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Stronger Together: The Cross-Cultural Coalition to Stop a Fossil Fuel Export Terminal in the Salish Sea

Thesis (Master's)--University of Washington, 2016-06

Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure

Thesis (Ph.D.)--University of Washington, 2016-06

tRNASer(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes

Exogenous transfer RNAs (tRNAs) favor translation of bovine papillomavirus 1 wild-type (wt) L1 mRNA in in vitro translation systems (Zhou et al. 1999, J. Virol., 73, 4972-4982). We, therefore, investigated whether papillomavirus (PV) wt L1 protein expression could be enhanced in eukaryotic cells following exogenous tRNA supplementation. Both Chinese hamster ovary (CHO) and Cos1 cells, transfected with PV1 wt L1 genes, effectively transcribed the genes but did not translate them. However, L1 protein translation was demonstrated following co-transfection with the L1 gene and a gene expressing tRNA(Ser)(CGA). Cell lines, stably transfected with a bovine papillomavirus 1 (BPV1) wt L1 expression construct, produced L1 protein after the transfection of the tRNA(Ser)(CGA) gene, but not following the transfection with basal vectors, suggesting that tRNA(Ser)(CGA) gene enhanced wt L1 translation as a result of endogenous tRNA alterations and phosphorylation of translation initiation factors elF4E and elF2alpha in the tRNA(Ser)(CGA) transfected L1 cell lines. The tRNA(Ser)(CGA) gene expression significantly reduced translation of L1 proteins expressed from codon-modified (HB) PV L1 genes utilizing mammalian preferred codons, but had variable effects on translation of green fluorescent proteins (GFPs) expressed from six serine GFP variants. The changes of tRNA pools appear to match the codon composition of PV wt and HB L1 genes and serine GFP variants to regulate translation of their mRNAs. These findings demonstrate for the first time in eukaryotic cells that translation of the target genes can be differentially influenced by the provision of a single tRNA expression construct.

Gene codon composition determines differentiation-dependent expression of a viral capsid gene in keratinocytes in vitro and in vivo

By establishing mouse primary keratinocytes (KCs) in culture, we were able, for the first time, to express papillomavirus major capsid (L1) proteins by transient transfection of authentic or codon-modified L1 gene expression plasmids. We demonstrate in vitro and in vivo that gene codon composition is in part responsible for differentiation-dependent expression of L1 protein in KCs. L1 mRNA was present in similar amounts in differentiated and undifferentiated KCs transfected with authentic or codon-modified L1 genes and had a similar half-life, demonstrating that L1 protein production is posttranscriptionally regulated. We demonstrate further that KCs substantially change their tRNA profiles upon differentiation. Aminoacyl-tRNAs from differentiated KCs but not undifferentiated KCs enhanced the translation of authentic L1 mRNA, suggesting that differentiation-associated change to tRNA profiles enhances L1 expression in differentiated KCs. Thus, our data reveal a novel mechanism for regulation of gene expression utilized by a virus to direct viral capsid protein expression to the site of virion assembly in mature KCs. Analysis of two structural proteins of KCs, involucrin and keratin 14, suggests that translation of their mRNAs is also regulated, in association with KC differentiation in vitro, by a similar mechanism

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E-coli genome

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms. (c) 2005 Elsevier Ltd. All rights reserved.

Optimal eradication: when to stop looking for an invasive plant

The notion of being sure that you have completely eradicated an invasive species is fanciful because of imperfect detection and persistent seed banks. Eradication is commonly declared either on an ad hoc basis, on notions of seed bank longevity, or on setting arbitrary thresholds of 1% or 5% confidence that the species is not present. Rather than declaring eradication at some arbitrary level of confidence, we take an economic approach in which we stop looking when the expected costs outweigh the expected benefits. We develop theory that determines the number of years of absent surveys required to minimize the net expected cost. Given detection of a species is imperfect, the optimal stopping time is a trade-off between the cost of continued surveying and the cost of escape and damage if eradication is declared too soon. A simple rule of thumb compares well to the exact optimal solution using stochastic dynamic programming. Application of the approach to the eradication programme of Helenium amarum reveals that the actual stopping time was a precautionary one given the ranges for each parameter.

