Ribonuclease P (RNaseP) generates the mature 5' end of tRNAs by removing 5'leader sequences from pre-tRNAs. In vitro, the RNA subunit is sufficient to catalyze this reaction and is therefore a ...ribozyme. The kinetic analysis of RNase P-mediated catalysis is complicated because product release is normally rate-limiting. Furthermore, the intermolecular nature of the cleavage reaction precludes many applications of in vitro selection schemes to the analysis of RNaseP. To examine and manipulate the RNase P function more effectively, we designed a pair of ribozymes in which the RNase P RNA is covalently linked to a pre-tRNA substrate. To facilitate intramolecular cleavage, pre-tRNA molecules were tethered to circulatory permuted RNaseP RNA molecules at nucleotides implicated in substrate binding. These "active-site-tethered" pre-tRNA-RNaseP RNA conjugates undergo accurate and efficient self-cleavage in vitro, with first-order reaction rates equivalent to the rate of the chemical step of the native RNase P reaction. Unlike most ribozymes, RNase P recognizes its substrate through tertiary RNA-RNA interactions, rather than through extensive Watson-Crick base-pairing. However, the development of the active-site-tethered conjugates has led us to create a sequence-specific endonuclease, termed Endo.P. In the Endo.P configuration, the 3'half of the pre-tRNA acceptor stem binds exogenous RNA substrates via Watson-Crick base-pairing; the bound substrate is subsequently cleaved at the predicted site. The demonstration of sequence-specific cleavage by Endo.P expands the potential of RNase P and its derivatives as reagents in gene therapy.
A detailed comparative analysis of archaeal RNase P RNA
structure and a comparison of the resulting structural
information with that of the bacterial RNA reveals that
the archaeal RNase P RNAs are ...strikingly similar to those
of Bacteria. The differences between the secondary structure
models of archaeal and bacterial RNase P RNA have largely
disappeared, and even variation in the sequence and structure
of the RNAs are similar in extent and type. The structure
of the cruciform (P7–11) has been reevaluated on
the basis of a total of 321 bacterial and archaeal sequences,
leading to a model for the structure of this region of
the RNA that includes an extension to P11 that consistently
organizes the cruciform and adjacent highly-conserved sequences.
Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from ...culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low alpha -diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high alpha -diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.
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We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational ...expense of molecular dynamics simulations often group multiple atoms into a single "coarse-grained" interaction site, which leads to a loss of chemical resolution. In this work we convert this shortcoming into a feature and use identical coarse-grained models to represent molecules that share non-reactive characteristics but react by different mechanisms. As a proof of concept we use this approach to simulate and investigate distinct, yet similar, trifunctional isocyanurate resin formulations that polymerize by either chain- or step-growth. Since the underlying molecular mechanics of these models are identical, all emergent differences are a function of the reaction mechanism only. We find that the microscopic morphologies resemble related all-atom simulations and that simulated mechanical testing reasonably agrees with experiment.
A study of registers and records in accident and emergency departments in the London area was conducted to investigate the time course of an epidemic of asthma after a thunderstorm, characteristics ...of patients affected and the demand on emergency medical resources. The study supported the hypothesis that "thunderstorm associated asthma" is related to aeroallergens.
For decades, a wide variety of observations spanning the radio through optical and on to the x-ray have attempted to uncover signs of type Ia supernovae (SNe Ia) interacting with a circumstellar ...medium (CSM). The goal of these studies is to constrain the nature of the hypothesized SN Ia mass-donor companion. A continuous CSM is typically assumed when interpreting observations of interaction. However, while such models have been successfully applied to core-collapse SNe, the assumption of continuity may not be accurate for SNe Ia, as shells of CSM could be formed by pre-supernova eruptions (novae). In this work, we model the interaction of SNe with a spherical, low density, finite-extent CSM and create a suite of synthetic radio synchrotron light curves. We find that CSM shells produce sharply peaked light curves, and identify a fiducial set of models that all obey a common evolution and can be used to generate radio light curves for interaction with an arbitrary shell. The relations obeyed by the fiducial models can be used to deduce CSM properties from radio observations; we demonstrate this by applying them to the non-detections of SN 2011fe and SN 2014J. Finally, we explore a multiple shell CSM configuration and describe its more complicated dynamics and resultant radio light curves.
Abstract Objective: To investigate the time course of an epidemic of asthma after a thunderstorm, characteristics of patients affected, and the demand on emergency medical resources. Design: Study of ...registers and records in accident and emergency departments and questionnaire to staff. Setting: London area. Subjects: All patients presenting at 12 accident and emergency departments with asthma or other airways disease. Main outcome measures: Numbers of patients, clinical features, information on shortage of resources—equipment, drugs, and staff. Results: The epidemic had a sudden onset on 24 June 1994; 640 patients with asthma or other airways disease attended during 30 hours from 1800 on 24 June, nearly 10 times the expected number. Over half (365) the patients were aged 21 to 40 years. A history of hay fever was recorded in 403 patients; for 283 patients this was the first known attack of asthma; a history of chronic obstructive airways disease was recorded in 12 patients. In all, 104 patients were admitted (including five to an intensive care unit). Several departments ran out of equipment or drugs, called in additional doctors, or both. Conclusions: This study supports the view that this epidemic was larger than previously reported epidemics and the hypothesis that “thunderstorm associated asthma” is related to aeroallergens. Demands on resources were considerable; a larger proportion of patients needing intensive care would have caused greater problems. Key messages Key messages People affected by thunderstorm associated asthma are characteristically young atopic adults who either are not known to have previously had asthma or are asthmatic but probably do not have steroid inhaler prophylaxis Thunderstorm associated asthma seems to have had a benign course in most patients in this epidemic, but many patients presenting to accident and emergency departments should not induce complacency in the treatment of acute asthma This kind of “major incident” puts a strain on emergency medical services in a way not usually anticipated because all hospitals in an area may be affected
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