Development of agarose gel electrophoresis as a novel method to monitor lignin degradation

Lignin represents the sole bulk alternative source of sustainable aromatic platform chemicals that are otherwise produced by the petrochemical industry (Gillet et al., 2017). Currently there is no high-throughput analytical technique that can be used to quantify or assess the degradation of polymeric lignin. This has significantly held back research within this field, as information about polymeric lignin is crucial if a process is to be developed to efficiently valorise it. The aim of this project was to use agarose gel electrophoresis to develop a novel technique to quantify and assess changes in the structure of polymeric lignin. Another aim was to utilise agarose gel electrophoresis to assess the quantity of low molecular weight aromatic products produced by lignin degradation. Agarose gel electrophoresis has, for the first time, been shown in this study to separate effectively polymeric lignin from low molecular weight components. Electrophoretic variables such as pH, voltage, gel-type, buffer, level and edge- effects have been explored and optima determined. Migrating bands have been characterized and confirmed by multiple methods, as lignin. Band visualisation and quantification techniques have been developed to quantify and assess the polymeric fraction of a lignin sample. Purified samples of lignin have been prepared by cutting bands from the gel and extracting into solution. The method has been shown to separate Kraft, protobind and organosolv lignins corresponding to their respective molecular weight to charge (m/z) distribution, and the results were closely comparable to laborious analyses using Gel Permeation Chromatography (GPC). Electrophoresis with 1% agarose gel in sodium borate buffer at pH 8.75 was found to be highly effective in assessing the concentration and m/z distribution of polymeric lignin after biological, chemical and hydrothermal degradation. Trace profiles of the imaged bands show possible differences in the mechanisms of degradation and indicate lignin shape as another mobility factor. High throughput methods were developed with 40 simultaneous lanes. The method was also shown to be successful in separating low molecular weight products from polymeric lignin, and therefore has the potential to be used to assess the production of platform chemicals

Rapid, Precise, and High-Sensitivity Acquisition of Paleomagnetic and Rock-Magnetic Data: Development of a Low-Noise Automatic Sample Changing System for Superconducting Rock Magnetometers

Among Earth sciences, paleomagnetism is particularly linked to the statistics of large sample sets as a matter of historical development and logistical necessity. Because the geomagnetic field varies over timescales relevant to sedimentary deposition and igneous intrusion, while the fidelity of recorded magnetization is modulated by original properties of rock units and by alteration histories, "ideal" paleomagnetic results measure remanent magnetizations of hundreds of samples at dozens of progressive demagnetization levels, accompanied by tests of magnetic composition on representative sister specimens. We present an inexpensive, open source system for automating paleomagnetic and rock magnetic measurements. Using vacuum pick-and-place technology and a quartz-glass sample holder, the system can in one hour measure remanent magnetizations, as weak as a few pAm2, of ~30 specimens in two vertical orientations with measurement errors comparable to those of the best manual systems. The system reduces the number of manual manipulations required per specimen ~8 fold

Orion Absolute Navigation System Progress and Challenges

The Orion spacecraft is being designed as NASA's next-generation exploration vehicle for crewed missions beyond Low-Earth Orbit. The navigation system for the Orion spacecraft is being designed in a Multi-Organizational Design Environment (MODE) team including contractor and NASA personnel. The system uses an Extended Kalman Filter to process measurements and determine the state. The design of the navigation system has undergone several iterations and modifications since its inception, and continues as a work-in-progress. This paper seeks to benchmark the current state of the design and some of the rationale and analysis behind it. There are specific challenges to address when preparing a timely and effective design for the Exploration Flight Test (EFT-1), while still looking ahead and providing software extensibility for future exploration missions. The primary measurements in a Near-Earth or Mid-Earth environment consist of GPS pseudorange and deltarange, but for future explorations missions the use of star-tracker and optical navigation sources need to be considered. Discussions are presented for state size and composition, processing techniques, and consider states. A presentation is given for the processing technique using the computationally stable and robust UDU formulation with an Agee-Turner Rank-One update. This allows for computational savings when dealing with many parameters which are modeled as slowly varying Gauss-Markov processes. Preliminary analysis shows up to a 50% reduction in computation versus a more traditional formulation. Several state elements are discussed and evaluated, including position, velocity, attitude, clock bias/drift, and GPS measurement biases in addition to bias, scale factor, misalignment, and non-orthogonalities of the accelerometers and gyroscopes. Another consideration is the initialization of the EKF in various scenarios. Scenarios such as single-event upset, ground command, pad alignment, cold start are discussed as are strategies for whole and partial state updates as well as covariance considerations. Strategies are given for dealing with latent measurements and high-rate propagation using multi-rate architecture. The details of the rate groups and the data ow between the elements is discussed and evaluated

