Microbial Diversity Across an Oxygen Gradient Using Large-scale Phylogenetic-based Analysis of Marine Metagenomes

Insufficient reference sequence data for annotation of unknown environmental sequences and metagenomes has driven efforts to find alternative annotation methods that mitigate biases from missing information. The use of phylogenetic-placement algorithms shows promise as a robust sequence annotation technique that deals with missing reference information by allowing for annotation of sequences at internal nodes of a phylogenetic tree. However, using these methods for community level surveys of the thousands of genes found in metagenomes requires powerful computational systems and sophisticated software workflows. The main goal of this thesis is to outline a phylogenetic analysis pipeline built to process environmental metagenomic samples using the pplacer software suite, and a pilot study performed with this software pipeline to investigate community-level patterns in gene diversity for a marine oxygen minimum zone (OMZ) off the coast of Chile, South America. Reference sequence data was used to create a custom database and custom reference packages for 9,204 functional housekeeping genes, along with small sub-unit ribosomal genes (SSU) by Domain. A comparative analysis of metagenomic samples from the OMZ using our pipeline shows that while functional and SSU genes show similar spatial patterns of diversity across the oxygen gradient, higher overall diversity was identified via the functional genes. Ecologically relevant functional genes showed higher levels of diversity than either the total from all functional genes or SSU ribosomal genes, underlining the importance of diversity in ecosystem functions

A flight investigation with a STOL airplane flying curved, descending instrument approach paths

A flight investigation using a De Havilland Twin Otter airplane was conducted to determine the configurations of curved, 6 deg descending approach paths which would provide minimum airspace usage within the requirements for acceptable commercial STOL airplane operations. Path configurations with turns of 90 deg, 135 deg, and 180 deg were studied; the approach airspeed was 75 knots. The length of the segment prior to turn, the turn radius, and the length of the final approach segment were varied. The relationship of the acceptable path configurations to the proposed microwave landing system azimuth coverage requirements was examined

Adolescent amphetamine exposure elicits dose-specific effects on monoaminergic neurotransmission and behaviour in adulthood.

Despite the growing non-medical consumption of amphetamine (Amph) during adolescence, its long-term neurobiological and behavioural effects have remained largely unexplored. The present research sought to characterize the behavioural profile and electrophysiological properties of midbrain monoaminergic neurons in adult rodents after Amph exposure during adolescence. Adolescent rats were administered vehicle, 0.5, 1.5, or 5.0 mg/kg.d Amph from postnatal day (PND) 30–50. At adulthood (PND 70), rats were tested in an open-field test (OFT) and elevated plus maze (EPM), paralleled by in-vivo extracellular recordings of serotonin (5-HT), dopamine (DA) and norepinephrine (NE) neurons from the dorsal raphe nucleus, ventral tegmental area, and locus coeruleus, respectively. 5-HT firing in adulthood was increased in rats that had received Amph (1.5 mg/kg.d) during adolescence. At this regimen, DA firing activity was increased, but not NE firing. Conversely, the highest Amph dose regimen (5.0 mg/kg.d) enhanced NE firing, but not DA or 5-HT firing rates. In the OFT, Amph (1.5 mg/kg.d) significantly increased the total distance travelled, while the other doses were ineffective. In the EPM, all three Amph doses increased time spent in the open arms and central platform, as well as the number of stretch-attend postures made. Repeated adolescent exposure to Amph differentially augments monoaminergic neuronal firing in a dose-specific fashion in adulthood, with corresponding alterations in locomotion, risk assessment (stretch-attend postures and central platform occupancy) and risk-taking behaviours (open-arm exploration). Thus, adolescent Amph exposure induces long-lasting neurophysiological alterations that may have implications for drug-seeking behaviour in the future

Sorption behaviour of per- and polyfluoroalkyl substances (PFASs) in tropical soils

