Iron limitation and the role of siderophores in marine Synechococcus

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2009Marine cyanobacteria in the genus Synechococcus are widely distributed and contribute significantly to global primary productivity. In many parts of the ocean their growth is limited by a lack of iron, an essential nutrient that is virtually insoluble in seawater. To overcome this, Synechococcus have evolved a number of strategies to acquire iron. Gene distribution, metagenomics and a novel immunological flow cytometry assay in the Costa Rica Upwelling Dome were used to estimate the importance of Fe stress. Genomic and metagenomic measures suggest that iron limitation is, paradoxically, more severe in coastal and upwelling areas than in the open ocean, where iron is less abundant. A serological assay found significant differences in the vertical distribution of the Fe stress protein IdiA over just a few meters. Despite average surface ocean iron concentrations of just 0.07 nM, most marine oligotrophic cyanobacteria lack iron-binding siderophores that are present in many heterotrophic marine bacteria. Siderophores are widely distributed in the surface ocean and compose an important portion of the pool of natural ligands that bind >99% of all soluble Fe. In bottle incubations from the Sargasso Sea we found the addition of Fe complexed to an excess of the siderophore desferrioxamine B (DFB) limited Synechococcus growth and stimulated the growth of heterotrophic bacteria in a concentration dependent manner. Laboratory work revealed that excess DFB decreased Synechococcus growth beyond Fe-limited controls at concentrations as low as 20-40 nM. The inhibition was aggravated by light but it could be reversed by the addition of Fe. The DFB inhibition could not be explained by thermodynamic or kinetic models of Fe’ or co-limitation with other metals. DFB may interact with some aspect of cellular physiology to directly inhibit cyanobacterial growth.Funding for this research was provided by Grant NSF-OCE0352241 from the National Science Foundation to Eric A. Webb and grants 495 and 495.01 from the Gordon and Betty Moore Foundation, grants DE-F602-07ER64506 and DE-F602- 08ER64516 from the Department of Energy, and grant Z792093-02 (C-MORE) from the University of Hawaii, to Sallie W. Chisholm

The application of transactional fairness to the gambling sector

The idea of ‘fairness’ in consumer protection has been discussed for a long time. However, more recently there has been a renewed focus on the use of unfair pricing practices and terms in consumer markets and regulators and lawmakers are responding. Practices which can be considered unfair often emerge as companies develop new and innovative ways to engage with consumers including offering different prices and / or terms to different sets of customers. Being ‘fair and open’ is an important principle for gambling regulation. In that context, this paper focusses on fairness in gambling markets and seeks to develop a framework comprising of general principles against which the fairness of gambling terms can be assessed. The findings of this paper could have impacts not only on the behaviour of firms but could also offer consistency across markets and in regulation

Iron limitation and the role of Siderophores in marine Synechococcus

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections."June 2009."Includes bibliographical references.Marine cyanobacteria in the genus Synechococcus are widely distributed and contribute significantly to global primary productivity. In many parts of the ocean their growth is limited by a lack of iron, an essential nutrient that is virtually insoluble in seawater. To overcome this, Synechococcus have evolved a number of strategies to acquire iron. Gene distribution, metagenomics and a novel immunological flow cytometry assay in the Costa Rica Upwelling Dome were used to estimate the importance of Fe stress. Genomic and metagenomic measures suggest that iron limitation is, paradoxically, more severe in coastal and upwelling areas than in the open ocean, where iron is less abundant. A serological assay found significant differences in the vertical distribution of the Fe stress protein IdiA over just a few meters. Despite average surface ocean iron concentrations of just 0.07 nM, most marine oligotrophic cyanobacteria lack iron-binding siderophores that are present in many heterotrophic marine bacteria. Siderophores are widely distributed in the surface ocean and compose an important portion of the pool of natural ligands that bind >99% of all soluble Fe. In bottle incubations from the Sargasso Sea we found the addition of Fe complexed to an excess of the siderophore desferrioxamine B (DFB) limited Synechococcus growth and stimulated the growth of heterotrophic bacteria in a concentration dependent manner.(cont.) Laboratory work revealed that excess DFB decreased Synechococcus growth beyond Fe-limited controls at concentrations as low as 20-40 nM. The inhibition was aggravated by light but it could be reversed by the addition of Fe. The DFB inhibition could not be explained by thermodynamic or kinetic models of Fe' or co-limitation with other metals. DFB may interact with some aspect of cellular physiology to directly inhibit cyanobacterial growth.by Adam R. Rivers.Ph.D

