Slippage Model Research Articles

Sequence Element Required for Efficient −1 Ribosomal Frameshifting in Red Clover Necrotic Mosaic Dianthovirus

The RNA−1 of the bipartite red clover necrotic mosaic dianthovirus (RCNMV) genome encodes the 88-kDa polymerase. The polymerase is translated from both 5′ proximal and internal open reading frames by a −1 ribosomal frameshifting event. A shifty heptanucleotide conforming to the simultaneous slippage model is identified, and a downstream stem-loop structure and atypical pseudoknot are predicted. A β-glucuronidase reporter assay identified a 118-nucleotide element containing both the shifty heptanucleotide and the predicted secondary structures that were required for efficient −1 ribosomal frameshift expressionin vivo. A series of site-directed and compensatory mutations affecting the base-paired regions of the predicted secondary structure were introduced into a RCNMV RNA−1 cDNA clone from which infectious transcripts were derived. Mutations that destroyed the predicted pseudoknot had no effect on frameshifting efficiencyin vitroor infectivity of the virus, whereas mutations destabilizing the stem-loop structure abolished both ribosomal frameshiftingin vitroand biological activity. These results demonstrate the essential role of a predicted secondary structure that does not involve a pseudoknot in the expression of the RCNMV polymerase by ribosomal frameshifting.

Microsatellite variation and evolution in the Mimulus guttatus species complex with contrasting mating systems.

Mutational variability at microsatellite loci is shaped by both population history and the mating system. In turn, alternate mating systems in flowering plants can resolve aspects of microsatellite loci evolution. Five species of yellow monkeyflowers (Mimulus sect. Simiolis) differing for historical rates of inbreeding were surveyed for variation at six microsatellite loci. High levels of diversity at these loci were found in both outcrossing and selfing taxa. In line with allozyme studies, inbreeders showed more partitioning of diversity among populations, and diversity in selfing taxa was lower than expected from reductions in effective population size due to selfing alone, suggesting the presence of either population bottlenecks or background selection in selfers. Evaluation of the stepwise mutation model (a model of DNA replication slippage) suggests that these loci evolve in a stepwise fashion. Inferred coalescent times of microsatellite alleles indicate that past bottlenecks of population size or colonization events were important in reducing diversity in the inbreeding taxon.

Replication bypass and mutagenic effect of alpha-deoxyadenosine site-specifically incorporated into single-stranded vectors.

alpha-2'-Deoxyadenosine (alpha) is a major adenine lesion produced by gamma-ray irradiation of DNA under anoxic conditions. In this study, single-stranded recombinant M13 vectors containing alpha were constructed and transfected into Escherichia coli to assess lethal and mutagenic effects of this lesion. The data for alpha were further compared with those obtained with M13 vectors containing normal A or a model abasic site (F) at the same site. The transfection assay revealed that alpha constituted a moderate block to DNA replication. The in vivo replication capacity to pass through alpha was approximately 20% relative to normal A, but 20-fold higher than that of F constituting an almost absolute replication block. Similar data were obtained by in vitro replication of oligonucleotide templates containing alpha or F by E.coli DNA polymerase I. The mutagenic consequence of replicating M13 DNA containing alpha was analyzed by direct DNA sequencing of progeny phage. Mutagenesis was totally targeted at the site of alpha introduced into the vector. Mutation was exclusively a single nucleotide deletion and no base substitutions were detected. The deletion frequency associated alpha was dependent on the 3'-nearest neighbor base: with the 3'-nearest neighbor base T mutation (deletion) frequency was 26%, whereas 1% with the 3'-nearest neighbor base G. A possible mechanism of the single nucleotide deletion associated with alpha is discussed on the basis of the misinsertion-strand slippage model.

Flux dynamics and c-axis resistive dissipation in the mixed state of high-temperature superconductors The case of (La 1− xSr x) 2CuO 4

We take the single-crystalline (La 1− x Sr x ) 2CuO 4 system ( x = 0.068) as an example to study flux dynamics in the mixed state of high- T c superconductors by systematically measuring its c-axis resistivity, ϱ c , as a function of temperature, magnetic-field intensity and magnetic-field orientation with respect to the ab-plane. We firstly show the experimental evidence that excludes the contribution of Lorentz force driven flux motion to the c-axis resistive dissipation. Furthermore, we argue that neither the vortex dynamics for conventional anisotropic superconductors nor the two-dimensional pancake vortices model is appropriate for the present system. We then demonstrate the difficulty of the previously considered Lorentz force free dissipation models in explaining the present experimental observations. Finally, a phenomenological model is introduced, in which the phase slippage model developed by Ambegaokar and Halperin is extended to the case of the c-axis resistivity by taking into account the following two main features: (1) the intrinsic layered structures along the c-axis, and (2) the irreversibility line, T irr( H), corresponding to a vortex glass-liquid transition. To show the advantages of the present model, we compare the model with the experimental ϱ c ( T, H) data for H|| C, which gives excellent agreement in almost the whole transition region (five decades).

