Passive broadband full Stokes polarimeter using a Fresnel cone

Light's polarisation contains information about its source and interactions, from distant stars to biological samples. Polarimeters can recover this information, but reliance on birefringent or rotating optical elements limits their wavelength range and stability. Here we present a static, single-shot polarimeter based on a Fresnel cone - the direct spatial analogue to the popular rotating quarter-wave plate approach. We measure the average angular accuracy to be 2.9 (3.6) degrees for elliptical(linear) polarisation states across the visible spectrum, with the degree of polarisation determined to within 0.12(0.08). Our broadband full Stokes polarimeter is robust, cost-effective, and could find applications in hyper-spectral polarimetry and scanning microscopy.Comment: 6 Pages, 4 Figure

Transposon and deletion mutagenesis of genes involved in perchlorate reduction in Azospira suillum PS.

UnlabelledAlthough much work on the biochemistry of the key enzymes of bacterial perchlorate reduction, chlorite dismutase, and perchlorate reductase has been published, understanding of the molecular mechanisms of this metabolism has been somewhat hampered by the lack of a clear model system amenable to genetic manipulation. Using transposon mutagenesis and clean deletions, genes important for perchlorate reduction in Azospira suillum PS have been identified both inside and outside the previously described perchlorate reduction genomic island (PRI). Transposon mutagenesis identified 18 insertions in 11 genes that completely abrogate growth via reduction of perchlorate but have no phenotype during denitrification. Of the mutants deficient in perchlorate reduction, 14 had insertions that were mapped to eight different genes within the PRI, highlighting its importance in this metabolism. To further explore the role of these genes, we also developed systems for constructing unmarked deletions and for complementing these deletions. Using these tools, every core gene in the PRI was systematically deleted; 8 of the 17 genes conserved in the PRI are essential for perchlorate respiration, including 3 genes that comprise a unique histidine kinase system. Interestingly, the other 9 genes in the PRI are not essential for perchlorate reduction and may thus have unknown functions during this metabolism. We present a model detailing our current understanding of perchlorate reduction that incorporates new concepts about this metabolism.ImportanceAlthough perchlorate is generated naturally in the environment, groundwater contamination is largely a result of industrial activity. Bacteria capable of respiring perchlorate and remediating contaminated water have been isolated, but relatively little is known about the biochemistry and genetics of this process. Here we used two complementary approaches to identify genes involved in perchlorate reduction. Most of these genes are located on a genomic island, which is potentially capable of moving between organisms. Some of the genes identified are known to be directly involved in the metabolism of perchlorate, but other new genes likely regulate the metabolism in response to environmental signals. This work has uncovered new questions about the regulation, energetics, and evolution of perchlorate reduction but also presents the tools to address them

Structure and evolution of chlorate reduction composite transposons.

UnlabelledThe genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration.ImportanceGenome sequencing has identified, for the first time, chlorate reduction composite transposons. These transposons are constructed with flanking insertion sequences that differ in type and orientation between organisms, indicating that this mobile element has formed multiple times and is important for dissemination. Apart from core metabolic enzymes, very little is known about the genetic factors involved in chlorate reduction. Comparative analysis has identified several genes that may also be important, but the relative absence of accessory genes suggests that this mobile metabolism relies on host systems for electron transport, regulation, and cofactor synthesis. Phylogenetic analysis of Cld and ClrA provides support for the hypothesis that chlorate reduction was built multiple times from type II dimethyl sulfoxide (DMSO) reductases and cld. In at least one case, cld has been coopted from a perchlorate reduction island for this purpose. This work is a significant step toward understanding the genetics and evolution of chlorate reduction

SONTRAC—A low background, large area solar neutron spectrometer

SONTRAC is a scintillating fiber neutron detector designed to measure solar flare neutrons from a balloon or spacecraft platform. The instrument is comprised of alternating orthogonal planes of scintillator fibers viewed by photomultiplier tubes and image intensifier/CCD camera optics. It operates by tracking the paths of recoil protons from the double scatter of 20 to 200 MeV neutrons off hydrogen in the plastic scintillator, thereby providing the necessary information to determine the incident neutron direction and energy. SONTRAC is also capable of detecting and measuring high-energy gamma rays \u3e20 MeV as a “solid-state spark chamber.” The self-triggering and track imaging features of a prototype for tracking in two dimensions have been demonstrated in calibrations with cosmic-ray muons, 14 to ∼65 MeV neutrons and ∼20 MeV protons

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1.

