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

Determining the Extent of Market and Extent of Resource for Stated Preference Survey Design Using Mapping Methods

Determining the appropriate survey population and the commodity to be valued are among the most fundamental design decisions for stated preference (SP) surveys. However, often little information is available about who in the population holds measurable value for the resource (the extent of the market) and their perceptions regarding the scope of the resource to be valued (the extent of the resource). In this paper, we present a novel approach using cognitive mapping interview techniques to shed light on these design questions. The method also provides ancillary information that assists in the interpretation of information collected during focus groups and through SP survey administration. The approach was developed and tested as part of an ongoing study on environmental degradation associated with acidification in the Southern Appalachian Mountain region. Although damage from acidification in the study region is broad, it is not clear whether residents of this region care, in both a use and nonuse sense, about resources in their states of residence, in neighboring states, on public lands, or more broadly across the region. From a pilot study, we found that participants show a significant home-state preference in the number and size of natural areas that they value within the larger Southern Appalachian Mountain region. However, this preference is not strong enough to suggest that the market for improving these resources is solely constrained to residents of the state in which the resource is located.stated preference, cognitive mapping, extent of market, extent of resource, definition of commodity

Hormone Receptor and ERBB2 Status in Gene Expression Profiles of Human Breast Tumor Samples

The occurrence of large publically available repositories of human breast tumor gene expression profiles provides an important resource to discover new breast cancer biomarkers and therapeutic targets. For example, knowledge of the expression of the estrogen and progesterone hormone receptors (ER and PR), and that of the ERBB2 in breast tumor samples enables choice of therapies for the breast cancer patients that express these proteins. Identifying new biomarkers and therapeutic agents affecting the activity of signaling pathways regulated by the hormone receptors or ERBB2 might be accelerated by knowledge of their expression levels in large gene expression profiling data sets. Unfortunately, the status of these receptors is not invariably reported in public databases of breast tumor gene expression profiles. Attempts have been made to employ a single probe set to identify ER, PR and ERBB2 status, but the specificity or sensitivity of their prediction is low. We enquired whether estimation of ER, PR and ERBB2 status of profiled tumor samples could be improved by using multiple probe sets representing these three genes and others with related expression

How Does Retirement Planning Software Handle Postretirement Realities?

Many risks must be managed during the post-retirement period. This chapter explores retirement planning software that provides individuals and advisors the opportunity to perform a range of calculations to help them in retirement planning. We link results from surveys and research by the Society of Actuaries to show how the software handles post-retirement risks. We find that approaches to managing these risks are often not well-integrated

Bicalutamide as an Androgen Blocker With Secondary Effect of Promoting Feminization in Male-to-Female Transgender Adolescents

PURPOSE: The purpose of the study was to describe the novel use of bicalutamide in transgender youth. METHODS: This is a retrospective review of patients with gender dysphoria followed in the pediatric endocrine clinic at Riley Hospital for Children. RESULTS: Of 104 patients with gender dysphoria, 23 male-to-female adolescents received bicalutamide 50 mg daily as a second-line puberty blocker after insurance company denial of a gonadotropin-releasing hormone analog. Six patients received estrogen concurrently. Of 13 patients treated exclusively with bicalutamide seen in follow-up, 84.6% had breast development within 6 months, the majority being ≥ Tanner stage III. CONCLUSIONS: Bicalutamide may be an alternative to gonadotropin-releasing hormone analogs in transgender male-to-female youth who are also ready to undergo physical transition

The management and cost of surgical site infection in patients undergoing surgery for spinal metastasis

Background Surgical site infection (SSI) is a serious potential complication of spinal surgery. SSI can impact significantly on in-patient hospitalisation and the costs associated with extra care. Aim To investigate the management of patients experiencing SSI following surgery for spinal metastatic tumours, and to estimate the costs associated with SSI in this context. Methods Patients experiencing SSI following spinal tumour surgery at a large spinal surgery centre between January 2009 and December 2012 were identified. Existing case notes were reviewed and patient and procedural data, details of the infection and treatment interventions were collected. A bottom-up approach to calculating costs associated with infection was used for patients experiencing SSI and compared with a quasi-random sample of similar patients without SSI. Findings The mean cost of treating patients with SSI was significantly greater than costs associated with those without SSI (p=0.019). Mean cost of in-patient hospital stay was 60% higher in patients with SSI compared to those without SSI (p=0.004). In-patient hospital stay alone accounted for 59% of total costs. Return to theatre was the second most costly intervention overall, accounting for 38% of costs, and was the most expensive single intervention involved in the treatment of SSI. Conclusion SSI significantly increases healthcare costs for patients undergoing surgery for spinal metastasis, with prolonged in-patient hospitalisation and return to theatre for wound management being major contributors. The actual total cost to society derived from SSI in this patient group is likely to be far beyond just the direct costs to healthcare providers

Electron-Electron Bremsstrahlung Emission and the Inference of Electron Flux Spectra in Solar Flares

Although both electron-ion and electron-electron bremsstrahlung contribute to the hard X-ray emission from solar flares, the latter is normally ignored. Such an omission is not justified at electron (and photon) energies above $\sim 300$ keV, and inclusion of the additional electron-electron bremsstrahlung in general makes the electron spectrum required to produce a given hard X-ray spectrum steeper at high energies. Unlike electron-ion bremsstrahlung, electron-electron bremsstrahlung cannot produce photons of all energies up to the maximum electron energy involved. The maximum possible photon energy depends on the angle between the direction of the emitting electron and the emitted photon, and this suggests a diagnostic for an upper cutoff energy and/or for the degree of beaming of the accelerated electrons. We analyze the large event of January 17, 2005 observed by RHESSI and show that the upward break around 400 keV in the observed hard X-ray spectrum is naturally accounted for by the inclusion of electron-electron bremsstrahlung. Indeed, the mean source electron spectrum recovered through a regularized inversion of the hard X-ray spectrum, using a cross-section that includes both electron-ion and electron-electron terms, has a relatively constant spectral index $\delta$ over the range from electron kinetic energy $E = 200$ keV to $E = 1$ MeV. However, the level of detail discernible in the recovered electron spectrum is not sufficient to determine whether or not any upper cutoff energy exists.Comment: 7 pages, 5 figures, submitted to Astrophysical Journa

Quasiexcitons in Incompressible Quantum Liquids

Photoluminescence (PL) has been used to study two-dimensional incompressible electron liquids in high magnetic fields for nearly two decades. However, some of the observed anomalies coincident with the fractional quantum Hall effect are still unexplained. We show that emission in these systems occurs from fractionally charged "quasiexciton" states formed from trions correlated with the surrounding electrons. Their binding and recombination depend on the state of both the electron liquid and the involved trion, predicting discontinuities in PL and sensitivity to sample parameters.Comment: 4 pages, 4 figure