VIRAL RNA ELEMENTS AND HOST GENES AFFECTING RNA RECOMBINATION IN TOMBUSVIRUSES

RNA recombination is a major factor driving viral evolution and contributing to new disease outbreaks. Therefore, understanding the mechanism of RNA recombination can help scientists to develop longer lasting antiviral strategies. Tombusviruses are one of the best model RNA viruses to study RNA virus recombination. My goals were to dissect the mechanism of tombusviral RNA recombination. To do so, in my thesis, I describe my results on the roles of (i) the viral replicase and the viral RNA templates; and (ii) the effect of host factors on tombusvirus recombination events. To study the mechanism of RNA recombination without the influence of selection pressure on the emerging recombinants, we developed an in vitro RNA recombination assay based on viral RNA templates and purified viral replicase preparations. Using this in vitro assay, we demonstrated that replicase driven template switching is the mechanism of recombination, whereas RNA ligation seems less likely to be a major mechanism. In addition, we also studied the role of RNA substrates, in more detail. Our results showed that viral replicase preferred to use functional RNA domains in the acceptor RNAs over random switching events. Host factors may also play important roles in RNA recombination. Using yeast as a model system for studying replication and recombination of a tombusvirus replicon, we identified 9 host genes affecting tombusvirus RNA recombination. Separate deletion of five of these genes enhanced generation of novel viral RNA recombinants. Further studies on one of these genes, XRN1, a 5-3 exoribonuclease, indicated that it might be involved in degradation of tombusvirus RNAs. Lack of Xrn1p resulted in accumulation of truncated (partially degraded) replicon RNAs, which became good templates for RNA recombination. To further study Xrn1p, we overexpressed Xrn4p of Arabidopsis thaliana, a functional analogue of the yeast Xrn1p, in Nicotiana benthamiana plants. After superinfecting the Xrn4p-overexpressing N. benthamiana with tombusvirus, truncated tombusvirus genomic and subgenomic RNA1 were observed. Some of the identified tombusvirus variants were infectious in protoplasts and could systemically infected N. benthamiana plants. Overall, this is the first report that a single host gene can affect rapid viral evolution and RNA recombination

Leveling Maintenance Mechanism by Using the Fabry-Perot Interferometer with Machine Learning Technology

This study proposes a method for maintaining parallelism of the optical cavity of a laser interferometer using machine learning. The Fabry-Perot interferometer is utilized as an experimental optical structure in this research due to its advantage of having a brief optical structure. The supervised machine learning method is used to train algorithms to accurately classify and predict the tilt angle of the plane mirror using labeled interference images. Based on the predicted results, stepper motors are fixed on a plane mirror that can automatically adjust the pitch and yaw angles. According to the experimental results, the average correction error and standard deviation in 17-grid classification experiment are 32.38 and 11.21 arcseconds, respectively. In 25-grid classification experiment, the average correction error and standard deviation are 19.44 and 7.86 arcseconds, respectively. The results show that this parallelism maintenance technology has essential for the semiconductor industry and precision positioning technology

Deferoxamine retinopathy: spectral domain-optical coherence tomography findings

Al-Djamiʿ li Ibn al-BaïtharNumérisation effectuée à partir d'un document de substitution

Deferoxamine retinopathy: spectral domain-optical coherence tomography findings

BACKGROUND: To describe the spectral domain optical coherence tomography (SD-OCT) findings of a patient who developed pigmentary retinopathy following high-dose deferoxamine administration. CASE PRESENTATION: A 34-year-old man with thalassemia major complained of nyctalopia and decreased vision following high-dose intravenous deferoxamine to treat systemic iron overload. Fundus examination revealed multiple discrete hypo-pigmented lesions at the posterior pole and mid-peripheral retina. Recovery was partial following cessation of desferrioxamine six weeks later. A follow-up SD-OCT showed multiple accumulated hyper-reflective deposits primarily in the choroid, retina pigment epithelium (RPE), and inner segment and outer segment (IS/OS) junction. CONCLUSION: Deferoxamine retinopathy primarily targets the RPE–Bruch membrane–photoreceptor complex, extending from the peri-fovea to the peripheral retina with foveola sparing. An SD-OCT examination can serve as a simple, noninvasive tool for early detection and long-term follow-up

Analysis of Heat Transfer Mechanism for Shelf Vacuum Freeze-Drying Equipment

Vacuum freeze-drying technology is applicable to the process of high heat-sensitive products. Due to the long drying period and extremely low processing temperature and pressure, the uniform and efficiency of heat transfer fluid temperature in shelf are critical for product quality. Therefore, in this study, the commercial computer fluid dynamics (CFD) software, FLUENT, was utilized for three-dimension numerical simulation of the shelf vacuum freeze-drying process. The influences of different inlet and outlet positions for shelves on the uniformity of the flow rate and temperature were discussed. Moreover, it explored the impacts on the temperature gradient of shelves after heat exchange of different flow rates and low temperature materials. In order to reduce the developing time and optimize the design, the various secondary refrigerants in different plies of shelves were investigated. According to the effect of heat exchange between different flow rates and low temperature layer material shelves on the temperature gradient of shelves surface, the minimum temperature gradient was 20 L/min, and the maximum was 2.5 L/min

Factors Affecting Aluminum Dissolve from Acidified Water Purification Sludge

Recovering resources from water purification sludge (WPS) have been gradually stipulated in environmental protection laws and regulations in many nations. Hence, reusing the WPS is becoming an important topic, and recovering alum from WPS is one of the many practical alternatives. Most previous research efforts have been conducted on studying the amphoteric characteristic of aluminum hydroxide for investigating the optimum pH range to dissolve the Al(III) species from WPS, but it has been lack of reaction kinetics or mechanisms related discussion. Therefore, in this investigation, water purification sludge (WPS) solution was broken by ultrasound to make particle size of reactants smaller, specific surface area larger. According to the reaction kinetics, these phenomena let the dissolved aluminum salt quantity increased and the reaction rate go faster

Metabolic classification of microbial genomes using functional probes

<p>Abstract</p> <p>Background</p> <p>Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on the evolutionary relationships of organisms, classifications of the genomes based on alternative points of view may help advance our understanding of the delicate relationships of organisms.</p> <p>Results</p> <p>We have developed a proteome-based method for classifying microbial species. This classification method uses a set of probes comprising short, highly conserved amino acid sequences. For each genome, <it>in silico </it>translation is performed to obtained its proteome, based on which a probe-set frequency pattern is generated. Then, the probe-set frequency patterns are used to cluster the proteomes/genomes.</p> <p>Conclusions</p> <p>Features of the proposed method include a high running speed in challenge of a large number of genomes, and high applicability for classifying organisms with incomplete genome sequences. Moreover, the probe-set clustering method is sensitive to the metabolic phenotypic similarities/differences among species and is thus supposed potential for the classification or differentiation of closely-related organisms.</p