Redfield ratios revisited: Removing the biasing effect of anthropogenic CO2

Redfield ratios of remineralization are calculated based on chemical data analysis on isopycnal surfaces. The concentrations of dissolved inorganic carbon used in this study were corrected for the anthropogenic CO2 content as estimated with a back-calculation technique. The corrections increased the apparent carbon remineralization by 25-30%, thus proving important for the reliable estimation of Redfield carbon ratios in the presence of anthropogenic CO2. Best estimates from this study largely confirm the more recently published Redfield ratios of remineralization. The following results were obtained for the latitude range 3-41°N along 20-29°W in the Northeast Atlantic Ocean: Corg: P ratio = 123 ± 10; Corg : N ratio = 7.2 ± 0.8; -O2 :Corg ratio = 1.34 ± 0.06; -O2 : P ratio = 165 ± 15; N: P ratio = 17.5 ± 2.0. These ratios are in close agreement with the average composition of phytoplankton and represent respiration of organic matter consisting on average of 52% protein, 36% polysaccharide, and 12% lipid

Effects of poisons and preservatives on the composition of organic matter in a sediment trap experiment

Fluxes and molecular compositions of a group of major biochemical classes (lipids, lignin, pigments, amino acids, and carbohydrates) were compared among sediment traps treated with different poisons and preservatives and deployed for 1–2 months in a coastal marine environment. Fluxes and compositions of biochemicals were significantly more variable than bulk particle fluxes and elemental compositions. This observation was attributed to a greater influence of dead zooplankton “swimmers” in treated traps rather than differences in microbial decomposition due to the various treatments. Molecular compositions, especially of lipids, confirm the influence of zooplankton swimmers on the biochemical composition of the particulate material in treated traps compared to untreated controls even when large swimmers had been removed. An inventory of the major biochemicals we measured accounted for 25–45% of the organic carbon in our samples, with amino acids and sugars making up the bulk (80–90%) of the identified carbon

Effects of poisons and preservatives on the fluxes and elemental compositions of sediment trap materials

Bulk particle fluxes and organic elemental compositions were compared among sediment traps treated with different poisons and preservatives. The traps (3:1 open cylinders) were deployed for 1–2 months at 30 and 60 m depths in a coastal marine environment. The tested treatments included mercuric chloride, mixed antibiotics, sodium azide, formalin, chloroform, and salt, along with untreated controls. Fluxes of bulk particulate material and weight percentages of organic carbon measured for differently treated traps deployed simultaneously at the same depth both varied by an average of ±8% of the mean value. Great numbers of large (\u3e850 μm) zooplankton swimmers were removed by sieving from bulk sediment trap samples treated with formalin and mercuric chloride, and to a lesser extent from those treated with azide and chloroform. The \u3c850 μm “sediment” fractions of the formalin- and mercuric chloride-treated samples were characterized by slightly elevated %OC concentrations and lowered (C/N) ratios, apparently resulting from smaller swimmers that were not separated by sieving. Overall, problems involved with sample and treatment washout, and swimmer artifacts in poisoned traps affected measured fluxes and elemental compositions more than differences that could be clearly attributed to microbial degradation

Young organic matter as a source of carbon dioxide outgassing from Amazonian rivers

Rivers are generally supersaturated with respect to carbon dioxide, resulting in large gas evasion fluxes that can be a significant component of regional net carbon budgets. Amazonian rivers were recently shown to outgas more than ten times the amount of carbon exported to the ocean in the form of total organic carbon or dissolved inorganic carbon. High carbon dioxide concentrations in rivers originate largely from in situ respiration of organic carbon, but little agreement exists about the sources or turnover times of this carbon. Here we present results of an extensive survey of the carbon isotope composition ({sup 13}C and {sup 14}C) of dissolved inorganic carbon and three size-fractions of organic carbon across the Amazonian river system. We find that respiration of contemporary organic matter (less than 5 years old) originating on land and near rivers is the dominant source of excess carbon dioxide that drives outgassing in mid-size to large rivers, although we find that bulk organic carbon fractions transported by these rivers range from tens to thousands of years in age. We therefore suggest that a small, rapidly cycling pool of organic carbon is responsible for the large carbon fluxes from land to water to atmosphere in the humid tropics

