Slippage Model Research Articles

Most low‐level microsatellite instability in colorectal cancers can be explained without an elevated slippage rate

Many cancers show a low level of microsatellite slippage and are labelled MSI-L (microsatellite instability--low). However, it is unclear whether this slippage can be attributed to some underlying genetic change that results in a mutator phenotype, analogous to mismatch repair deficiency in MSI-H cancers, or whether the apparent instability is the result of relatively frequent normal somatic slippage. Here, we have used a mathematical model of microsatellite slippage during cancer growth to estimate the degree of microsatellite slippage expected in a cancer due to normal somatic slippage. We compared the model to the slippage observed in 42 non-MSI-H cancers that were macro-dissected into four distinct regions and genotyped at N = 9 microsatellite loci. When the slippage rate was set at mu = 10(-5) per locus per division, ten cancers showed a level of slippage in at least one region that was too severe to be expected from normal somatic slippage alone, suggesting that these cancers had acquired MSI-L. Only one of these ten cancers had putative MSI-L in all four regions. When we considered a slightly higher slippage rate of mu = 5 x 10(-5), none of the cancers showed a degree of slippage that could not be reasonably explained by normal somatic slippage. Counting the number of 'unstable' loci was a poor indicator of putative MSI-L status. We conclude that most low-level microsatellite instability in colorectal cancers can be explained without requiring an elevated slippage rate during neoplastic development, and hence there is little evidence for a discrete MSI-L group of cancers. Putative MSI-L status is indicated by the presence of at least one locus that has multiple alleles that differ by at least five motif repeats from the germline. If an underlying genetic change does cause MSI-L, it appears to be a relatively uncommon event that occurs late in oncogenesis.

Double complex mutations involvingF8andFUNDC2caused by distinct break-induced replication

Genomic rearrangements are a well-recognized cause of genetic disease and can be formed by a variety of mechanisms. We report a complex rearrangement causing severe hemophilia A, identified and further characterized using a range of PCR-based methods, and confirmed using array-comparative genomic hybridization (array-CGH). This rearrangement consists of a 15.5-kb deletion/16-bp insertion located 0.6 kb from a 28.1-kb deletion/263-kb insertion at Xq28 and is one of the most complex rearrangements described at a DNA sequence level. We propose that the rearrangement was generated by distinct but linked cellular responses to double strand breakage, namely break-induced replication (BIR) and a novel model of break-induced serial replication slippage (SRS). The copy number of several genes is affected by this rearrangement, with deletion of part of the Factor VIII gene (F8, causing hemophilia A) and the FUNDC2 gene, and duplication of the TMEM185A, HSFX1, MAGEA9, and MAGEA11 genes. As the patient exhibits no clinically detectable phenotype other than hemophilia A, it appears that the biological effects of the other genes involved are not dosage-dependent. This investigation has provided novel insights into processes of DNA repair including BIR and the first description of SRS during repair in a pathological context.

Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana

The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated--such as the position of a locus within the chromosome, or imperfect repeats--appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.

High-Grade Slippage of the Lumbar Spine in a Rat Model of Spondylolisthesis

Radiographic and histologic evaluation of spondylolisthesis in a rat model. To investigate the effects of etodolac, a cox-2 inhibitor, on the severity of spondylolisthesis in a 4-week-old rat model. Spondylolisthesis occurs associated with spondylolysis in some pediatric patients. In such patients, the percent of forward slippage varies individually ranging between 0% and 100%. The factors determining the severity of forward slippage have not been clarified as yet. In earlier studies, we found that growth plate stress fracture was the basic lesion and that slippage was a consequence of the stress fracture. Hence, we hypothesized that the capacity of bone healing might be an important determinant of the degree of forward slippage. A lumbar spine slippage model was prepared in 4-week-old rats with vertebral physis fracture. To disrupt the fracture healing, the cyclooxygenase-2 (cox-2) inhibitor etodolac was used, and its effects on slippage and deformity were evaluated radiologically and histologically. In the etodolac group, forward slip significantly increased (P < 0.05) to the Meyerding Grade III while in the control rats it was Grade I or II. Bone remodeling of the vertebral body was suppressed by etodolac. Histologically, epiphyseal separation with slippage was observed in all the control and etodolac-treated rats. However, in the etodolac-treated group, the epiphyseal plate was greatly separated and did not present periosteal thickening at the physis fracture site. Vertebral forward slippage occurred in young rats after epiphyseal separation. In the etodolac group, slippage increased as deterioration of the bone healing capacity increased. Poor bony healing is suggested as one of the determinants of high-grade spondylolisthesis in children and adolescents.

Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms

Gross genomic rearrangements involving deletions in the CFTR gene have recently been found to account for approximately 20% of unidentified cystic fibrosis (CF) chromosomes in both French and Italian patients. Using QMPSF and walking quantitative DHPLC, six novel mutations (three simple deletions, two complex deletions with short insertions of 3-6 bp, and a complex deletion with a 182 bp inverted downstream sequence) were characterized by screening 274 unidentified CF chromosomes from 10 different countries. These lesions increase the total number of fully characterized large CFTR genomic rearrangements involving deletions to 21. Systematic analysis of the 42 associated breakpoints indicated that all 21 events were caused by nonhomologous recombination. Whole gene complexity analysis revealed a significant correlation between regions of low sequence complexity and the locations of the deletion breakpoints. Known recombination-promoting motifs were noted in the vicinity of the breakpoints. A total of 11 simple deletions were potentially explicable in terms of the classical model of replication slippage. However, the complex deletions appear to have arisen via multiple mechanisms; three of the five complex deletions with short insertions and both examples of large inverted insertions (299 and 182 bp, respectively) can be explained by either a model of serial replication slippage in cis (SRScis) or SRS in trans (SRStrans). Finally, the nature and distribution of large genomic rearrangements in the CFTR gene were compared and contrasted with those of two other genes, DMD and MSH2, with a view to gaining a broader understanding of DNA sequence context in mediating the diverse underlying mutational mechanisms.

Determination of frictional conditions between electrode array and endosteum lining for use in cochlear implant models

Frictional conditions between the electrode array (in cochlear implants) and the endosteum lining covering the walls of the interior scala tympani structure strongly influence the sliding behaviour of the electrode array. Friction coefficients, determined by a simple but effective method based on the impending slippage model of electrode arrays sliding over the endosteum lining are reported in this paper. In this study, friction coefficients of the Nucleus standard straight and the Contour arrays have been determined with and without lubricants applied on the endosteum lining. In the absence of applied lubricants, friction coefficients were found to be 0.19 for the Nucleus standard straight array and 0.12 for the Contour array. Application of lubricants (glycerin and sorbelene) has the potential to lower the friction coefficient for Nucleus standard straight array (0.12 and 0.15) and for the Contour array (0.04 and 0.08). These results are used in finite element models to predict accurately the trajectories of electrode arrays and sliding contact pressures on cochlear structures to evaluate the likelihood of damage sustained during insertion.

Complex gene rearrangements caused by serial replication slippage

The now-classical model of replication slippage can in principle account for both simple deletions and tandem duplications associated with short direct repeats. Invariably, a single replication slippage event is invoked, irrespective of whether simple deletions or tandem duplications are involved. However, we recently identified three complex duplicational insertions that could also be accounted for by a model of serial replication slippage. We postulate that a sizeable proportion of hitherto inexplicable complex gene rearrangements may be explained by such a model. To test this idea, and to assess the generality of our initial findings, a number of complex gene rearrangements were selected from the Human Gene Mutation Database (HGMD). Some 95% (20/21) of these mutations were found to be explicable by twin or multiple rounds of replication slippage, the sole exception being a double deletion in the F9 gene that is associated with DNA sequences that appear capable of adopting non-B conformations. Of the 20 complex gene rearrangements, 19 (seven simple double deletions, one triple deletion, two double mutational events comprising a simple deletion and a simple insertion, six simple indels that may constitute a novel and non-canonical class of gene conversion, and three complex indels) were compatible with the model of serial replication slippage in cis; the remaining indel in the MECP2 gene, however, appears to have arisen via interchromosomal replication slippage in trans. Our postulate that serial replication slippage may account for a variety of complex gene rearrangements has therefore received broad support from the study of the above diverse series of mutations.

