Controlled evolution of an RNA enzyme

It is generally thought that prior to the origin of protein synthesis, life on earth was based on self-replicating RNA molecules. This idea has become especially popular recently due to the discovery of catalytic RNA (ribozymes). RNA has both genotypic and phenotypic properties, suggesting that it is capable of undergoing Darwinian evolution. RNA evolution is likely to have played a critical role in the early history of life on earth, and thus is important in considering the possibility of life elsewhere in the solar system. We have constructed an RNA-based evolving system in the laboratory, combining amplification and mutation of an RNA genotype with selection of a corresponding RNA phenotype. This system serves as a functional model of a primitive organism. It can also be used as a tool to explore the catalytic potential of RNA. By altering the selection constraints, we are attempting to modify the substrate specificity of an existing ribozyme in order to develop ribozymes with novel catalytic function. In this way, we hope to gain a better understanding of RNA's catalytic versatility and to assess its suitability for the role of primordial catalyst. All of the RNA enzymes that are known to exist in contemporary biology carry out cleavage/ligation reactions involving RNA substrates. The Tetrahymena ribozyme, for example, catalyzes phosphoester transfer between a guanosine containing and an oligopyrimidine containing substrate. We tested the ability of mutant forms of the Tetrahymena ribozyme to carry out a comparable reaction using DNA, rather than RNA substrate. An ensemble of structural variants of the ribozyme was prepared and tested for their ability to specifically cleave d(GGCCCTCT-A3TA3TA) at the phosphodiester bond following the sequence CCCTCT. We recovered a mutant form of the enzyme that cleaves DNA more efficiently than does the wild-type. Beginning with this selected mutant we have now scattered random mutations throughout the ribozyme and have begun an evolutionary search to further expand the catalytic repertoire of RNA

Spanning tree generating functions and Mahler measures

We define the notion of a spanning tree generating function (STGF) $\sum a_n z^n$, which gives the spanning tree constant when evaluated at $z=1,$ and gives the lattice Green function (LGF) when differentiated. By making use of known results for logarithmic Mahler measures of certain Laurent polynomials, and proving new results, we express the STGFs as hypergeometric functions for all regular two and three dimensional lattices (and one higher-dimensional lattice). This gives closed form expressions for the spanning tree constants for all such lattices, which were previously largely unknown in all but one three-dimensional case. We show for all lattices that these can also be represented as Dirichlet $L$-series. Making the connection between spanning tree generating functions and lattice Green functions produces integral identities and hypergeometric connections, some of which appear to be new.Comment: 26 pages. Dedicated to F Y Wu on the occasion of his 80th birthday. This version has additional references, additional calculations, and minor correction

The asymptotic quasi-stationary states of the two-dimensional magnetically confined plasma and of the planetary atmosphere

We derive the differential equation governing the asymptotic quasi-stationary states of the two dimensional plasma immersed in a strong confining magnetic field and of the planetary atmosphere. These two systems are related by the property that there is an intrinsic constant length: the Larmor radius and respectively the Rossby radius and a condensate of the vorticity field in the unperturbed state related to the cyclotronic gyration and respectively to the Coriolis frequency. Although the closest physical model is the Charney-Hasegawa-Mima (CHM) equation, our model is more general and is related to the system consisting of a discrete set of point-like vortices interacting in plane by a short range potential. A field-theoretical formalism is developed for describing the continuous version of this system. The action functional can be written in the Bogomolnyi form (emphasizing the role of Self-Duality of the asymptotic states) but the minimum energy is no more topological and the asymptotic structures appear to be non-stationary, which is a major difference with respect to traditional topological vortex solutions. Versions of this field theory are discussed and we find arguments in favor of a particular form of the equation. We comment upon the significant difference between the CHM fluid/plasma and the Euler fluid and respectively the Abelian-Higgs vortex models.Comment: Latex 126 pages, 7 eps figures included. Discussion on various forms of the equatio

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed

Non-perturbative corrections to mean-field behavior: spherical model on spider-web graph

We consider the spherical model on a spider-web graph. This graph is effectively infinite-dimensional, similar to the Bethe lattice, but has loops. We show that these lead to non-trivial corrections to the simple mean-field behavior. We first determine all normal modes of the coupled springs problem on this graph, using its large symmetry group. In the thermodynamic limit, the spectrum is a set of $\delta$-functions, and all the modes are localized. The fractional number of modes with frequency less than $\omega$ varies as $\exp (-C/\omega)$ for $\omega$ tending to zero, where $C$ is a constant. For an unbiased random walk on the vertices of this graph, this implies that the probability of return to the origin at time $t$ varies as $\exp(- C' t^{1/3})$, for large $t$, where $C'$ is a constant. For the spherical model, we show that while the critical exponents take the values expected from the mean-field theory, the free-energy per site at temperature $T$, near and above the critical temperature $T_c$, also has an essential singularity of the type $\exp[ -K {(T - T_c)}^{-1/2}]$.Comment: substantially revised, a section adde

Supersymmetric Extension of the Quantum Spherical Model

In this work, we present a supersymmetric extension of the quantum spherical model, both in components and also in the superspace formalisms. We find the solution for short/long range interactions through the imaginary time formalism path integral approach. The existence of critical points (classical and quantum) is analyzed and the corresponding critical dimensions are determined.Comment: 21 pages, fixed notation to match published versio

A statistical mechanical description of metastable states and hysteresis in the 3D soft-spin random-field model at T=0