A critical evaluation of interlaboratory data on total, elemental, and isotopic carbon in the carbonaceous particle reference material, NIST SRM 1649a

Because of increased interest in the marine and atmospheric sciences in elemental carbon (EC), or black carbon (BC) or soot carbon (SC), and because of the difficulties in analyzing or even defining this pervasive component of particulate carbon, it has become quite important to have appropriate reference materials for intercomparison and quality control. The NIST "urban dust" Standard Reference Material? SRM 1649a is useful in this respect, in part because it comprises a considerable array of inorganic and organic species, and because it exhibits a large degree of (14C) isotopic heterogeneity, with biomass carbon source contributions ranging from about 2 % (essentially fossil aliphatic fraction) to about 32 % (polar fraction). A primary purpose of this report is to provide documentation for the new isotopic and chemical particulate carbon data for the most recent (31 Jan. 2001) SRM 1649a Certificate of Analysis. Supporting this is a critical review of underlying international intercomparison data and methodologies, provided by 18 teams of analytical experts from 11 institutions. Key results of the intercomparison are: (1) a new, Certified Value for total carbon (TC) in SRM 1649a; (2) 14C Reference Values for total carbon and a number of organic species, including for the first time 8 individual PAHs; and (3) elemental carbon (EC) Information Values derived from 13 analytical methods applied to this component. Results for elemental carbon, which comprised a special focus of the intercomparison, were quite diverse, reflecting the confounding of methodological-matrix artifacts, and methods that tended to probe more or less refractory regions of this universal, but ill-defined product of incomplete combustion. Availability of both chemical and 14C speciation data for SRM 1649a holds great promise for improved analytical insight through comparative analysis (e.g., fossil/ biomass partition in EC compared to PAH), and through application of the principle of isotopic mass balance.Carrie, L. A., Benner, B. A., Kessler, J. D., Klinedinst, D. B., Klouda, G. A., Marolf, J. V., . . . Schmid, H. (2002). A Critical Evaluation of Interlaboratory Data on Total, Elemental, and Isotopic Carbon in the Carbonaceous Particle Reference Material, NIST SRM 1649a. Journal of Research of the National Institute of Standards and Technology, 107(3), 279-298

Multiplex Immunoassay of Lower Genital Tract Mucosal Fluid from Women Attending an Urban STD Clinic Shows Broadly Increased IL1ß and Lactoferrin

BACKGROUND: More than one million new cases of sexually transmitted diseases (STDs) occur each day. The immune responses and inflammation induced by STDs and other frequent non-STD microbial colonizations (i.e. Candida and bacterial vaginosis) can have serious pathologic consequences in women including adverse pregnancy outcomes, infertility and increased susceptibility to infection by other pathogens. Understanding the types of immune mediators that are elicited in the lower genital tract by these infections/colonizations can give important insights into the innate and adaptive immune pathways that are activated and lead to strategies for preventing pathologic effects. METHODOLOGY/PRINCIPAL FINDINGS: 32 immune mediators were measured by multiplexed immunoassays to assess the immune environment of the lower genital tract mucosa in 84 women attending an urban STD clinic. IL-3, IL-1ß, VEGF, angiogenin, IL-8, ß2Defensin and ß3Defensin were detected in all subjects, Interferon-α was detected in none, while the remaining mediators were detected in 40% to 93% of subjects. Angiogenin, VEGF, FGF, IL-9, IL-7, lymphotoxin-α and IL-3 had not been previously reported in genital mucosal fluid from women. Strong correlations were observed between levels of TNF-α, IL-1ß and IL-6, between chemokines IP-10 and MIG and between myeloperoxidase, IL-8 and G-CSF. Samples from women with any STD/colonization had significantly higher levels of IL-8, IL-3, IL-7, IL-1ß, lactoferrin and myeloperoxidase. IL-1ß and lactoferrin were significantly increased in gonorrhea, Chlamydia, cervicitis, bacterial vaginosis and trichomoniasis. CONCLUSIONS/SIGNIFICANCE: These studies show that mucosal fluid in general appears to be an environment that is rich in immune mediators. Importantly, IL-1ß and lactoferrin are biomarkers for STDs/colonizations providing insights into immune responses and pathogenesis at this mucosal site

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/