In vitro synthesis of uniform poly(dG)-poly(dC) by Klenow exo- fragment of polymerase I

In this paper, we describe a production procedure of the one-to-one double helical complex of poly(dG)–poly(dC), characterized by a well-defined length (up to 10 kb) and narrow size distribution of molecules. Direct evidence of strands slippage during poly(dG)–poly(dC) synthesis by Klenow exo− fragment of polymerase I is obtained by fluorescence resonance energy transfer (FRET). We show that the polymer extension results in an increase in the separation distance between fluorescent dyes attached to 5′ ends of the strands in time and, as a result, losing communication between the dyes via FRET. Analysis of the products of the early steps of the synthesis by high-performance liquid chromatography and mass spectroscopy suggest that only one nucleotide is added to each of the strand composing poly(dG)–poly(dC) in the elementary step of the polymer extension. We show that proper pairing of a base at the 3′ end of the primer strand with a base in sequence of the template strand is required for initiation of the synthesis. If the 3′ end nucleotide in either poly(dG) or poly(dC) strand is substituted for A, the polymer does not grow. Introduction of the T-nucleotide into the complementary strand to permit pairing with A-nucleotide results in the restoration of the synthesis. The data reported here correspond with a slippage model of replication, which includes the formation of loops on the 3′ ends of both strands composing poly(dG)–poly(dC) and their migration over long-molecular distances (μm) to 5′ ends of the strands.

Large apparent interfacial slippage at polyelectrolyte-perfluorocarbon interfaces on a quartz crystal resonator.

The apparent negative areal mass densities obtained for a polyelectrolyte multilayer on a quartz crystal resonator in contact with four different perfluorocarbon liquids are explained by the interfacial slippage between the multilayer and the liquids. It is shown that the zone of interfacial slipping can be conveniently treated as a separate layer with distinct physical parameters. Three models of slippage were taken into a closer study. In the first model, the so-called de Gennes model, a very thin gas-filled cavity is formed between the moving phase and the stationary phase. The second model is based on the slipping layer consisting of water. In the third model, the so-called "true slipping" model, it is assumed that the particle velocity has a discontinuity at the interface. In each case, the slipping admittances and slippage lengths as well as the corrected areal mass densities were calculated from the experimental data. Although no unambiguous experimental evidence was found to favor strongly any of these three models, the slightly smaller variation in the slipping admittance and the areal mass density seems to give more credibility to the de Gennes model.

Sliding Friction at a Rubber/Brush Interface

We study the friction of a poly(dimethylsiloxane) (PDMS) rubber network sliding, at low velocity, on a substrate on which PDMS chains are end-tethered. We thus clearly evidence the contribution to friction of the pullout mechanism of chain ends that penetrate into the network. This interfacial dissipative process is systematically investigated by probing the velocity dependence of the friction stress and its variations with the grafting density and molecular weight of the tethered chains. This allows us to confirm semiquantitatively the picture of arm retraction relaxation of the grafted chains proposed in models of slippage at a network/brush interface.

Vertebral forward slippage in immature lumbar spine occurs following epiphyseal separation and its occurrence is unrelated to disc degeneration: is the pediatric spondylolisthesis a physis stress fracture of vertebral body?

Radiographic and histologic evaluation of a rat model of lumbar spine slippage. To clarify the pathomechanism of slippage in the immature spine. There are controversial hypotheses regarding the pathogenesis of slippage of the pediatric spine with pars defects. Some studies supported that disc degeneration was its cause, while others indicated the growth plate injury was the cause. An immature lumbar spine slippage model in 4-week-old rats was used. Following posterior destabilizing surgery, the lumbar spine was radiographically and histologically examined at 1, 3, 5, and 7 days after surgery. Radiographically, slippage occurred about 7% in the % slip on day 7, and no slippage was observed before day 5. Histologically, epiphyseal separation also appeared on day 7; before day 5, the growth plate showed no abnormalities. Within 7 days after the operation, the anulus fibrosus did not show any sign indicating degeneration. The nucleus pulposus was also normal up to day 7. The findings of this study support the hypothesis that vertebral forward slippage of the immature spine occurs following epiphyseal separation and its occurrence is unrelated to disc degeneration.

Oculopharyngeal muscular dystrophy (OPMD) due to a small duplication in the PABPN1 gene.