UnlabelledDespite evidence for the prevalence of horizontal gene transfer of respiratory genes, little is known about how pathways functionally integrate within new hosts. One example of a mobile respiratory metabolism is bacterial chlorate reduction, which is frequently encoded on composite transposons. This implies that the essential components of the metabolism are encoded on these mobile elements. To test this, we heterologously expressed genes for chlorate reduction from Shewanella algae ACDC in the non-chlorate-reducing Shewanella oneidensis MR-1. The construct that ultimately endowed robust growth on chlorate included cld, a cytochrome c gene, clrABDC, and two genes of unknown function. Although strain MR-1 was unable to grow on chlorate after initial insertion of these genes into the chromosome, 11 derived strains capable of chlorate respiration were obtained through adaptive evolution. Genome resequencing indicated that all of the evolved chlorate-reducing strains replicated a large genomic region containing chlorate reduction genes. Contraction in copy number and loss of the ability to reduce chlorate were also observed, indicating that this phenomenon was extremely dynamic. Although most strains contained more than six copies of the replicated region, a single strain with less duplication also grew rapidly. This strain contained three additional mutations that we hypothesized compensated for the low copy number. We remade the mutations combinatorially in the unevolved strain and determined that a single nucleotide polymorphism (SNP) upstream of cld enabled growth on chlorate and was epistatic to a second base pair change in the NarP binding sequence between narQP and nrfA that enhanced growth.ImportanceThe ability of chlorate reduction composite transposons to form functional metabolisms after transfer to a new host is an important part of their propagation. To study this phenomenon, we engineered Shewanella oneidensis MR-1 into a chlorate reducer. We defined a set of genes sufficient to endow growth on chlorate from a plasmid, but found that chromosomal insertion of these genes was nonfunctional. Evolution of this inoperative strain into a chlorate reducer showed that tandem duplication was a dominant mechanism of activation. While copy number changes are a relatively rapid way of increasing gene dosage, replicating almost 1 megabase of extra DNA is costly. Mutations that alleviate the need for high copy number are expected to arise and eventually predominate, and we identified a single nucleotide polymorphism (SNP) that relieved the copy number requirement. This study uses both rational and evolutionary approaches to gain insight into the evolution of a fascinating respiratory metabolism

Continued Developments in the Modeling of Complex Dimension and Orientation Variation in Split D Differential Eddy Current Probes

Over the past few years, the complexity of models for split D differential eddy current probes has increased significantly. Moving from rather simplistic models where coils and cores were modeled symmetrically to the current state where validation can be done using very asymmetric coils [1, 2, 3]. Last year results showing a large amount of modeling error for variation in the orientation of the various components of a split D probe were presented. As a follow-on to this effort, additional modeling work has been performed looking into alleviating this error. One of the major factors being investigated this year is increasing mesh resolution. Convergence and statistical analysis will be performed on the data to determine the appropriate mesh resolution necessary for future modeling efforts involving orientation variation is needed. Recent work has addressed a model validation study using a large split D probe scanned over a notch at various orientations. Data from the previously described simulations will be compared to the experimental data collected. By running the simulations at various mesh resolutions, it is anticipated that a pattern will emerge detailing how the mesh resolution needs to changes to achieve comparable levels of accuracy as the probe orientation varies

Development of a Hard X-Ray Polarimeter for Astrophysics

We have been developing a Compton scatter polarimeter for measuring the linear polarization of hard X-rays (100-300 keV) from astrophysical sources. A laboratory prototype polarimeter has been used to successfully demonstrate the reliability of our Monte Carlo simulation code and to demonstrate our ability to generate a polarized photon source in the lab. Our design concept places a self-containedpolarimeter module on the front-end of a a 5-inch position sensitive PMT (PSPMT). We are currently working on the fabrication of a science model based on this PSPMT concept. Although the emphasis of our development effort is towards measuring hard X-rays from solar flares, our design has the advantage that it is sensitive over a rather large field-of-view (\u3e1 steradian), a feature that makes it especially attractive for γ-ray burst studie

Development of a hard X-ray polarimeter for astrophysics

We have been developing a Compton scatter polarimeter for measuring the linear polarization of hard X-rays (100-300 keV) from astrophysical sources. A laboratory prototype polarimeter has been used to successfully demonstrate the reliability of our Monte Carlo simulation code and to demonstrate our ability to generate a polarized photon source in the lab. Our design concept places a self-containedpolarimeter module on the front-end of a a 5-inch position sensitive PMT (PSPMT). We are currently working on the fabrication of a science model based on this PSPMT concept. Although the emphasis of our development effort is towards measuring hard X-rays from solar flares, our design has the advantage that it is sensitive over a rather large field-of-view (\u3e1 steradian), a feature that makes it especially attractive for γ-ray burst studies