Prokaryotic ribosomes recode the HIV-1 gag-pol-1 frameshift sequence by an E/P site post-translocation simultaneous slippage mechanism.

The mechanism favoured for -1 frameshifting at typical retroviral sites is a pre-translocation simultaneous slippage model. An alternative post-translocation mechanism would also generate the same protein sequence across the frameshift site and therefore in this study the strategic placement of a stop codon has been used to distinguish between the two mechanisms. A 26 base pair frameshift sequence from the HIV-1 gag-pol overlap has been modified to include a stop codon immediately 3' to the heptanucleotide frameshift signal, where it often occurs naturally in retroviral recoding sites. Stop codons at the 3'-end of the heptanucleotide sequence decreased the frame-shifting efficiency on prokaryote ribosomes and the recording event was further depressed when the levels of the release factors in vivo were increased. In the presence of elevated levels of a defective release factor 2, frameshifting efficiency in vivo was increased in the constructs containing the stop codons recognized specifically by that release factor. These results are consistent with the last six nucleotides of the heptanucleotide slippery sequence occupying the ribosomal E and P sites, rather than the P and A sites, with the next codon occupying the A site and therefore with a post-translocation rather than a pre-translocation -1 slippage model.

Paramyxovirus mRNA editing leads to G deletions as well as insertions.

Paramyxoviruses are thought to edit their P gene mRNAs co-transcriptionally, by a mechanism in which the polymerase stutters and reads the same template base more than once. Sendai virus (SeV) and bovine parainfluenza virus type 3 (bPIV3) are closely related viruses, but SeV edits its P gene mRNA with the insertion of a single G residue (at approximately 50% frequency) within the sequence 5' A6G3, whereas bPIV3 inserts 1 to approximately 6 Gs at roughly equal frequency within the sequence 5' A6G4. When SeV synthetic mini-genomes containing either SeV or bPIV3 P gene editing cassettes are expressed from cDNA in cells which are also transfected with the SeV NP, P and L genes, the virus-specific editing patterns were reproduced. Since the bPIV3 editing pattern was reproduced in a system that is otherwise completely SeV, this suggests that all the information for the virus-specific editing patterns is due to the RNA sequence itself. Unexpectedly, the length of the template C run was found to be critical, even though it varies from 3 to 7 nucleotides in length in different viruses. Expanding this template C run first led to attenuation of the insertion phenotype, and then to deletions rather than insertions. A stuttering or slippage model to account for these events has been further refined to include a pressure which displaces the nascent strand in a given direction once it has disengaged from the template, and the similarities of this model to those which account for readthrough of cellular RNA polymerase transcription blocks are discussed.

Identification and Analysis of the Site of -1 Ribosomal Frameshifting in Red Clover Necrotic Mosaic Virus

The genomic RNA-1 of red clover necrotic mosaic dianthovirus (RCNMV) contains the heptanucleotide GGAUUUU that precedes the termination codon of the 5′ proximal p27 open reading frame (ORF). This heptanucleotide is followed by a sequence with the potential to form a stable, complex secondary structure. Translation of RNA-1 is postulated to utilize a -1 ribosomal frameshifting mechanism to express the 88-kDa viral RNA polymerase. Using site-directed mutagenesis together with cell-free translation to monitor frameshifting and a biological assay of the mutants in plants, we establish the role of the GGAUUUU as the site where -1 ribosomal frameshifting occurs. The frameshifting signal sequence conforms to the simultaneous slippage model. Stop codons flanking the shifty signal are not required for frameshifting but the p27 ORF termination codon is necessary for maintaining optimal infectivity of the virus. Mutations abolishing the RCNMV RNA-1 internal p57 ORF initiation codon did not affect infectivity of the virus, suggesting that this cistron is only expressed in vivo as an 88-kDa ribosomal frameshifting product. Shifty heptanucleotide signals from a number of animal retroviruses and RNA plant viruses facilitate RCNMV frameshifting in vitro. However, only a limited number of the heterologous shifty heptanucleotides were functional in plant cells. We suggest that specific shifty tRNA populations in the cell facilitate viral-1 ribosomal frameshifting. This analysis also suggests that the slippery sequence requirements are not identical in mammalian and in plant systems.

