Development and application of a real-time polymerase chain reaction assay for the myxozoan parasite Henneguya ictaluri

Proliferative gill disease (PGD) caused by the myxozoan parasite Henneguya ictaluri is one of the most devastating parasitic infections in channel catfish aquaculture. Currently, there is no effective treatment for H. ictaluri and the unpredictable outbreaks can result in 100% mortality. Management strategies have been developed to prevent losses in newly stocked fingerlings by evaluating the PGD status of a pond prior to stocking, which is difficult since resident fish may not show clinical signs even when actinospore levels are lethal to naive fish. Current diagnostic methods are limited to the identification of an active infection and methods of predicting potential outbreaks have several limitations. The PGD status of a pond to be stocked can be determined using sentinel fish exposures which are labor intensive and require a source of parasite free fish. These limitations necessitated the development of more rapid and efficient means of determining actinospore concentrations to determine the risk of losing fish prior to stocking. The development of a quantitative real-time polymerase chain reaction (QPCR) assay provided a more rapid, sensitive and quantitative method of diagnosing active infections and also provides a means to predict potential PD outbreaks and determine the PGD status of a pond prior to stocking. Another approach in the control of this parasite is the identification of a less susceptible culturable species or to identify traits that could be targeted in a selective breeding program. Challenge studies have shown that the closely related blue catfish (Ictalurus furcatus) does not exhibit as severe an inflammatory response to H. ictaluri and mortalities are significantly lower than in channel catfish. Comparisons of PGD severity and H. ictaluri infection in channel catfish, blue catfish and channel x blue catfish backcross hybrids by gross examination, histopathology and the newly developed H. ictaluri real-time PCR (QPCR) assay supported previous research suggesting the life cycle of the parasite can not be completed as efficiently through the blue catfish host. This dissertation describes the development and validation of a QPCR assay to detect H. ictaluri in both fish tissues and environmental samples and the application of this assay in both research and production settings

NS2 is dispensable for efficient assembly of hepatitis C virus-like particles in a bipartite trans-encapsidation system.

Infectious hepatitis C virus (HCV) particle production in the genotype 2a JFH-1-based cell culture system involves non-structural proteins in addition to canonical virion components. NS2 has been proposed to act as a protein adaptor, co-ordinating the early stages of virion assembly. However, other studies have identified late-acting roles for this protein, making its precise involvement in infectious particle production unclear. Using a robust, bipartite trans-encapsidation system based upon baculovirus expression of HCV structural proteins, we have generated HCV-like particles (HCV-LP) in the absence of NS2 with overt similarity to wild-type virions. HCV-LP could transduce naive cells with trans-encapsidated subgenomic replicon RNAs and shared similar biochemical and biophysical properties with JFH-1 HCV. Both genotype 1b and JFH-1 intracellular HCV-LP were produced in the absence of NS2, whereas restoring NS2 to the JFH-1 system dramatically enhanced secreted infectivity, consistent with a late-acting role. Our system recapitulated authentic HCV particle assembly via trans-complementation of bicistronic, NS2-deleted, chimeric HCV, which is otherwise deficient in particle production. This closely resembled replicon-mediated NS2 trans-complementation, confirming that baculovirus expression of HCV proteins did not unduly affect particle production. Furthermore, this suggests that separation of structural protein expression from replicating HCV RNAs that are destined to be packaged alleviates an early stage requirement for NS2 during particle formation. This highlights our current lack of understanding of how NS2 mediates assembly, yet comparison of full-length and bipartite systems may provide further insight into this process

Warming seas increase cold-stunning events for Kemp’s ridley sea turtles in the northwest Atlantic

Since the 1970s, the magnitude of turtle cold-stun strandings have increased dramatically within the northwestern Atlantic. Here, we examine oceanic, atmospheric, and biological factors that may affect the increasing trend of cold-stunned Kemp’s ridleys in Cape Cod Bay, Massachusetts, United States of America. Using machine learning and Bayesian inference modeling techniques, we demonstrate higher cold-stunning years occur when the Gulf of Maine has warmer sea surface temperatures in late October through early November. Surprisingly, hatchling numbers in Mexico, a proxy for population abundance, was not identified as an important factor. Further, using our Bayesian count model and forecasted sea surface temperature projections, we predict more than 2,300 Kemp’s ridley turtles may cold-stun annually by 2031 as sea surface temperatures continue to increase within the Gulf of Maine. We suggest warmer sea surface temperatures may have modified the northerly distribution of Kemp’s ridleys and act as an ecological bridge between the Gulf Stream and nearshore waters. While cold-stunning may currently account for a minor proportion of juvenile mortality, we recommend continuing efforts to rehabilitate cold-stunned individuals to maintain population resiliency for this critically endangered species in the face of a changing climate and continuing anthropogenic threats

Secondary organic aerosol 3. Urban/regional scale model of size- and composition-resolved aerosols