The sorption behaviour of three perfluoroalkyl substances (PFASs), namely perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorohexane sulfonic acid (PFHxS), was determined on 28 tropical soils. Tropical soils are often highly weathered, richer in sesquioxides than temperate soils and may contain variable charge minerals. There are little data on sorption of PFASs in tropical soils. The highest Kd values were found for PFOS with mean values ranging from 0 to 31.6 L/kg. The Kd values for PFOA and PFHxS ranged from 0 to 4.9 L/kg and from 0 to 5.6 L/kg, respectively. While these values are in the range of literature sorption data, the average Kd values for PFOS and PFOA from the literature were 3.7 times and 3.6 times higher, respectively, than those measured in this study. Stepwise regression analysis did explain some of the variance, but with different explanatory variables for the different PFASs. The main soil properties explaining sorption for PFOS and PFOA were oxalate-extractable Al and pH, and for PFHxS was pH

Application of a column selection system and DryLab software for high-performance liquid chromatography method development

Abstract This paper describes a strategy for the development of chromatographic methods for drug candidates based upon the use of simple MS compatible mobile phases and optimization of the chromatographic selectivity through variations of the stationary phase and mobile phase pH. The strategy employs an automated column selection system and a series of HPLC columns, varying in hydrophobicity and silanol activity, in combination with DryLab software to develop chromatographic methods for the separation of mixtures of bupivacaine and its metabolites; acidic, basic, and neutral compounds; and atenolol, nitrendipine, and their degradation products

Protein hydrolysates from boarfish (Capros aper) and Atlantic salmon (Salmo salar) skin gelatin improve metabolic control in genetically obese diabetic (ob/ob) mice

There is increasing interest in dietary protein for management of Type 2 diabetes mellitus (T2DM) and obesity. The effects of twice-daily oral administration of a salmon skin gelatin hydrolysate (SSGH, 50 mg/kg), boarfish protein hydrolysate (BPH, (50 mg/kg), metformin (200 mg/kg), or saline control, were investigated in ob/ob mice. Non-fasting blood glucose was significantly reduced with SSGH (p < 0.01), BPH (p < 0.001) and metformin (p < 0.001), which were reflected in reductions in glycated haemoglobin (HbA1c) (p < 0.001, p < 0.01 and p < 0.01, respectively). Responses to oral and intraperitoneal glucose tolerance were improved (p < 0.05–0.01), as well as circulating plasma lipid profiles (p < 0.05–0.001). Chronic BPH treatment increased circulating plasma insulin (p < 0.01), whereas SSGH improved insulin sensitivity (p < 0.05), versus respective controls. All treatments significantly reduced energy intake (p < 0.05–0.001) versus (ob/ob) controls, without affecting overall bodyweight. These findings suggest that fish hydrolysates mediate potent anti-diabetic actions similar to metformin and might be suitable for the management and prevention of T2DM

Observation of laser pulse propagation in optical fibers with a SPAD camera

Recording processes and events that occur on sub-nanosecond timescales poses a difficult challenge. Conventional ultrafast imaging techniques often rely on long data collection times, which can be due to limited device sensitivity and/or the requirement of scanning the detection system to form an image. In this work, we use a single-photon avalanche detector array camera with pico-second timing accuracy to detect photons scattered by the cladding in optical fibers. We use this method to film supercontinuum generation and track a GHz pulse train in optical fibers. We also show how the limited spatial resolution of the array can be improved with computational imaging. The single-photon sensitivity of the camera and the absence of scanning the detection system results in short total acquisition times, as low as a few seconds depending on light levels. Our results allow us to calculate the group index of different wavelength bands within the supercontinuum generation process. This technology can be applied to a range of applications, e.g., the characterization of ultrafast processes, time-resolved fluorescence imaging, three-dimensional depth imaging, and tracking hidden objects around a corner. © The Author(s) 20171541sciescopu

A Radio Pulsar/X-ray Binary Link

Radio pulsars with millisecond spin periods are thought to have been spun up by transfer of matter and angular momentum from a low-mass companion star during an X-ray-emitting phase. The spin periods of the neutron stars in several such low-mass X-ray binary (LMXB) systems have been shown to be in the millisecond regime, but no radio pulsations have been detected. Here we report on detection and follow-up observations of a nearby radio millisecond pulsar (MSP) in a circular binary orbit with an optically identified companion star. Optical observations indicate that an accretion disk was present in this system within the last decade. Our optical data show no evidence that one exists today, suggesting that the radio MSP has turned on after a recent LMXB phase.Comment: published in Scienc