We present a formalism for computing the complexity of metastable states and the zero-temperature magnetic hysteresis loop in the soft-spin random-field model in finite dimensions. The complexity is obtained as the Legendre transform of the free-energy associated to a certain action in replica space and the hysteresis loop above the critical disorder is defined as the curve in the field-magnetization plane where the complexity vanishes; the nonequilibrium magnetization is therefore obtained without having to follow the dynamical evolution. We use approximations borrowed from condensed-matter theory and based on assumptions on the structure of the direct correlation functions (or proper vertices), such as a local approximation for the self-energies, to calculate the hysteresis loop in three dimensions, the correlation functions along the loop, and the second moment of the avalanche-size distribution.Comment: 28 pages, 12 figure

Orotracheal intubation in infants performed with a stylet versus without a stylet

Background: Neonatal endotracheal intubation is a common and potentially life-saving intervention. It is a mandatory skill for neonatal trainees, but one that is difficult to master and maintain. Intubation opportunities for trainees are decreasing and success rates are subsequently falling. Use of a stylet may aid intubation and improve success. However, the potential for associated harm must be considered. Objectives To compare the benefits and harms of neonatal orotracheal intubation with a stylet versus neonatal orotracheal intubation without a stylet. Search methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library; MEDLINE; Embase; the Cumulative Index to Nursing and Allied Health Literature (CINAHL), and previous reviews. We also searched cross-references, contacted expert informants, handsearched journals, and looked at conference proceedings. We searched clinical trials registries for current and recently completed trials. We conducted our most recent search in April 2017. Selection criteria All randomised, quasi–randomised, and cluster-randomised controlled trials comparing use versus non-use of a stylet in neonatal orotracheal intubation. Data collection and analysis: Two review authors independently assessed results of searches against predetermined criteria for inclusion, assessed risk of bias, and extracted data. We used the standard methods of the Cochrane Collaboration, as documented in the Cochrane Handbook for Systemic Reviews of Interventions, and of the Cochrane Neonatal Review Group. Main results: We included a single-centre non-blinded randomised controlled trial that reported a total of 302 intubation attempts in 232 infants. The median gestational age of enrolled infants was 29 weeks. Paediatric residents and fellows performed the intubations. We judged the study to be at low risk of bias overall. Investigators compared success rates of first-attempt intubation with and without use of a stylet and reported success rates as similar between stylet and no-stylet groups (57% and 53%) (P = 0.47). Success rates did not differ between groups in subgroup analyses by provider level of training and infant weight. Results showed no differences in secondary review outcomes, including duration of intubation, number of attempts, participant instability during the procedure, and local airway trauma. Only 25% of all intubations took less than 30 seconds to perform. Study authors did not report neonatal morbidity nor mortality. We considered the quality of evidence as low on GRADE analysis, given that we identified only one unblinded study. Authors' conclusions: Current available evidence suggests that use of a stylet during neonatal orotracheal intubation does not significantly improve the success rate among paediatric trainees. However, only one brand of stylet and one brand of endotracheal tube have been tested, and researchers performed all intubations on infants in a hospital setting. Therefore, our results cannot be generalised beyond these limitations

Packing and Hausdorff measures of stable trees

In this paper we discuss Hausdorff and packing measures of random continuous trees called stable trees. Stable trees form a specific class of L\'evy trees (introduced by Le Gall and Le Jan in 1998) that contains Aldous's continuum random tree (1991) which corresponds to the Brownian case. We provide results for the whole stable trees and for their level sets that are the sets of points situated at a given distance from the root. We first show that there is no exact packing measure for levels sets. We also prove that non-Brownian stable trees and their level sets have no exact Hausdorff measure with regularly varying gauge function, which continues previous results from a joint work with J-F Le Gall (2006).Comment: 40 page

The SHEDS-Wood Model: Incorporation of Observational Data to Estimate Exposure to Arsenic for Children Playing on CCA-Treated Wood Structures

BACKGROUND: Lumber treated with chromated copper arsenate (CCA) compounds has been used in residential outdoor wood structures and public playgrounds. The U.S. Environmental Protection Agency (EPA) has conducted a probabilistic assessment of children’s exposure to arsenic using the Stochastic Human Exposure and Dose Simulation model for the wood preservative scenario (SHEDS-Wood). The assessment relied on data derived from an experimental study conducted using adult volunteers and designed to result in maximum hand and wipe loadings to estimate the residue–skin transfer efficiency. Recent analyses of arsenic hand-loading data generated by studies of children actively involved in playing on CCA-treated structures indicate that the transfer efficiency coefficient and hand-loading estimates derived from the experimental study significantly overestimate the amount that occurs during actual play. OBJECTIVES: Our goal was to assess the feasibility of using child hand-loading data in the SHEDS-Wood model and their impact on exposure estimates. METHODS: We used data generated by the larger of the studies of children in SHEDS-Wood, instead of the distributions used by U.S. EPA. We compared our estimates of the lifetime average daily dose (LADD) and average daily dose (ADD) with those derived by the U.S. EPA. RESULTS: Our analysis indicates that data from observational studies of children can be used in SHEDS-Wood. Our estimates of the mean (and 95th percentile) LADD and ADD were 27% (10%) and 29% (15%) of the estimates derived by U.S. EPA. CONCLUSION: We recommend that the SHEDS-Woods model use data from studies of children actively playing on playsets to more accurately estimate children’s actual exposures to CCA