 2. Hindcasts for 2005–2007 reveal interannual variability in retentiveness

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C09005, doi:10.1029/2008JC004948.A persistent gyre at the mouth of the Bay of Fundy results from a combination of tidal rectification and buoyancy forcing. Here we assess recent interannual variability in the strength of the gyre using data assimilative model simulations. Realistic hindcast representations of the gyre are considered during cruises in 2005, 2006, and 2007. Assimilation of shipboard and moored acoustic Doppler current profiler velocities is used to improve the skill of the simulations, as quantified by comparison with nonassimilated drifter trajectories. Our hindcasts suggest a weakening of the gyre system during May 2005. Retention of simulated passive particles in the gyre during that period was highly reduced. A recovery of the dense water pool in the deep part of the basin by June 2006 resulted in a return to particle retention characteristics similar to climatology. Retention estimates reached a maximum during May 2007 (subsurface) and June–July 2007 (near surface). Interannual variability in the strength of the gyre was primarily modulated by the stratification of the dense water pool inside the Grand Manan Basin. These changes in stratification were associated with mixing conditions the preceding fall–winter and/or advectively driven modification of water mass properties.The preparation of this paper was supported by NSF grant OCE-0430724, NIEHS grant 1P50-ES01274201 (Woods Hole Center for Oceans and Human Health), andNOAAgrant NA06NOS4780245 (GOMTOX). Additional support was provided by NSF grant DMS-0417769

Cerebral blood volume, genotype and chemosensitivity in oligodendroglial tumours

INTRODUCTION: The biological factors responsible for differential chemoresponsiveness in oligodendroglial tumours with or without the −1p/−19q genotype are unknown, but tumour vascularity may contribute. We aimed to determine whether dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) could distinguish molecular subtypes of oligodendroglial tumour, and examined the relationship between relative cerebral blood volume (rCBV) and outcome following procarbazine, lomustine and vincristine (PCV) chemotherapy. METHODS: Pretherapy rCBV was calculated and inter- and intraobserver variability assessed. Allelic imbalance in 1p36, 19q13, 17p13, 10p12–15, and 10q22–26 and p53 mutation (exons 5–8) were determined. rCBV was compared with genotype and clinicopathological characteristics (n=37) and outcome following PCV chemotherapy (n=33). RESULTS: 1p/19q loss was seen in 6/9 grade II oligodendrogliomas, 6/14 grade II oligoastrocytomas, 4/4 grade III oligodendrogliomas, and 3/10 grade III oligoastrocytomas. rCBV measurements had good inter- and intraobserver variability, but did not distinguish histology subtype or grade. Tumours with 1p/19q loss had higher rCBV values (Student’s t-test P=0.001). Receiver operating characteristic analysis revealed a cut-off of 1.59 for identifying genotype (sensitivity 92%, specificity 76%). Tumours with high and low rCBV showed response to chemotherapy. The −1p/−19q genotype, but not rCBV, was strongly associated with response, progression-free and overall survival following PCV chemotherapy. Tumours with high rCBV and intact 1p/19q were associated with shorter progression-free and overall patient survival than those with intact 1p/19q and low rCBV or high rCBV and 1p/19q loss. CONCLUSION: rCBV identifies oligodendroglial tumours with 1p/19q loss, but does not predict chemosensitivity. The prognostic significance of rCBV may differ in oligodendroglial tumours with or without the −1p/−19q genotype

Rice grain cadmium concentrations in the global supply-chain

One of cadmium’s major exposure routes to humans is through rice consumption. The concentrations of cadmium in the global polished (white), market rice supply-chain were assessed in 2270 samples, purchased from retailers across 32 countries, encompassing 6 continents. It was found on a global basis that East Africa had the lowest cadmium with a median for both Malawi and Tanzania at 4.9 μg/kg, an order of magnitude lower than the highest country, China with a median at 69.3 μg/kg. The Americas were typically low in cadmium, but the Indian sub-continent was universally elevated. In particular certain regions of Bangladesh had high cadmium, that when combined with the high daily consumption rate of rice of that country, leads to high cadmium exposures. Concentrations of cadmium were compared to the European Standard for polished rice of 200 μg/kg and 5% of the global supply-chain exceeded this threshold. For the stricter standard of 40 μg/kg for processed infant foods, for which rice can comprise up to 100% by composition (such as rice porridges, puffed rice cereal and cakes), 25% of rice would not be suitable for making pure rice baby foods. Given that rice is also elevated in inorganic arsenic, the only region of the world where both inorganic arsenic and cadmium were low in grain was East Africa