Early Folding Biases in the Folding Free-Energy Surface of βα-Repeat Proteins: A Dissertation

Early events in folding can determine if a protein is going to fold, misfold, or aggregate. Understanding these deterministic events is paramount for de novo protein engineering, the enhancement of biopharmaceutical stabilities, and understanding neurodegenerative diseases including amyotrophic lateral sclerosis and Alzheimer\u27s disease. However, the physicochemical and structural biases within high energy states of protein biopolymers are poorly understood. A combined experimental and computational study was conducted on the small β/α-repeat protein CheY to determine the structural basis of its submillisecond misfolding reaction to an off-pathway intermediate. Using permutations, we were able to discriminate between the roles of two proposed mechanisms of folding; a nucleation condensation model, and a hydrophobic collapse model driven by the formation of clusters of isoleucine, leucine, and valine (ILV) residues. We found that by altering the ILV cluster connectivity we could bias the early folding events to either favor on or off-pathway intermediates. Structural biases were also experimentally observed in the unfolded state of a de novo designed synthetic β/α-repeat protein, Di-III_14. Although thermodynamically and kinetically 2-state, Di-III_14 has a well structured unfolded state that is only observable under native-favoring conditions. This unfolded state appears to retain native-like structure, consisting of a hydrophobic 7 core (69% ILV) stabilized by solvent exposed polar groups and long range electrostatic interactions. Together, these results suggest that early folding events are largely deterministic in these two systems. Generally, low contact order ILV clusters favor local compaction and, in specific cases, long range electrostatic interactions may have stabilizing effects in higher energy states

Corrections to Finite Size Scaling in Percolation

A 1/L-expansion for percolation problems is proposed, where L is the lattice finite length. The square lattice with 27 different sizes L = 18, 22 ... 1594 is considered. Certain spanning probabilities were determined by Monte Carlo simulations, as continuous functions of the site occupation probability p. We estimate the critical threshold pc by applying the quoted expansion to these data. Also, the universal spanning probability at pc for an annulus with aspect ratio r=1/2 is estimated as C = 0.876657(45)

False vacuum decay in kink scattering

In this work we consider kink-antikink and antikink-kink collisions in a modified $\phi^4$ model with a false vacuum characterized by a dimensionless parameter $\epsilon$. The usual $\phi^4$ model is recovered for $\epsilon=0$. We investigate the $\epsilon<<1$ regime where the kink in the presence of false vacuum can be understood as a small deformation of the standard kink for the $\phi^4$ model. We show that the attractive interaction between the kink-antikink pair leads to a rich scattering pattern, in some cases delaying considerably the false vacuum decay.Comment: 16 pages, 17 figure

ANÁLISE DE TRANSMISSÃO E DA DINÂMICA DE MODIFICAÇÃO DE GENÓTIPOS DE Mycobacterium tuberculosis NA REGIÃO METROPOLITANA DE VITÓRIA ES EM UM INTERVALO DE 10 ANOS

Introdução: Técnicas de tipagem molecular têm colaborado para o entendimento da dinâmica de transmissão da tuberculose (TB). Apesar de inúmeros trabalhos terem sido publicados a esse respeito, poucos estudos, no entanto, foram realizados levando-se em consideração a dinâmica de modificação dos perfis genotípicos de M. tuberculosis (Mtb) em um intervalo de tempo longo. Objetivos: Caracterizar os genótipos e identificar os fatores de risco associados com transmissão recente e tamanho de cluster de Mtb na Região Metropolitana de Vitória ES (RMV) e analisar a dinâmica de modificação dos genótipos de Mtb na Região Metropolitana de Vitória ES em intervalo de 10 anos. Métodos: Este estudo foi constituído de duas partes. Primeira parte: Estudo transversal de casos novos de TB diagnosticados na RMV, entre 2000 e 2010 para identificar fatores de risco associados à transmissão recente da TB e o tamanho do cluster de Mtb. A genotipagem dos isolados de Mtb foi realizada com base nos métodos de RFLP IS 6110, Spoligotyping e na análise de deleção RDRio. Foram realizados Modelos de regressão hierárquica polinomial para identificar os fatores associados com o tamanho do cluster. Segunda Parte: Estudo observacional para analisar a dinâmica de modificação dos genótipos de Mtb na RMV em intervalo de 10 anos (com cortes transversais nos períodos de 2000 2001 e 2011) com base nas técnicas de RFLP IS 6110 e MIRU- VNTR 24 loci tendo como fonte de dados registros laboratoriais e o SINAN. Resultados: Primeira Parte: Dentre os 959 isolados de Mtb, 461 (48%) casos pertenciam a um cluster. Nossos modelos de regressão polinomial mostraram que os isolados de Mtb pertencentes a família LAM e ao genótipo RDRio foram mais prováveis de estarem em clusters com 6-9 isolados (OR = 1,17, 95% IC 1,08 1,26; OR=1,25, 95% IC 1,14- 1,37; respectivamente) em relação aos outros grupos. Os pacientes com &#8805;10 isolados foram mais prováveis de pertencerem a família LAM e a família de RFLP ES14 (OR = 1,14, 95% IC 1,06 1,23; OR= 7,03, 95% IC 4,00 12,34, respectivamente). Segunda Parte: No período de 2000-2001, dentre os 329 isolados, 109 (33,2%) foram agrupados em 38 clusters enquanto, em 2011, dentre os 485 isolados de Mtb, 176 (36,2%) foram distribuídos em 39 clusters. Não houve diferença estatisticamente significativa entre os períodos analisados em relação a formação de um cluster (p=0,35). A análise dos padrões gerados pelo RFLP IS 6110 identificou 8 clusters, ao quais estão mais envolvidos com transmissão recente na RMV. A correlação entre as duas técnicas de genotipagem mostrou em 2000-2001 uma concordância de 42,1%, e 42,5% em 2011. Conclusão: Esses resultados confirmam que a família LAM e o genótipo RDRio são mais encontrados em clusters com 6-9 isolados, e que a família de RFLP ES14 é o genótipo mais prevalente na RMV, sugerindo que a proporção de casos de TB em uma cidade pode ser causada por um pequeno número de genótipos circulantes dentro de uma região e que fatores relacionados ao patógeno devem ser melhor estudados para melhoria no controle da doença. Palavras-chave: Mycobacterium tuberculosis, técnicas de genotipagem, epidemiologia molecular, dinâmica de modificação do Mtb

