Sources and transport of dissolved and particulate organic carbon in the Mississippi River estuary and adjacent coastal waters of the northern Gulf of Mexico

Dissolved organic carbon (DOC), stable carbon isotopic (delta(13)C) compositions of DOC and particulate organic carbon (POC), and elemental C/N ratios of POC were measured for samples collected from the lower Mississippi and Atchafalaya rivers and adjacent coastal waters in the northern Gulf of Mexico during the low flow season in June 2000 and high flow season in April 2001. These isotopic and C/N results combined with DOC measurements were used to assess the sources and transport of terrestrial organic matter from the Mississippi and Atchafalaya rivers to the coastal region in the northern Gulf of Mexico. delta(13)C values of both POC (-23.8parts per thousand to -26.8parts per thousand) and DOC (-25.0parts per thousand to -29.0parts per thousand) carried by the two rivers were more depleted than the values measured for the samples collected in the offshore waters. Strong seasonal variations in delta(13)C distributions were observed for both POC and DOC in the surface waters of the region. Fresh water discharge and horizontal mixing played important roles in the distribution and transport of terrestrial POC and DOC offshore. Our results indicate that both POC and DOC exhibited non-conservative behavior during the mixing especially in the mid-salinity range. Based on a simple two end-member mixing model, the comparison of the measured DOC-delta(13)C with the calculated conservative isotopic mixing curve indicated that there was a significant in situ production of marine-derived DOC in the mid- to high-salinity waters consistent with our in situ chlorophyll-a measurements. Our DOC-delta(13)C data suggest that a removal of terrestrial DOC mainly occurred in the high-salinity (>25) waters during the mixing. Our study indicates that the mid- to high- (10-30) salinity range was the most dynamic zone for organic carbon transport and cycling in the Mississippi River estuary. Variability in isotopic and elemental compositions along with variability in DOC and POC concentrations suggest that autochthonous production, bacterial utilization, and photo-oxidation could all play important roles in regulating and removing terrestrial DOC in the northern Gulf of Mexico and further study of these individual processes is warranted. (C) 2004 Elsevier B.V. All rights reserved.

Concentrations and distribution of organochlorine pesticides in shellfish from Changjiang estuary

To analyze and evaluate the status of organochlorine pollutants in the Changjiang (Yangtze River) estuary and adjacent waters, the concentrations of hexachlorocyclohexane (HCHs) and dichlorodiphenyltrichloroethane (DDTs) in shellfish collected in study area from 2006 to 2007 were determined with gas chromatography (GC). The concentration range of HCHs was (ND-12.13)x10(-3) mg/kg wet weight and averaged at 0.54x10(-3) mg/kg while the concentration of DDTs was in the range of (4.06-281.73) x10(-3) mg/kg with a mean of 57.52x10(-3) mg/kg in the survey areas. The concentrations of DDTs in the shellfish were higher than HCHs', so that DDTs could be considered as typical organochlorine pollutants in the areas. The concentrations of DDTs in the shellfish were higher than HCHs', so that DDTs could be considered as typical organochlorines pollutants. The HCHs in all the shellfish conformed to the first level of criterion (0.02 mg/kg) of the Marion Biology Quality (GB 18421-2001), and that of DDTs in most samples were beyond the first level (0.01 mg/kg) but conformed to the second level (0.10 mg/kg). On average, alpha-HCH and delta-HCH occupied the most part of HCHs, while O,P'-DDT and P,P'-DDT occupied the most part of DDTs. The concentrations of organocholorine pesticides in shellfish samples varied in site and in species. The highest level occurred at the Shengsi (SS), followed by Yangkougang (YKG), Lvsi (LS), Dongyuan (DY) and Beibayao (BBY), low concentrations were observed at Changsha (CS), Beidaodi (BDD), and Gouqi (GQ). The concentration of HCHs and DDTs in most sites decreased clearly from 2006 to 2007 except for YKG, DY, BDD, LYS, and SS. All of above results suggested that the study area was slightly affected by organochlorine pesticide, special by DDTs.

苏里格气田苏6加密井区山1-盒8层段河流沉积体系分析

Sulige gas field is located in Northwest of Yi-Shan Slope of the Ordos Basin. The Shan 1 Member of the Shanxi Formation and He8 Member of the ShiHeZi Formation are not only objective strata of research but also main producing strata of the Sulige Field. From core and wireline log data of 32 wells in well Su6 area of Sulige field, no less than six lithofaice types can be recognised. They are Gm,Sl,Sh,Sm,Sp,Fl,Fm. Box-shaped, bell-shaped, funnel-shaped and line-segment-shaped log are typcial gamma-ray log characters and shapes. The Depositonal system of the Shan1-He8 strata in research area have five bounding-surface hierarchies and was composed of six architectural elements, CH, LS,FF（CH）,SB,LA,GB. The depositional model of Shan 1 was the type of a sandy meandering river with natural levee, abandoned channels and crevasse splay. Channel depth of this model maybe 7-12 m and the fullest-bank flow can reach 14 m high. Based on analysis of depositional causes, a sandy braided river model for the depositional system of He 8 can be erected. It consists of active main channels, active chute channels, sheet-like sand bars, abandoned main channels and abandoned chute channels. Channel depth of this model can be 3-4 m with 9 m of highest flow. Six gamma-ray log cross sections show that the connectivity of sandbodies through Shan 1 Member is lower than He 8. Influenced by occurrence of mudy and silty deposits, vertical connectivity of sandbodies through He 8 is not high.