Tuning and Robustness Analysis for the Orion Absolute Navigation System

The Orion Multi-Purpose Crew Vehicle (MPCV) is currently under development as NASA's next-generation spacecraft for exploration missions beyond Low Earth Orbit. The MPCV is set to perform an orbital test flight, termed Exploration Flight Test 1 (EFT-1), some time in late 2014. The navigation system for the Orion spacecraft is being designed in a Multi-Organizational Design Environment (MODE) team including contractor and NASA personnel. The system uses an Extended Kalman Filter to process measurements and determine the state. The design of the navigation system has undergone several iterations and modifications since its inception, and continues as a work-in-progress. This paper seeks to show the efforts made to-date in tuning the filter for the EFT-1 mission and instilling appropriate robustness into the system to meet the requirements of manned space ight. Filter performance is affected by many factors: data rates, sensor measurement errors, tuning, and others. This paper focuses mainly on the error characterization and tuning portion. Traditional efforts at tuning a navigation filter have centered around the observation/measurement noise and Gaussian process noise of the Extended Kalman Filter. While the Orion MODE team must certainly address those factors, the team is also looking at residual edit thresholds and measurement underweighting as tuning tools. Tuning analysis is presented with open loop Monte-Carlo simulation results showing statistical errors bounded by the 3-sigma filter uncertainty covariance. The Orion filter design uses 24 Exponentially Correlated Random Variable (ECRV) parameters to estimate the accel/gyro misalignment and nonorthogonality. By design, the time constant and noise terms of these ECRV parameters were set to manufacturer specifications and not used as tuning parameters. They are included in the filter as a more analytically correct method of modeling uncertainties than ad-hoc tuning of the process noise. Tuning is explored for the powered-flight ascent phase, where measurements are scarce and unmodelled vehicle accelerations dominate. On orbit, there are important trade-off cases between process and measurement noise. On entry, there are considerations about trading performance accuracy for robustness. Process Noise is divided into powered flight and coasting ight and can be adjusted for each phase and mode of the Orion EFT-1 mission. Measurement noise is used for the integrated velocity measurements during pad alignment. It is also used for Global Positioning System (GPS) pseudorange and delta- range measurements during the rest of the flight. The robustness effort has been focused on maintaining filter convergence and performance in the presence of unmodeled error sources. These include unmodeled forces on the vehicle and uncorrected errors on the sensor measurements. Orion uses a single-frequency, non-keyed GPS receiver, so the effects due to signal distortion in Earth's ionosphere and troposphere are present in the raw measurements. Results are presented showing the efforts to compensate for these errors as well as characterize the residual effect for measurement noise tuning. Another robustness tool in use is tuning the residual edit thresholds. The trade-off between noise tuning and edit thresholds is explored in the context of robustness to errors in dynamics models and sensor measurements. Measurement underweighting is also presented as a method of additional robustness when processing highly accurate measurements in the presence of large filter uncertainties

The Effects of Fish Trap Mesh Size on Reef Fish Catch off Southeastern Florida

Catch and mesh selectivity of wire-meshed fish traps were tested for eleven different mesh sizes ranging from 13 X 13 mm (0.5 x 0.5") to 76 x 152 mm (3 X 6"). A total of 1,810 fish (757 kg) representing 85 species and 28 families were captured during 330 trap hauls off southeastern Florida from December 1986 to July 1988. Mesh size significantly affected catches. The 1.5" hexagonal mesh caught the most fish by number, weight, and value. Catches tended to decline as meshes got smaller or larger. Individual fish size increased with larger meshes. Laboratory mesh retention experiments showed relationships between mesh shape and size and individual retention for snapper (Lutjanidae), grouper (Serranidae), jack (Carangidae), porgy (Sparidae), and surgeonfish (Acanthuridae). These relationships may be used to predict the effect of mesh sizes on catch rates. Because mesh size and shape greatly influenced catchability, regulating mesh size may provide a useful basis for managing the commercial trap fishery

Dynamics of Capital Investment and Pollution Externalities in Wholesale Electricity Markets

