Kristopher Opron
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View article: Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis
Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis Open
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associa…
View article: Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis
Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis Open
Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease (COPD). Intermittent pulmonary exacerbations (PEx) in these co…
View article: WS18.1 Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection
WS18.1 Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection Open
View article: Obesity Is Associated with an Altered Airway Microbiome and Distinct Airway Microbiota-Immune Relationships in Asthma
Obesity Is Associated with an Altered Airway Microbiome and Distinct Airway Microbiota-Immune Relationships in Asthma Open
View article: Transcriptomic Profiles of Sepsis in the Human Brain
Transcriptomic Profiles of Sepsis in the Human Brain Open
View article: Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability
Measures of Cystic Fibrosis Airway Microbiota during Periods of Clinical Stability Open
Rationale: Differences in cystic fibrosis (CF) airway microbiota between periods of clinical stability and exacerbation of respiratory symptoms have been investigated in efforts to better understand microbial triggers of CF exacerba…
View article: A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code
A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code Open
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by se…
View article: Ribosome Structure, Function, and Early Evolution
Ribosome Structure, Function, and Early Evolution Open
Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel mot…
View article: Type-II tRNAs and Evolution of Translation Systems and the Genetic Code
Type-II tRNAs and Evolution of Translation Systems and the Genetic Code Open
Because tRNA is the core biological intellectual property that was necessary to evolve translation systems, tRNAomes, ribosomes, aminoacyl-tRNA synthetases, and the genetic code, the evolution of tRNA is the core story in evolution of life…
View article: Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study
Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study Open
Introduction Despite strong evidence that maturation patterns of the gut microbiome in early life influence the risk for childhood asthma, very little is known about gut microbiota patterns in adults with established asthma, and of greater…
View article: Hinge action versus grip in translocation by RNA polymerase
Hinge action versus grip in translocation by RNA polymerase Open
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were …
View article: Hinge action versus grip in translocation by RNA polymerase
Hinge action versus grip in translocation by RNA polymerase Open
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were …
View article: A model for genesis of transcription systems
A model for genesis of transcription systems Open
Repeating sequences generated from RNA gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. A simple and coherent story of life on earth is told from …
View article: A topological approach for proteinclassification
A topological approach for proteinclassification Open
Protein function and dynamics are closely related to its sequence and structure.However, prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classificat…
View article: Flexibility-Rigidity Index for Protein-Nucleic Acid Flexibility and Fluctuation Analysis
Flexibility-Rigidity Index for Protein-Nucleic Acid Flexibility and Fluctuation Analysis Open
Protein-nucleic acid complexes are important for many cellular processes including the most essential function such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been show…
View article: A topological approach for protein classification
A topological approach for protein classification Open
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classificat…
View article: Capturing protein multiscale thermal fluctuations
Capturing protein multiscale thermal fluctuations Open
Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a mult…
View article: Correlation function based Gaussian network models
Correlation function based Gaussian network models Open
Gaussian network model (GNM) is one of the most accurate and efficient methods for biomolecular flexibility analysis. However, the systematic generalization of the GNM has been elusive. We show that the GNM Kirchhoff matrix can be built fr…