DNA Sequence Determinants of Carcinogen-Induced Frameshift Mutagenesis

In order to examine the mechanisms of induced frameshift mutagenesis, we constructed double-stranded DNA plasmids which contain single N-2-acetylaminofluorene (AAF) adducts at specified positions within a run of contiguous guanine residues. The length of the homopolymeric run and the nature of the bases flanking the contiguous sequence were systematically varied. Monomodified plasmids were introduced into SOS-induced Escherichia coli, and -1 frameshift mutations were scored by means of a phenotypic assay. A strong positional effect of the DNA adduct within the contiguous sequence was observed irregardless of the nature of the flanking bases: the AAF-induced mutation frequency was 20-200-fold higher at the 3'-end of the contiguous sequence than at the 5'-end. In addition, for a given number of guanine residues flanking the GAAF adduct on its 5'-side, differences (up to 5-fold) in the induced mutation frequency were observed as a function of the base 3' to the adduct (CGGGAAFAT approximately CGGGAAFGT > CGGGAAFCT > CGGGAAFTT). These results are discussed, within the frame of an incorporation slippage model, in terms of differences in stability and occurrence of the slipped mutagenic intermediates.

Activated transport in the 2D electron solid in Si

We describe the characteristics of the temperature activated dc-transport observed in the insulating phase which occurs at dilute concentrations and low temperatures in high mobility 2D electron systems in Si. Our data show the existence of two different temperature regimes, one of which can be fitted well using the phase slippage model commonly applied to charge density waves.

Sequential slippage tests using Robbins-Lai's invariant confidence sequences

The paper deals with two kinds of location-slippage testing problems.The alternative hypothesis says that there is a single slippage in one kind of problems,and that there are multiple slippages in the other kind. In a location slippage model, by using Robbins' inequality, Robbins-Lai's invariant confidence sequences for slippage are constructed for both of the problems and sequential slippage tests using those confidence sequences are proposed.

Limits to the role of palindromy in deletion formation

We tested the effect of palindromy on deletion formation. This involved a study of reversion of insertion mutations in the pBR322 amp gene at a site where deletions end either in 9-bp direct repeats or in adjoining 4-bp direct repeats. Inserts of palindromic DNAs ranging from 10 to more than 26 bp and related nonpalindromic DNAs were compared. The frequency of deletions (selected as Ampr revertants) was stimulated by palindromy only at lengths greater than 26 bp. The 4-bp direct repeats, one component of which is located in the palindromic insert, were used preferentially as deletion endpoints with palindromes of at least 18 bp but not of 16 or 10 bp. We interpret these results with a model of slippage during DNA replication. Because deletion frequency and deletion endpoint location depend differently on palindrome length, we propose that different factors commit a molecule to undergo deletion and determine exactly where deletion endpoints will be.

Phase slippage in a magnetic field at intra- and intergranular Josephson junctions in high- Tc superconductors

The intra- and intergranular components of resistance in high- T c superconductors are modelled, after configurational averaging, as due to a single resistively shunted Josephson junction in each case. They are combined in series. A voltage develops across each junction due to thermally activated phase slippage. In the presence of a magnetic field slippage occurs at a faster rate and is accompanied by motion of the entire flux bundle in the junction. Data on thin films is fitted well by the model over a wide temperature range. The model predicts that in a flux density B the critical currents and activation energies at higher fields fall off as (ø 0/B) 1 2 /[D+(ø 0/B) 1 2 ] with D the junction width. Experimental data on thin films of YBa 2Cu 3O 7 agrees with this prediction for both types of junction. It also shows that neither the intra- nor the intergranular components of resistance are sensitive to the relative direction of macroscopic current and field down to low temperatures. Differences between the roles of the Lorentz force in flux creep and phase slippage models are discussed.

混繊糸および交織布を用いた一方向炭素繊維／ＰＥＥＫ複合材の試作と横方向引張り特性

Three types of unidirectional carbon fiber/PEEK composites are fabricated from : (a) prepreg sheet, (b) plain weave cloth ; warp : commingled yarn (1800 d) of carbon fiber with PEEK fiber, weft : PEEK yarn (70 d), (c) 5-shaft sateen weave cloth ; warp : carbon yarn (1800 d), weft : PEEK yarn (900 d). The transverse tensile properties are measured and compared with the theoretical predictions based on the perfect adhesion and interfacial slippage models. The transverse Young's moduli of the composites fabricated from (a) and (b) are in good agreement with the theoretical values based on the perfect adhesion model at the fiber/matrix interface. On the other hand, Young's modulus of the composite from (c) rather coincides with the prediction by the interfacial slippage model. The wettability and the interfacial adhesion between the carbon fiber and the PEEK resin are also investigated by the SEM observation of the fracture surface.

Outlier tests for logistic regression: A conditional approach

We consider exact conditional methods for identifying outliers in logistic regression data. Tests for a single outlier and multiple outliers are developed assuming a logistic slippage model. The p-values for these tests are determined using an explicit enumeration of all possible responses consistent with the observed value of the sufficient statistic. Justifications are given for preferring this computationally intensive approach to standard methods based on asymptotic approximations. The techniques are applied to two examples.