The field of environmental economics was built on the notion of internalizing into markets the social harm caused by pollution. This dissertation examines the implications of putting that idea into practice in the electric power generation sector, with a particular focus on market structure and short- and long-run industry dynamics. Environmental policy to mitigate climate change seeks to transform the capital composition of industries for the purpose of reducing carbon dioxide emissions. In deregulated wholesale electricity markets, firms may exercise long-run market power through investment and retirement decisions which affect future wholesale price settlement. In Chapter 1, I develop a dynamic structural model of the Texas electricity market spanning 2003-2019 to analyze how long-run market power exercise and environmental policy for reducing carbon emissions affect the capital composition of the industry over time. I find that market power exercise led to significant early fossil fuel plant retirements over this period, with an attendant decrease in consumer surplus on the order of $1.6 billion annually. Further counterfactual analysis suggests that federal production tax credits for wind power expanded the deployment of wind by approximately 73 percent, but the associated reductions in emissions were more than twice as costly as would have been achieved under a$20-per-ton carbon tax. In Chapter 2 I delve further into the issue of market structure and long-run dynamics. Economic theory suggests that setting the wholesale price of electricity at the marginal social cost of unmet demand during periods of scarcity results in optimal capacity investment in the presence of perfect competition. I examine the implications of applying this principle in a setting where competition is imperfect, and where the market was structured prior to the introduction of competition (deregulation) and therefore not established through firms’ profit maximizing behavior. I build a stylized model that approximates the effects of a scarcity price mechanism under the hourly demand distribution observed in the Texas wholesale electricity market in 2017. I use this model to demonstrate that the scarcity price mechanism may encourage incumbent firms with large portfolios to retire plants, and that firms with a threshold amount of existing infra-marginal generation capacity will be unwilling to invest in new capacity. I then use a dynamic structural model to demonstrate that the scarcity price mechanism introduced in Texas in 2014 accelerated turnover over the period 2014-2019 by driving greater retirement of capacity in addition to greater investment, relative to a counterfactual scenario in which the scarcity price design was not implemented. In Chapter 3 I shift my focus from long-run industry dynamics and environmental policy concerning a global pollutant (carbon dioxide) to short-run dynamics and harm from a local pollutant (ground-level ozone). NOx emissions are a precursor to ground-level ozone, a pernicious pollutant that is harmful to human health and ecosystems. Despite decades of regulations including NOx emissions pricing, and a corresponding precipitous decline in NOx emissions, episodic high-ozone events prevent many areas from achieving air quality standards. Theoretically, spatially or temporally differentiated emissions prices could be more cost-effective at reducing such events than a uniform price. To test this prediction, using data from the EPA and NOAA spanning 2001-2019, we use novel empirical strategies to estimate (1) the link between hourly emissions and high-ozone events and (2) hourly marginal abatement costs. The estimates form the basis for simulations that compare uniform and differentiated emissions pricing. Consistent with economic theory, differentiated emissions pricing is substantially more cost effective at reducing high-ozone events, but this advantage depends on the accuracy of the estimated NOx-ozone relationship

Compressor rotor failure due to fouling at Qatargas condensate refinery

Case Study•Process Overview •Hydrogen Recycle Compressor •The Problem •Performance Trends •Compressor Crash •Vibration analysis •Internal Inspection of Compressor •Investigation •Resolution •Lessons Learn

A Type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars

Objective: To determine the relationships between RepA/C2 plasmids carrying several antibiotic resistance genes found in isolates of Salmonella enterica serovars Ohio and Senftenberg from pigs. Methods: Illumina HiSeq was used to sequence seven S. enterica isolates. BLAST searches identified relevant A/C2 plasmid contigs, and contigs were assembled using PCR. Results: Two serovar Ohio isolates were ST329 and the five Senftenberg isolates were ST210. The A/C2 plasmids recovered from the seven isolates belong to Type 2 and contain two resistance islands. Their backbones were closely related, differing by five or fewer single nucleotide polymorphisms. The sul2-containing resistance island ARI-B is 19.9 kb and also contains the kanamycin and neomycin resistance gene aphA1, the tetracycline resistance gene tetA(D), and an erythromycin resistance gene, erm(42), not previously seen in A/C2 plasmids. A second 30.3 kb resistance island, RI-119, is in a unique location in the A/C2 backbone 8.2 kb downstream of rhs. RI-119 contained genes conferring resistance to apramycin, netilmicin, tobramycin (aacC4), hygromycin (hph), sulphonamides (sul1) and spectinomycin and streptomycin (aadA2). In one of the seven plasmids, this resistance region contained two IS26-mediated deletions. A discrete 5.7 kb segment containing the aacC4 and hph genes and bounded by IS26 on one side and the IR of Tn5393 on the other was identified. Conclusions: The presence of almost identical A/C2 plasmids in two serovars indicates a common origin. Type 2 A/C2 plasmids continue to evolve via addition of new resistance regions such as RI-119 and evolution of existing ones

A Type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars

Objective: To determine the relationships between RepA/C2 plasmids carrying several antibiotic resistance genes found in isolates of Salmonella enterica serovars Ohio and Senftenberg from pigs. Methods: Illumina HiSeq was used to sequence seven S. enterica isolates. BLAST searches identified relevant A/C2 plasmid contigs, and contigs were assembled using PCR. Results: Two serovar Ohio isolates were ST329 and the five Senftenberg isolates were ST210. The A/C2 plasmids recovered from the seven isolates belong to Type 2 and contain two resistance islands. Their backbones were closely related, differing by five or fewer single nucleotide polymorphisms. The sul2-containing resistance island ARI-B is 19.9 kb and also contains the kanamycin and neomycin resistance gene aphA1, the tetracycline resistance gene tetA(D), and an erythromycin resistance gene, erm(42), not previously seen in A/C2 plasmids. A second 30.3 kb resistance island, RI-119, is in a unique location in the A/C2 backbone 8.2 kb downstream of rhs. RI-119 contained genes conferring resistance to apramycin, netilmicin, tobramycin (aacC4), hygromycin (hph), sulphonamides (sul1) and spectinomycin and streptomycin (aadA2). In one of the seven plasmids, this resistance region contained two IS26-mediated deletions. A discrete 5.7 kb segment containing the aacC4 and hph genes and bounded by IS26 on one side and the IR of Tn5393 on the other was identified. Conclusions: The presence of almost identical A/C2 plasmids in two serovars indicates a common origin. Type 2 A/C2 plasmids continue to evolve via addition of new resistance regions such as RI-119 and evolution of existing ones

Turbomachinery Operation and Maintenance

Discussion Grou