Oculopharyngeal muscular dystrophy (OPMD) is a late onset autosomal dominant muscle disorder. The OPMD-locus has been mapped to chromosome 14q11.2-q13. The polyadenylate binding protein nuclear 1 (PABPN1; PABP2) gene has been identified as the mutated gene. The mutation consists of a short meiotically stable trinucleotide repeat in the first exon of PABPN1 gene. We have investigated Dutch OPMD patients from four unrelated families and identified a new mutation in two of the four families. Instead of a repeat expansion we found a duplication in the first exon of the PABPN1 gene (c.27_28ins12, p.11_12insAAAA). The identification of this new mutation supports the theory of unequal crossing-over as molecular mechanism causing the mutation in the PABPN1 gene responsible for OPMD, and not the slippage model.

Extremely complex pattern of microsatellite mutation in the germline of wheat exposed to the post-Chernobyl radioactive contamination

The molecular structure of rare variants at 13 microsatellite loci found in a population of wheat plants grown for one generation in the heavily contaminated 30 km exclusion zone around the Chernobyl Nuclear Power Plant and in a control population was compared. Evidence for rare alterations (variants) was obtained for all 13 loci, including gain and loss of repeats, as well as the complete loss of microsatellite bands. The ratio between gains and losses among variants in the control group was similar to that in the exposed group. Sequencing of variants at six microsatellite loci found in the exposed population revealed extremely complex pattern of germline mutations, including complete deletions of loci, a bias towards mutations with gains and losses of multiple repeat units, and relatively frequent insertions of DNA of unknown origin. The occurrence of large deletions at two loci may be attributed to direct and inverted repeats sequences located just upstream and downstream of the array. The results of our study also suggest that the majority of mutations within the studied wheat microsatellite loci are represented by gains and losses of multiple repeat units, implying that a simple model of replication slippage cannot account for mutation events at these loci. Our data also support the conclusion that the spectra of spontaneous and radiation-induced mutation in wheat may be similar.

Shear-thinning liquid films: macroscopic and asymptotic behaviour by quasi-self-similar solutions

We consider the spreading of a thin droplet of viscous liquid on a plane surface driven by capillarity in the complete wetting regime. In the case of constant viscosity, the no-slip condition leads to a force singularity at advancing contact lines. It is well known nowadays that the introduction of appropriate slip conditions removes this paradox and alters only logarithmically the macroscopic behaviour of solutions at intermediate timescales. Here, we investigate a different approach, which consists in keeping the no-slip condition and assuming instead a shear-thinning rheology. This relaxation leads, in lubrication approximation, to fourth order degenerate parabolic equations of quasilinear type. By analysing a class of quasi-self-similar solutions to these equations in the limit of Newtonian rheology, we obtain a scaling law in time for macroscopic quantities (such as macroscopic profile, effective contact-angle) which is only logarithmically affected by the shear-thinning parameters. As opposed to positive slippage models, the scaling law is uniform for large times as far as the macroscopic support is well defined, and thus could also describe the asymptotic behaviour of a large class of solutions for fixed shear-thinning rheology.

Micromechanics of plant tissues beyond the linear-elastic range.

We investigated the relation between cell wall structure and the resulting mechanical characteristics of different plant tissues. Special attention was paid to the mechanical behaviour beyond the linear-elastic range, the underlying micromechanical processes and the fracture characteristics. The previously proposed model of reorientation and slippage of the cellulose microfibrils in the cell wall [H.-CH. Spatz et al. (1999) J Exp Biol 202:3269-3272) was supported and is here refined, using measurements of the changes in microfibrillar angle during straining. Our model explains the widespread phenomenon of stress-strain curves with two linear portions of different slope and sheds light on the micromechanical processes involved in viscoelasticity and plastic yield. We also analysed the velocity dependence of viscoelasticity under the perspective of the Kelvin model, resolving the measured viscoelasticity into functions of a velocity-dependent and a velocity-independent friction. The influence of lignin on the above-mentioned mechanical properties was examined by chemical lignin extraction from tissues of Aristolochia macrophylla Lam. and by the use of transgenic plants of Arabidopsis thaliana (L.) Heynh. with reduced lignin content. Additionally, the influence of extraction of hemicelluloses on the mechanical properties was investigated as well as a cell wall mutant of Arabidopsis with an altered configuration of the cellulose microfibrils.