Forced retroevolution of an RNA bacteriophage

The operator hairpin ahead of the replicase gene in RNA bacteriophage MS2 contains overlapping signals for binding the coat protein and ribosomes. Coat protein binding inhibits further translation of the gene and forms the first step in capsid formation. The hairpin sequence was partially randomized to assess the importance of this structure element for the bacteriophage and to monitor alternative solutions that would evolve on the passaging of mutant phages. The evolutionary reconstruction of the operator failed in the majority of mutants. Instead, a poor imitation developed containing only some of the recognition signals for the coat protein. Three mutants were of particular interest in that they contained double nonsense codons in the lysis reading frame that runs through the operator hairpin. The simultaneous reversion of two stop codons into sense codons has a very low probability of occurring. Therefore the phage solved the problem by deleting the nonsense signals and, in fact, the complete operator, except for the initiation codon of the replicase gene. Several revertants were isolated with activities ranging from 1% to 20% of wild type. The operator, long thought to be a critical regulator, now appears to be a dispensable element. In addition, the results indicate how RNA viruses can be forced to step back to an attenuated form.

One-stop health centres:What co-location means for pharmacy

This paper examines the potential for the development of patient services that could arise from the co-location of pharmacies with medical practices in the new "one-stop" centres. A review of the pharmacy-specific literature shows limited understanding of influence of location upon service development and highlights a tension between the professional and commercial drives. The aim of the survey of health centre pharmacists was to describe the current patterns of integration in the primary health care team. The study demonstrates that co-location offers opportunities but that there are barriers linked to the loss of traditional commercial activity. © 2003 Elsevier Science Ltd. All rights reserved.

Patient anxiety and experiences associated with an outpatient "one-stop" "see and treat" hysteroscopy clinic

BACKGROUND: "One-stop" outpatient hysteroscopy clinics have become well established for the investigation and treatment of women with abnormal uterine bleeding. However, the advantages of these clinics may be offset by patient factors such as anxiety, pain, and dissatisfaction. This study aimed to establish patients' views and experiences of outpatient service delivery in the context of a one-stop diagnostic and therapeutic hysteroscopy clinic, to determine the amount of anxiety experienced by these women and compare this with other settings, and to determine any predictors for patient preferences. METHODS: The 20-item State-Trait Anxiety Inventory was given to 240 women attending a one-stop hysteroscopy clinic: to 73 consecutive women before their appointment in a general gynecology clinic and to 36 consecutive women attending a chronic pelvic pain clinic. The results were compared with published data for the normal female population, for women awaiting major surgery, and for women awaiting a colposcopy clinic appointment. In addition, a questionnaire designed to ascertain patients' views and experiences was used. Logistic regression analysis was used to delineate the predictive values of diagnostic or therapeutic hysteroscopy, and to determine their effect on the preference of patients to have the procedure performed under general anesthesia in the future. RESULTS: Women attending the hysteroscopy clinic in this study reported significantly higher levels of anxiety than those attending the general gynecology clinic (median, 45 vs 39; p = 0.004), but the levels of anxiety were comparable with those of women attending the chronic pelvic pain clinic (median, 45 vs 46; p = 0.8). As compared with the data from the normal female population (mean, 35.7) and those reported for women awaiting major surgery (mean, 41.2), the levels of anxiety experienced before outpatient hysteroscopy clinic treatment were found to be higher (mean, 45.7). Only women awaiting colposcopy (6-item mean score, 51.1 +/- 13.3) experienced significantly higher anxiety scores than the women awaiting outpatient hysteroscopy (6-item mean score, 47.3 +/- 13.9; p = 0.002). Despite their anxiety, most women are satisfied with the outpatient hysteroscopy "see and treat" service. High levels of anxiety, particularly concerning pain but not operative intervention, were significant predictors of patients desiring a future procedure to be performed under general anesthesia. CONCLUSIONS: Outpatient hysteroscopy is associated with significant anxiety, which increases the likelihood of intolerance for the outpatient procedure. However, among those undergoing operative therapeutic procedures, dissatisfaction was not associated with the outpatient setting.