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

A Dust Twin of Cas A: Cool Dust and 21-micron Silicate Dust Feature in the Supernova Remnant G54.1+0.3

We present infrared (IR) and submillimeter observations of the Crab-like supernova remnant (SNR) G54.1+0.3 including 350 micron (SHARC-II), 870 micron (LABOCA), 70, 100, 160, 250, 350, 500 micron (Herschel) and 3-40 micron (Spitzer). We detect dust features at 9, 11 and 21 micron and a long wavelength continuum dust component. The 21 micron dust coincides with [Ar II] ejecta emission, and the feature is remarkably similar to that in Cas A. The IRAC 8 micron image including Ar ejecta is distributed in a shell-like morphology which is coincident with dust features, suggesting that dust has formed in the ejecta. We create a cold dust map that shows excess emission in the northwestern shell. We fit the spectral energy distribution of the SNR using the continuous distributions of ellipsoidal (CDE) grain model of pre-solar grain SiO2 that reproduces the 21 and 9 micron dust features and discuss grains of SiC and PAH that may be responsible for the 10-13 micron dust features. To reproduce the long-wavelength continuum, we explore models consisting of different grains including Mg2SiO4, MgSiO3, Al2O3, FeS, carbon, and Fe3O4. We tested a model with a temperature-dependent silicate absorption coefficient. We detect cold dust (27-44 K) in the remnant, making this the fourth such SNR with freshly-formed dust. The total dust mass in the SNR ranges from 0.08-0.9 Msun depending on the grain composition, which is comparable to predicted masses from theoretical models. Our estimated dust masses are consistent with the idea that SNe are a significant source of dust in the early Universe.Comment: MNRAS: accepted on June 28, 2018 and published on July 4, 201

In-situ measurements of the optical absorption of dioxythiophene-based conjugated polymers

Conjugated polymers can be reversibly doped by electrochemical means. This doping introduces new sub-bandgap optical absorption bands in the polymer while decreasing the bandgap absorption. To study this behavior, we have prepared an electrochemical cell allowing measurements of the optical properties of the polymer. The cell consists of a thin polymer film deposited on gold-coated Mylar behind which is another polymer that serves as a counterelectrode. An infrared transparent window protects the upper polymer from ambient air. By adding a gel electrolyte and making electrical connections to the polymer-on-gold films, one may study electrochromism in a wide spectral range. As the cell voltage (the potential difference between the two electrodes) changes, the doping level of the conjugated polymer films is changed reversibly. Our experiments address electrochromism in poly(3,4-ethylene-dioxy-thiophene) (PEDOT) and poly(3,4-dimethyl-propylene-dioxy-thiophene) (PProDOT-Me$_2$). This closed electrochemical cell allows the study of the doping induced sub-bandgap features (polaronic and bipolaronic modes) in these easily oxidized and highly redox switchable polymers. We also study the changes in cell spectra as a function of polymer thickness and investigate strategies to obtain cleaner spectra, minimizing the contributions of water and gel electrolyte features

Predictive Monitoring for Respiratory Decompensation Leading to Urgent Unplanned Intubation in the Neonatal Intensive Care Unit

Background: Infants admitted to the neonatal intensive care unit (NICU), and especially those born with very low birth weight (VLBW; \u3c 1,500 g), are at risk for respiratory decompensation requiring endotracheal intubation and mechanical ventilation. I ntubation and mechanical ventilation are associated with increased morbidity, particularly in urgent unplanned cases. Methods: We tested the hypothesis that the systemic response associated with respiratory decombensation can be detected from physiological monitoring and that statistical models of bedside monitoring data can identify infants at increased risk of urgent unplanned intubation. We studied 287 VLBW infants consecutively admitted to our NICU and found 96 events in 51 patients, excluding intUbations occurring within. 12h of a previous extubation. Results: In order of importance in a multivariable statistical model, we found that the characteristics of reduced O-2 satura, tion, especially as heart rate was falling; increased heart rate correlation with respiratory rate; and the amount of apnea were aIF significant independent pr,edictors.\u27 The predictive model, validated internally by bootStrap, had a receiver-operating characteristic area of 0.84 + / - 0.04. Conclusion: We propose that predictive monitoring in the NICU for urgent unplanned intubation may improve outcomes by allowing clinicians to intervene noninvasively before intubation is required

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.

BackgroundDesulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations.ResultsThe functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.ConclusionsEven though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion

Immunocompetent murine models for the study of glioblastoma immunotherapy.

Glioblastoma remains a lethal diagnosis with a 5-year survival rate of less than 10%. (NEJM 352:987-96, 2005) Although immunotherapy-based approaches are capable of inducing detectable immune responses against tumor-specific antigens, improvements in clinical outcomes are modest, in no small part due to tumor-induced immunosuppressive mechanisms that promote immune escape and immuno-resistance. Immunotherapeutic strategies aimed at bolstering the immune response while neutralizing immunosuppression will play a critical role in improving treatment outcomes for glioblastoma patients. In vivo murine models of glioma provide an invaluable resource to achieving that end, and their use is an essential part of the preclinical workup for novel therapeutics that need to be tested in animal models prior to testing experimental therapies in patients. In this article, we review five contemporary immunocompetent mouse models, GL261 (C57BL/6), GL26 (C57BL/6) CT-2A (C57BL/6), SMA-560 (VM/Dk), and 4C8 (B6D2F1), each of which offer a suitable platform for testing novel immunotherapeutic approaches

Mixing of Supersonic Streams

The Strutjet approach to Rocket Based Combined Cycle (RBCC) propulsion depends upon fuel-rich flows from the rocket nozzles and turbine exhaust products mixing with the ingested air for successful operation in the ramjet and scramjet modes. A model of the Strutjet device has been built and is undergoing test to investigate the mixing of the streams as a function of distance from the Strutjet exit plane. Initial cold flow testing of the model is underway to determine both, the behavior of the ingested air in the duct and to validate the mixing diagnostics. During the tests, each of the two rocket nozzles ejected up to two pounds mass per second into the 13.6 square inch duct. The tests showed that the mass flow of the rockets was great enough to cause the entrained air to go sonic at the strut, which is the location of the rocket nozzles. More tests are necessary to determine whether the entrained air chokes due to the reduction in the area of the duct at the strut (a physical choke), or because of the addition of mass inside the duct at the nozzle exit (a Fabri choke). The initial tests of the mixing diagnostics are showing promise