The California Institute of Technology (CIT) three-dimensional urban/regional atmospheric model is used to perform comprehensive gas- and aerosol-phase simulations of the 8 September 1993 smog episode in the South Coast Air Basin of California (SoCAB) using the atmospheric chemical mechanism of part 1 [Griffin et al., 2002] and the thermodynamic module of part 2 [Pun et al., 2002]. This paper focuses primarily on simulations of secondary organic aerosol (SOA) and determination of the species and processes that lead to this SOA. Meteorological data and a gas and particulate emissions inventory for this episode were supplied directly by the South Coast Air Quality Management District. A summer 1993 atmospheric sampling campaign provides data against which the performance of the model is evaluated. Predictions indicate that SOA formation in the SoCAB is dominated by partitioning of hydrophobic secondary products of the oxidation of anthropogenic organics. The biogenic contribution to total SOA increases in the more rural eastern portions of the region, as does the fraction of hydrophilic SOA, the latter reflecting the increasing degree of oxidation of SOA species with atmospheric residence time

A Simple Approach for State-Action Abstraction using a Learned MDP Homomorphism

Animals are able to rapidly infer from limited experience when sets of state action pairs have equivalent reward and transition dynamics. On the other hand, modern reinforcement learning systems must painstakingly learn through trial and error that sets of state action pairs are value equivalent -- requiring an often prohibitively large amount of samples from their environment. MDP homomorphisms have been proposed that reduce the observed MDP of an environment to an abstract MDP, which can enable more sample efficient policy learning. Consequently, impressive improvements in sample efficiency have been achieved when a suitable MDP homomorphism can be constructed a priori -- usually by exploiting a practioner's knowledge of environment symmetries. We propose a novel approach to constructing a homomorphism in discrete action spaces, which uses a partial model of environment dynamics to infer which state action pairs lead to the same state -- reducing the size of the state-action space by a factor equal to the cardinality of the action space. We call this method equivalent effect abstraction. In a gridworld setting, we demonstrate empirically that equivalent effect abstraction can improve sample efficiency in a model-free setting and planning efficiency for modelbased approaches. Furthermore, we show on cartpole that our approach outperforms an existing method for learning homomorphisms, while using 33x less training data.Comment: Previously Presented at the Multi-disciplinary Conference on Reinforcement Learning and Decision Making (RLDM) 202

Predicting the response of a submillimeter bolometer to cosmic rays

Bolometers designed to detect. submillimeter radiation also respond to cosmic, gamma, and x rays. Because detectors cannot be fully shielded from such energy sources, it is necessary to understand the effect of a photon or cosmic-ray particle being absorbed. The resulting signal (known as a glitch) can then be removed from raw data. We present measurements using an Americium-241 gamma radiation source to irradiate a prototype bolometer for the High Frequency Instrument in the Planck Surveyor satellite. Our measurements showed no variation in response depending on where the radiation was absorbed, demonstrating that the bolometer absorber and thermistor thermalize quickly. The bolometer has previously been fully characterized both electrically and optically. We find that using optically measured time constants underestimates the time taken for the detector to recover from a radiation absorption event. However, a full thermal model for the bolometer, with parameters taken from electrical and optical measurements, provides accurate time constants. Slight deviations from the model were seen at high energies; these can be accounted for by use of an extended model

Synthetic Cationic Autoantigen Mimics Glatiramer Acetate Persistence at the Site of Injection and Is Efficacious Against Experimental Autoimmune Encephalomyelitis

A synthetic peptide, K-PLP, consisting of 11-unit poly-lysine (K11) linked via polyethylene glycol (PEG) to proteolipid protein epitope (PLP) was synthesized, characterized, and evaluated for efficacy in ameliorating experimental autoimmune encephalomyelitis (EAE) induced by PLP. K-PLP was designed to mimic the cationic nature of the relapsing-remitting multiple sclerosis treatment, glatiramer acetate (GA). With a pI of ~10, GA is able to form visible aggregates at the site of injection via electrostatic interactions with the anionic extracellular matrix. Aggregation further facilitates the retention of GA at the site of injection and draining lymph nodes, which may contribute to its mechanism of action. K-PLP with a pI of ~11, was found to form visible aggregates in the presence of glycosaminoglycans and persist at the injection site and draining lymph nodes in vivo, similar to GA. Additionally, EAE mice treated with K-PLP showed significant inhibition of clinical symptoms compared to free poly-lysine and to PLP, which are the components of K-PLP. The ability of the poly-lysine motif to retain PLP at the injection site, which increased the local exposure of PLP to immune cells may be an important factor affecting drug efficacy

Effect of Sorting and Feeding Optaflexx on Performance and Economics of Long Yearling Steers

A two-year experiment evaluated the effects of sorting long yearling steers by initial feedlot BW and supplementing 200 mg/steer of Optaflexx daily the last 28 days of the feeding period on ADG, F/G, carcass characteristics and profitability. Feedlot ADG, F/G, and profitability were not effected by sorting. However, sorted cattle exhibited increased fat thickness, increased ribeye area, and increased percentage of carcasses with a yield grade of four or higher. Supplementing Optaflexx the last 28 days of the feeding period had no effect on feedlot performance, carcass characteristics, or profitability

Effect of Sorting and Feeding Optaflexx on Performance and Economics of Long Yearling Steers

A two-year experiment evaluated the effects of sorting long yearling steers by initial feedlot BW and supplementing 200 mg/steer of Optaflexx daily the last 28 days of the feeding period on ADG, F/G, carcass characteristics and profitability. Feedlot ADG, F/G, and profitability were not effected by sorting. However, sorted cattle exhibited increased fat thickness, increased ribeye area, and increased percentage of carcasses with a yield grade of four or higher. Supplementing Optaflexx the last 28 days of the feeding period had no effect on feedlot performance, carcass characteristics, or profitability