辣椒氟平均含量及其影响因素研究

西南地区是我国燃煤污染型氟中毒流行最为严重的地区，同时也是我国主要辣椒优异种质资源的分布地之一。大量的研究已经证明，辣椒和玉米等食物在用煤火烘干过程中可以吸收富集燃煤过程释放到大气中的氟，因此由燃煤型氟污染引起的食物型氟中毒也不断受到关注。 国内外至今缺乏对辣椒氟的背景值、平均含量以及影响其含量变化的因素的系统研究，只有部分研究者对燃煤型地方性氟中毒地区的辣椒进行了零星的调查分析，所采样品具有很大的局限性，远远不能代表辣椒整体的氟含量水平；且国内外迄今尚无辣椒氟含量的卫生标准，由于辣椒与其他食物和蔬菜相比具有其特殊性，而目前国家有关食品中氟的限量标准（GB2762-2005）对辣椒而言明显不合适，因此只有在对辣椒中氟的含量进行充分调查研究，才能有针对性地制定出更为科学合理的卫生标准，才能为辣椒是否受到氟污染的判别及防止辣椒氟污染提供理论依据。本研究的目的、方法、结果及结论如下所示。 目的：调查我国西南部分地区新鲜辣椒及干辣椒的氟含量水平，了解辣椒中氟的分布规律，进而确定新鲜辣椒中氟的污染判别值并探讨辣椒氟污染的防治措施。方法：按照《食品中氟的测定》（GB/T 5009.18-2003）方法对采自西南77个县市的新鲜辣椒（176个）及干辣椒（296个）进行氟的含量测定，根据地区、辣椒品种、干燥方式、储存时间及赋存状态，对辣椒中氟的含量进行统计分析。结果：采自农田的新鲜辣椒氟的几何平均含量为8.9mg•kg-1（干重，176个样，置信度95％），干辣椒样品氟的几何平均含量为19.6mg•kg-1（干重，296个样，置信度95％）。结论：研究证实辣椒的干燥与储存方式不当是导致辣椒氟污染的主要原因；通过对新鲜辣椒中氟含量的研究，证实我国现行的食品中氟限量标准(GB2762-2005)并不适用于辣椒，建议以24.7mg•kg-1 (干重)、5.2mg•kg-1 (鲜重)为新鲜辣椒氟污染判别值。

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with a matrix of carbon nanotubes for the analysis of low-mass compounds in environmental samples

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for environmental analysis has been mainly focused on qualitative analysis of high-mass molecules, such as toxins, humic acid, and microorganisms. Herein,we describe a novel MALDI-TOF-MS method with a matrix of oxidized carbon nanotubes for analysis of low-mass compounds in environmental samples. A number of chemicals in the environment were qualitatively analyzed by the present method, and it was found that most of them, especially the highly polar chemicals, were measurable with high sensitivity. With the intrinsic ability to measure high-mass chemicals, this method can compensate for the current shortage of methods for environmental analysis for the measurement of highly polar or high-mass chemicals. For sample analysis, arsenic speciation in Chinese traditional medicines was qualified and diphenylolpropane in water samples was quantified. With the relatively high tolerance of the method to interfering molecules, a simple pretreatment or even no pretreatment could be employed before MS detection. Furthermore, this method can be employed in a high-throughput format.

Metallic foam processing from the liquid state

Cox, S.J., Bradley, G. and Weaire, D. (2001) Metallic foam processing from the liquid state: the competition between solidification and drainage. Eur. Phys. J. AP 14:87-97. Sponsorship: This research was supported by the Prodex programme of ESA, and is a contribution to ESA contract C14308/AO-075-99. SJC was supported by Enterprise Ireland and a Marie Curie fellowship. GB was supported by the HPC Programme of TCD.

A Hybrid GLR Algorithm for Parsing with Epsilon Grammars

We give a hybrid algorithm for parsing epsilon grammars based on Tomita's non-ϵ-grammar parsing algorithm ([Tom86]) and Nozohoor-Farshi's ϵ-grammar recognition algorithm ([NF91]). The hybrid parser handles the same set of grammars handled by Nozohoor-Farshi's recognizer. The algorithm's details and an example of its use are given. We also discuss the deployment of the hybrid algorithm within a GB parser, and the reason an ϵ grammar parser is needed in our GB parser.