Evaluation of US Federal Guidelines (Primary Response Incident Scene Management [PRISM]) for Mass Decontamination of Casualties During the Initial Operational Response to a Chemical Incident

Study objective The aim of this study was to evaluate the clinical and operational effectiveness of US federal government guidance (Primary Response Incident Scene Management [PRISM]) for the initial response phase to chemical incidents. Methods The study was performed as a large-scale exercise (Operation DOWNPOUR). Volunteers were dosed with a chemical warfare agent simulant to quantify the efficacy of different iterations of dry, ladder pipe system, or technical decontamination. Results The most effective process was a triple combination of dry, ladder pipe system, and technical decontamination, which attained an average decontamination efficiency of approximately 100% on exposed hair and skin sites. Both wet decontamination processes (ladder pipe system and technical decontamination, alone or in combination with dry decontamination) were also effective (decontamination efficiency >96%). In compliant individuals, dry decontamination was effective (decontamination efficiency approximately 99%), but noncompliance (tentatively attributed to suboptimal communication) resulted in significantly reduced efficacy (decontamination efficiency approximately 70%). At-risk volunteers (because of chronic illness, disability, or language barrier) were 3 to 8 times slower than ambulatory casualties in undergoing dry and ladder pipe system decontamination, a consequence of which may be a reduction in the overall rate at which casualties can be processed. Conclusion The PRISM incident response protocols are fit for purpose for ambulatory casualties. However, a more effective communication strategy is required for first responders (particularly when guiding dry decontamination). There is a clear need to develop more appropriate decontamination procedures for at-risk casualties.Peer reviewedFinal Published versio

Judicial Review, Irrationality, and the Legitimacy of Merits-Review

The definition of the irrationality ground of judicial review recognises the constitutional principle of the separation of powers, in allowing for judicial control of the executive only very rarely. The author in a previous article in this study found that the courts, on occasions, had intervened in circumstances where administrative decisions arguably were not irrational. To this end, the purpose of this article is to assess the constitutionality of these seemingly low standards of irrationality. The author does so by reference either to the manner of review employed—the use of the proportionality principle, for example—or the context of the administrative decision under scrutiny, such as the infringement of the applicant’s fundamental rights. The author finds that the cases from the previous article where low standards of irrationality were arguably adopted were, in fact, legitimate according to these chosen methods of evaluation. However, this is an interim conclusion because, for reasons of word length, the author is unable to complete a full assessment here. It is therefore proposed that a subsequent article will continue to examine the constitutionality of these cases. Furthermore, the author will also try and establish a zone of executive decision-making, for reasons of democracy, where the courts are excluded from irrationality review. If the author is unsuccessful in this regard, the final conclusion of this study will inevitably be that low standards of judicial intervention exist without limit—a clear assault on the constitutional principle stated above

Graviton Excitations and Lorentz-Violating Gravity with Cosmological Constant

Motivated by the interest raised by the problem of Lorenz-symmetry violating gauge theories in connetion with gravity models, this contribution sets out to provide a general method to systematically study the excitation spectrum of gravity actions which include a Lorentz-symmetry breaking Chern-Simons-type action term for the spin connection. A complete set of spin-type operators is found which accounts for the (Lorentz) violation parameter to all orders and graviton propagators are worked out in a number of different situations

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis [version 1; referees: 2 approved]

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github

Stable large area drop-on-demand deposition of a conductive polymer ink for 3D-printed electronics, enabled by bio-renewable co-solvents

Development of conductive polymer ink formulations with reliable jetting stability and physical properties could offer sustainable routes for scaling-up the 3D-printing of electronics. We report a new poly(3,4-ethylenedioxythiophene) polystyrene sulphonate (PEDOT:PSS) ink formulation, InkCG, using bio-renewable solvents dihydrolevoglucosenone (cyrene) and glycerol carbonate (GC) as an alternative to commonly used dimethyl sulfoxide (DMSO). These green organic co-solvents enhance jetting reliability and long-term stability of the ink and improve electrical properties of the deposited PEDOT:PSS layers, compared to the commonly used DMSO-containing ink formulations. We achieve large-area and high-fidelity electronic devices (array of 140 devices) with reproducible electrical performance through inkjet-based 3D printing. Enhanced performance stability is observed under cyclic bending, thermal annealing, UV or IR exposure, offering exciting opportunities for sustainable deposition of PEDOT:PSS for large-area 3D printing and its exploitation in heterostructures and flexible electronics