横等方性繊維を用いた一方向繊維複合材への界面すべりモデルの適用

In a preceding paper, the interfacial slippage model of the unidirectional fiber composite was developed assuming that the fiber and the matrix were both isotropic. By the use of this model, the elastic moduli and the stress distribution in the transverse cross-section of the composite can be predicted. In this paper, the interfacial slippage model has been extended to the composite reinforced with transversely isotropic fiber. The predicted transverse Young's moduli of the unidirectional carbon fiber/PEEK composites are compared with the experimental results. In the experiment, two types of unidirectional carbon fiber/PEEK composites are prepared : (a) from prepreg sheet and (b) from the cloth woven using the warp of carbon fiber and the weft of PEEK fiber. The transverse Young's modulus of the specimen (a) coincides with the theoretical results assuming the perfect adhesion at the carbon fiber/PEEK interface. On the other hand, the experimental result, of specimen (b) rather coincides with the theoretical prediction based on the interfacial slippage model.

Identification of a Type I Outlier in an Autoregressive Model

Let a realization of a time series be given, which coincides with that of an autoregressive Process except for a single observation. The location of this value is assumed to be known. In order to desctibe the outlier a slippage model is used. In this paper we deal with the testing problem, Whether an outlier is present or not If some parameters x are assumed to be know, we are able to give a UMPU test (x) In the case x unknown we replace x by a suitable estimator x and obtain a test (x). Severak tests are introduced and the asymptotic distributions of the test statistics are derived. A comparison of the asymptotic power functins shows that is the best of these tests.

Vaccinia virus late transcripts generated in vitro have a poly(A) head.

A cell free system mediating accurate transcription of vaccinia virus genes was established using lysates of cells in the late phase of infection. Vaccinia late genes are faithfully transcribed in this extract whereas cellular pol II and pol III promoters are not recognized. The late viral transcripts contain a poly(A) head of approximately 35 nt at the 5' end which is not co-linearly encoded in the externally added template. The transcripts obtained in vitro are indistinguishable from the mature in vivo RNAs. The poly(A) head is synthesized de novo and its formation appears to be directly coupled to the transcription of the gene. The synthesis of the poly(A) head transcripts in vitro is consistent with a proposed slippage model.

A Note on Restricted Maximum Likelihood Estimation with an Alternative Outlier Model

SUMMARY For single outliers in normal theory fixed effects models a mean slippage model is commonly used. An alternative is to model the outlier as arising from an unknown observation with inflated variance. Maximum likelihood estimates for the position of the outlier under the two models need not agree. This paper considers maximizing a restricted part of the likelihood to estimate the variance parameters and characterizes these estimates in terms of standard least squares parameters. It is shown that the residual variance and outlier position are the same under both models.

Relationship of net chloride flow across the human erythrocyte membrane to the anion exchange mechanism.

The parallel effects of the anion transport inhibitor DIDS (4,4'-diisothiocyanostilbene-2,2'-disulfonate) on net chloride flow and on chloride exchange suggest that a major portion of net chloride flow takes place through the anion exchange system. The "slippage" model postulates that the rate of net anion flow is determined by the movement of the unloaded anion transport site across the membrane. Both the halide selectivity of net anion flow and the dependence of net chloride flux on chloride concentration over the range of 75 to 300 mM are inconsistent with the slippage model. Models in which the divalent form of the anion exchange carrier or water pores mediate net anion flow are also inconsistent with the data. The observations that net chloride flux increases with chloride concentration and that the DIDS-sensitive component tends to saturate suggest a model in which net anion flow involves "transit" of anions through the diffusion barriers in series with the transport site, without any change in transport site conformation such as normally occurs during the anion exchange process. This model is successful in predicting that the anion exchange inhibitor NAP-taurine, which binds to the modifier site and inhibits the conformational change, has less effect on net chloride flow than on chloride exchange.

The relationship between microseismicity and high pore pressures during hydraulic stimulation experiments in low permeability granitic rocks

Several hundred microearthquakes with local magnitudes ranging between −4 and −2 were recorded during hydraulic stimulation experiments at the hot dry rock demonstration site, Fenton Hill, New Mexico. These events are probably caused by shear failure induced by high pore fluid pressures. Since the event locations seem to cluster in a narrow band near the hydraulic fracture, we were able to use micro‐seismic techniques to locate the hydraulic fracture and monitor its growth. We calculate the minimum pore pressure increase necessary to induce rock failure using a simple model of slippage on preexisting fractures. By comparing a pore pressure distribution, calculated using a one‐dimensional diffusion model with the distribution of event foci, we demonstrate that high pore pressures are a probable cause for these microearthquakes. Stress drops for these microearthquakes, calculated from spectral parameters, increased by a factor of 3 during the course of the experiment. The stress drop increase correlates with a migration of seismic activity away from the injection well bore, which suggests relatively low in situ shear stresses near the well bore caused by strain release in this region during previous pressurizations.