Iron oxide dissolution and solubility in the presence of siderophores

Abstract.: Iron is an essential trace nutrient for most known organisms. The iron availability is limited by the solubility and the slow dissolution kinetics of iron-bearing mineral phases, particularly in pH neutral or alkaline environments such as carbonatic soils and ocean water. Bacteria, fungi, and plants have evolved iron acquisition systems to increase the bioavailability of iron in such environments. A particularly efficient iron acquisition system involves the solubilization of iron by siderophores. Siderophores are biogenic chelators with high affinity and specificity for iron complexation. This review focuses on the geochemical aspects of biological iron acquisition. The significance of iron-bearing minerals as nutrient source for siderophore-promoted iron acquisition has been confirmed in microbial culture studies. Due to the extraordinary thermodynamic stability of soluble siderophore-iron complexes, siderophores have a pronounced effect on the solubility of iron oxides over a wide pH range. Very small concentrations of free siderophores in solution have a large effect on the solution saturation state of iron oxides. This siderophore induced disequilibrium can drive dissolution mechanisms such as proton-promoted or ligand-promoted iron oxide dissolution. The adsorption of siderophores to oxide surfaces also induces a direct siderophore-promoted surface-controlled dissolution mechanism. The efficiency of siderophores for increasing the solubility and dissolution kinetics of iron oxides are compared to other natural and anthropogenic ligand

Bolzano on the intransparency of content

Content, according to Bolzano, is intransparent: our knowledge of certain essential features of the contents of our contentful mental acts (such as their identity and composition) is often severely limited. In this paper, I identify various intransparency theses Bolzano is committed to and present and evaluate the defence he offers for his view. I argue that while his intransparency theses may be correct, his defence is unsuccessful. Moreover, I argue that improving on his defence would require substantially modifying his general epistemology of content

Internal tree cycling and atmospheric archiving of mercury: examination with concentration and stable isotope analyses

Trees predominantly take up mercury (Hg) from the atmosphere via stomatal assimilation of gaseous elemental Hg (GEM). Hg is oxidised in leaves/needles and transported to other tree anatomy including bole wood where it can be stored long-term. Using Hg associated with growth rings facilitates archiving of historical GEM concentrations. Nonetheless, there are significant knowledge gaps on the cycling of Hg within trees. We investigate Hg archived in tree rings, internal tree Hg cycling, and differences in Hg uptake mechanisms in Norway spruce and European larch sampled within 1 km of a HgCl2 contaminated site using total Hg (THg) and Hg stable isotope analyses. Tree ring samples are indicative of significant increases in THg concentrations (up to 521&micro;g&middot;kg-1) from background period (BGP; facility closed; 1992&mdash;present) to secondary industrial period (2ndIP; no HgCl2 wood treatment; 1962&ndash;1992) to primary industrial period (1stIP; active HgCl2 wood treatment; &asymp;1900&ndash;1962). Mass dependent fractionation (MDF) Hg stable isotope data are shifted negative during industrial periods (&delta;202Hg: 1stIP: 4.32&plusmn;0.15 &permil;; 2ndIP: 4.04&plusmn;0.32 &permil;; BGP: 2.83&plusmn;0.74 &permil;; 1SD). Even accounting for a &asymp; 2.6 &permil; MDF shift associated with stomatal uptake, these data are indicative of emissions derived from industrial activity being enriched in lighter isotopes associated with HgCl2 reduction and Hg0 volatilisation. Similar MDF (&delta;202Hg: 3.90&plusmn;0.30 &permil;; 1SD) in bark Hg (137&plusmn;105&micro;g&middot;kg-1) suggests that stomatal assimilation and downward transport is also the dominant uptake mechanism for bark Hg (reflective of negative stomatal uptake MDF shift) rather than deposition to bark. THg was enriched in sapwood of all sampled trees across both tree species. This may indicate long-term storage of a fraction of Hg in sapwood or xylem solution. These data advance our understanding of the physiological processing of Hg within trees and provide critical direction to future research into the use of trees as archives for historical atmospheric Hg.</p

From aptamer-based biomarker discovery to diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay

Recently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community

STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design

BackgroundMicrosatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant markers, a feature missing from most other similar tools.ResultsOur extensions to the STADEN package provide the following functionality to facilitate microsatellite (and also minisatellite) marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps with different search criteria one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package.ConclusionThe STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex microsatellite marker design. It gives the user detailed control over the workflow, enabling flexible combinations of manual and automated analysis steps. The software is available under the OpenBSD License [1,2]. The high efficiency of our automated marker design workflow has been confirmed in three microsatellite development projects

Circumstellar Structure around Evolved Stars in the Cygnus-X Star Formation Region

We present observations of newly discovered 24 micron circumstellar structures detected with the Multiband Imaging Photometer for Spitzer (MIPS) around three evolved stars in the Cygnus-X star forming region. One of the objects, BD+43 3710, has a bipolar nebula, possibly due to an outflow or a torus of material. A second, HBHA 4202-22, a Wolf-Rayet candidate, shows a circular shell of 24 micron emission suggestive of either a limb-brightened shell or disk seen face-on. No diffuse emission was detected around either of these two objects in the Spitzer 3.6-8 micron Infrared Array Camera (IRAC) bands. The third object is the luminous blue variable candidate G79.29+0.46. We resolved the previously known inner ring in all four IRAC bands. The 24 micron emission from the inner ring extends ~1.2 arcmin beyond the shorter wavelength emission, well beyond what can be attributed to the difference in resolutions between MIPS and IRAC. Additionally, we have discovered an outer ring of 24 micron emission, possibly due to an earlier episode of mass loss. For the two shell stars, we present the results of radiative transfer models, constraining the stellar and dust shell parameters. The shells are composed of amorphous carbon grains, plus polycyclic aromatic hydrocarbons in the case of G79.29+0.46. Both G79.29+0.46 and HBHA 4202-22 lie behind the main Cygnus-X cloud. Although G79.29+0.46 may simply be on the far side of the cloud, HBHA 4202-22 is unrelated to the Cygnus-X star formation region.Comment: Accepted by A