Deposition of silver nanoparticles in geochemically heterogeneous porous media: predicting affinity from surface composition analysis.

The transport of uncoated silver nanoparticles (AgNPs) in a porous medium composed of silica glass beads modified with a partial coverage of iron oxide (hematite) was studied and compared to that in a porous medium composed of unmodified glass beads (GB). At a pH lower than the point of zero charge (PZC) of hematite, the affinity of AgNPs for a hematite-coated glass bead (FeO-GB) surface was significantly higher than that for an uncoated surface. There was a linear correlation between the average nanoparticle affinity for media composed of mixtures of FeO-GB and GB collectors and the relative composition of those media as quantified by the attachment efficiency over a range of mixing mass ratios of the two types of collectors, so that the average AgNPs affinity for these media is readily predicted from the mass (or surface) weighted average of affinities for each of the surface types. X-ray photoelectron spectroscopy (XPS) was used to quantify the composition of the collector surface as a basis for predicting the affinity between the nanoparticles for a heterogeneous collector surface. A correlation was also observed between the local abundances of AgNPs and FeO on the collector surface.

Unrecognized pretransplant and donor‐derived cryptococcal disease in organ transplant recipients.

BACKGROUND: Cryptococcosis occurring ≤30 days after transplantation is an unusual event, and its characteristics are not known. METHODS: Patients included 175 solid-organ transplant (SOT) recipients with cryptococcosis in a multicenter cohort. Very early-onset and late-onset cryptococcosis were defined as disease occurring ≤30 days or >30 days after transplantation, respectively. RESULTS: Very early-onset disease developed in 9 (5%) of the 175 patients at a mean of 5.7 days after transplantation. Overall, 55.6% (5 of 9) of the patients with very early-onset disease versus 25.9% (43 of 166) of the patients with late-onset disease were liver transplant recipients (P = .05). Very early cases were more likely to present with disease at unusual locations, including transplanted allograft and surgical fossa/site infections (55.6% vs 7.2%; P < .001). Two very early cases with onset on day 1 after transplantation (in a liver transplant recipient with Cryptococcus isolated from the lung and a heart transplant recipient with fungemia) likely were the result of undetected pretransplant disease. An additional 5 cases involving the allograft or surgical sites were likely the result of donor‐acquired infection. CONCLUSIONS: A subset of SOT recipients with cryptococcosis present very early after transplantation with disease that appears to occur preferentially in liver transplant recipients and involves unusual sites, such as the transplanted organ or the surgical site. These patients may have unrecognized pretransplant or donor-derived cryptococcosis.

Mapping the complexity of transcription control in higher eukaryotes.

Recent genomic analyses suggest the importance of combinatorial regulation by broadly expressed transcription factors rather than expression domains characterized by highly specific factors.

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.

BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important. RESULTS: Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage. CONCLUSIONS: We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.

Unmasking a role for sex chromosomes in gene silencing.

Several sexually dimorphic phenotypes correlate with sex-chromosome dosage rather than with phenotypic sex. New research suggests that sex chromosome dimorphism helps to regulate gene silencing.

Smoothened signal transduction is promoted by G protein-coupled receptor kinase 2.

Deregulation of the Sonic hedgehog pathway has been implicated in an increasing number of human cancers. In this pathway, the seven-transmembrane (7TM) signaling protein Smoothened regulates cellular proliferation and differentiation through activation of the transcription factor Gli. The activity of mammalian Smoothened is controlled by three different hedgehog proteins, Indian, Desert, and Sonic hedgehog, through their interaction with the Smoothened inhibitor Patched. However, the mechanisms of signal transduction from Smoothened are poorly understood. We show that a kinase which regulates signaling by many "conventional" 7TM G-protein-coupled receptors, G protein-coupled receptor kinase 2 (GRK2), participates in Smoothened signaling. Expression of GRK2, but not catalytically inactive GRK2, synergizes with active Smoothened to mediate Gli-dependent transcription. Moreover, knockdown of endogenous GRK2 by short hairpin RNA (shRNA) significantly reduces signaling in response to the Smoothened agonist SAG and also inhibits signaling induced by an oncogenic Smoothened mutant, Smo M2. We find that GRK2 promotes the association between active Smoothened and beta-arrestin 2. Indeed, Gli-dependent signaling, mediated by coexpression of Smoothened and GRK2, is diminished by beta-arrestin 2 knockdown with shRNA. Together, these data suggest that GRK2 plays a positive role in Smoothened signaling, at least in part, through the promotion of an association between beta-arrestin 2 and Smoothened.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Evidence-ranked motif identification.

cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate sequences, it utilizes information across all sequence regions to search for high-scoring motifs. We apply cERMIT on a range of direct binding and overexpression datasets; it substantially outperforms state-of-the-art approaches on curated ChIP-chip datasets, and easily scales to current mammalian ChIP-seq experiments with data on thousands of non-coding regions.