Curricular offerings in seventy-five independent schools in New England.

Thesis (Ed.M.)--Boston Universit

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents

A twist in the tail : SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication

The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2′-hydroxyl acylation analysed by primer extension. Marked differences were found in the long-range interactions of SL9266 when the two widely used genotype 2a JFH-1 (HCVcc) and genotype 1b Con1b sub-genomic replicon systems were compared. In both genomes, there was evidence for interaction of the sub-terminal bulge loop of SL9266 and sequences around nucleotide 9110, though the replication phenotype of genomes bearing mutations that disrupted this interaction was fundamentally different. In contrast, a ‘kissing loop’ interaction between the terminal loop of SL9266 and sequences in the 3′-untranslated X-tail was only detectable in JFH-1-based genomes. In the latter, where both long-range interactions are present, they were independent, implying that SL9266 forms the core of an extended pseudoknot. The presence of the ‘kissing loop’ interaction inhibited the formation of SL9571 in the 3′-X-tail, an RNA structure implicated in genome replication. We propose that, SL9266 may contribute a switch function that modulates the mutually incompatible translation and replication events that must occur for replication of the positive-strand RNA genome of HCV

Постспленектомічний спленоз, як предиктор розвитку рецидиву хвороби Верльгофа

Спленектомія (СЕ) у хворих на хворобу Верльгофа (ХВ), виконується у випадку неефективності консервативного лікування цього тяжкого захворювання. Не зважаючи на високий ризик оперативного втручання, пов'язаний з притаманним для цього захворювання порушеннями в системі згортання крові, СЕ продовжує активно використовуватися , так як є найбільш ефективним методом лікування ХВ

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.Comment: 9 pages, 2 figure

Prediction of RNA secondary structure in hepatitis C and related viruses

The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognised. In this thesis several computational methods to detect RNA secondary structure in the coding regions of hepatitis C virus (HCV), hepatitis G virus (HGV)/GB virus C (GBV-C) and related viruses have been used. These include thermodynamic prediction of folding free energies (FFEs), evolutionary conservation of minimum energy structures between virus genotypes, suppression of synonymous variability and analysis of covariant and semi covariant substitutions in thermodynamically favoured structures. Each of the predictive methods provided evidence for conserved RNA secondary structure in the core and NS5B encoding regions of HCV and throughout the entire coding region of HGV/GBV-C.Positions in the HCV genome with predicted RNA structure localise precisely to regions of marked suppression of variability at synonymous sites, indicating that RNA structure constrains sequence change at what are generally regarded as phenotypically neutral sites. Combining these methods, the computational data obtained in this thesis demonstrates the existence of at least ten conserved stem loop structures within the NS5B coding region and three in that coding for the core protein both within the coding region of HCV. Analysis of the NS5B coding region and 3' untranslated region (3'UTR) of HGV/GBV-C indicates an even greater degree of RNA secondary structure. Remarkably, it appears from analysis of FFEs that extensive RNA secondary structure may exist along the entire length of both the HCV and HGV/GBV-C genomes, a finding with considerable implications for future functional studies.The existence of predicted RNA structures in the HCV genome was determined using controlled nuclease mapping of RNA transcripts from the core and NS5B regions under conditions which retained potential long-range RNA interactions. The pattern of cleavage sites of nucleases specific for single and double stranded RNA provided strong experimental support for structures previously predicted in this study. Electron microscopy was also used to directly visualise the RNA folding structure of HGV/GBV-C and provided some evidence for at least four structures within the NS5B coding region and long range RNA folding across the length of the virus genome.The degree of structural conservation between diverse HCV and HGV/GBV-C genotypes and related viruses suggests roles in virus replication, and/or RNA packaging for the discrete structures identified in this thesis. Whilst this role and that of the genome wide structure identified is currently not understood the structures predicted in this work are providing a starting point for such functional studies using the HCV replicon

Adaptive electronic throttle control of road vehicles

Previous work at Loughborough University has clearly demonstrated the gains that can be made in overall performance feel through the manipulation of the engine demand map. In particular the studies have shown the importance of the throttle progression, and the relationship between throttle pedal progression and wide-open throttle performance. These studies concluded with a clear set of design guidelines for the initial set up of a vehicle to achieve optimal performance feel for a population of drivers. These studies also highlighted the wide variation in response from different subjects indicating that further gains in satisfaction could be achieved if the demand map were optimised for each driver. Failing to provide optimum performance feel for the driver can result in reduced satisfaction, in turn making vehicles less saleable and more difficult to drive through the increased concentration needed to drive the vehicle. This thesis attempts to solve the problem of demographic and driver preference variation, by developing an electronic throttle system that adapts to driver preference. [Continues.