Gradual Internal Reforming of Ethanol in Solid Oxide Fuel cells

AbstractElectrolyte (yttria-stabilised zirconia, YSZ) supported solid oxide fuel cells (SOFCs) were fabricated using spin coating of standard LSM cathode and Ni-YSZ cermet anode. A ceria-based catalytic layer was deposited onto the anode with a special current collector design. Such a single cell configuration allows operation by gradual internal reforming of direct carbon-containing fuels. First, the fabricated single cells were operated with hydrogen to determine the optimised conditions of fuel concentration and flow rate regarding faradaïc efficiency. Then, the fuel was switched to dry ethanol and the cells were operated for several hours (100h) with good stability. Post-operation electron microcopy analyses revealed no carbon formation in the anode layer. The results indicate that the gradual internal reforming mechanism is effective, opening up the way to multi-fuel SOFCs, provided that a suitable catalyst layer and cell design are available

Prevalence of non-aureus Staphylococcus species causing intramammary infections in Canadian dairy herds

Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their importance as a group, the distribution of individual species needs to be determined. In the present study, NAS intramammary infection (IMI) was defined as a milk sample containing ≥1,000 cfu/mL in pure or mixed culture that was obtained from a cohort of cows assembled by the Canadian Bovine Mastitis Research Network. Overall, 6,213 (6.3%) of 98,233 quarter-milk samples from 5,149 cows and 20,305 udder quarters were associated with an NAS IMI. Of the 6,213 phenotypically identified NAS isolates, 5,509 (89%) were stored by the Canadian Bovine Mastitis Research Network Mastitis Pathogen Collection and characterized using partial sequencing of the rpoB housekeeping gene, confirming 5,434 isolates as NAS. Prevalence of each NAS species IMI was estimated using Bayesian models, with presence of a specific NAS species as the outcome. Overall quarter-level NAS IMI prevalence was 26%. The most prevalent species causing IMI were Staphylococcus chromogenes (13%), Staphylococcus simulans (4%), Staphylococcus haemolyticus (3%), Staphylococcus xylosus (2%), and Staphylococcus epidermidis (1%). The prevalence of NAS IMI as a group was highest in first-parity heifers and was evenly distributed throughout cows in parities ≥2. The IMI prevalence of some species such as S. chromogenes, S. simulans, and S. epidermidis differed among parities. Overall prevalence of NAS IMI was 35% at calving, decreased over the next 10 d, and then gradually increased until the end of lactation. The prevalence of S. chromogenes, Staphylococcus gallinarum, Staphylococcus cohnii, and Staphylococcus capitis was highest at calving, whereas the prevalence of S. chromogenes, S. haemolyticus, S. xylosus, and S. cohnii increased during lactation. Although the overall prevalence of NAS IMI was similar across barn types, the prevalence of S. simulans, S. xylosus, S. cohnii, Staphylococcus saprophyticus, S. capitis, and Staphylococcus arlettae IMI was higher in tie-stall barns; the prevalence of S. epidermidis IMI was lowest; and the prevalence of S. chromogenes and Staphylococcus sciuri IMI was highest in bedded-pack barns. Staphylococcus simulans, S. epidermidis, S. xylosus, and S. cohnii IMI were more prevalent in herds with intermediate to high bulk milk somatic cell count (BMSCC) and S. haemolyticus IMI was more prevalent in herds with high BMSCC, whereas other common NAS species IMI were equally prevalent in all 3 BMSCC categories. Distribution of NAS species IMI differed among the 4 regions of Canada. In conclusion, distribution differed considerably among NAS species IMI; therefore, accurate identification (species level) is essential for studying NAS epidemiology