Pressure and magnetic-field effects on the onset of dissipation inHg0.82Re0.18Ba2Ca2Cu3O8+δceramic superconductors

The pressure and magnetic-field effects on a ${\mathrm{Hg}}_{0.82}{\mathrm{Re}}_{0.18}{\mathrm{Ba}}_{2}{\mathrm{Ca}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{8+\mathrm{\ensuremath{\delta}}}$ sample with optimum oxygen content was studied. The onset temperature of the dissipation ${(T}_{\mathrm{on}})$ for a fixed applied magnetic field increases with the pressure. The ${H(T}_{\mathrm{on}})$ curves, taken at different pressures, may be superposed when ${T}_{\mathrm{on}}$ is scaled with the pressure-dependent critical temperature, ${T}_{c}(P),$ suggesting that the mechanism which leads to an increase of ${T}_{c}$ also improves the intergrain coupling. Our data are discussed in the frame of the phase slippage model giving some insight on the influence of the pressure on the transport properties of our sample.

Influence of the pressure on the onset of the dissipation in Hg 0.82Re 0.18Ba 2Ca 2Cu 3O 8+δ ceramic superconductor

The pressure (P) effect on a Hg 0.82Re 0.18Ba 2Ca 2Cu 3O 8+δ sample with optimum oxygen content is presented. The onset temperature of the dissipation (T co) increases with P. The T co(H) curves, taken at different pressures, are superposed when T co were scaled with T c(P), suggesting that the mechanism which leads to an increasing of T c also improves the intergran coupling. Our data is discussed in the frame of the phase slippage model giving some insight on the microscopic effects of the pressure.

Anionic phospholipids decrease the rate of slippage on the Ca2+-ATPase of sarcoplasmic reticulum

Accumulation of Ca(2+) by the Ca(2+)-ATPase of skeletal-muscle sarcoplasmic reticulum has been measured in reconstituted, sealed vesicles as a function of lipid composition. Measurements were performed in the presence of carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) to eliminate any effects of H(+) transport; in the presence of FCCP, addition of valinomycin had no effect on the level or rate of accumulation of Ca(2+) showing that, in the presence of FCCP, no electrical potential built up across the membrane. Levels of accumulation were low when the phospholipid was dioleoylphosphatidylcholine (DOPC), even though DOPC supports high ATPase activity. Inclusion of 10 mol% anionic phospholipid [dioleoylphosphatidic acid (DOPA) or dioleoylphosphatidylserine (DOPS)] led to higher levels of accumulation of Ca(2+), 10 mol% being the optimum concentration. Cardiolipin or phosphatidylinositol 4-phosphate were more effective than DOPA or DOPS in increasing accumulation of Ca(2+). Effects of anionic phospholipids were seen in the presence of an ATP-regenerating system to remove ADP, and in the presence of phosphate within the reconstituted vesicles to precipitate calcium phosphate. Rates of passive leak of Ca(2+) from the reconstituted vesicles were slow. The Ca(2+)-accumulation process was simulated assuming either simple passive leak of Ca(2+) from the vesicles or assuming slippage on the ATPase, a process in which the phosphorylated intermediate of the ATPase releases bound Ca(2+) on the cytoplasmic rather than the lumenal side of the membrane. The experimental data fitted to a slippage model, with anionic phospholipids decreasing the rate of slippage.

Modeling fiber slippage during the preforming process

AbstractUntil now, the pin‐jointed net model has been a widely used method for the prediction of preforming shape for woven fabrics. However, it deals only with pure trellising (or shear) and neglects other possible deformation modes. In some cases, there is evidence showing that other deformation modes have relevance to, and effectiveness in forming the final shape. A model considering only the shear mode will not result in an adequate prediction. In this study, a slippage model is developed to modify the pin‐jointed net model. Macrostructure of the fabrics is included in the slippage model in order to capture more deformation modes. Comparisons of experimental and simulation results are presented. It is shown that the numerical prediction using the slippage model has better agreement with experimental measurements.

Sequence context modulation of translesion synthesis at a single N-2-acetylaminofluorene adduct located within a mutation hot spot.

Oligonucleotides containing a single N-(deoxyguanosin-8-yl)acetylaminofluorene lesion (dGuo-C8-AAF) at each guanine residue of the sequence (5'-G1G2G3) have been used as templates for in vitro primer extension reactions by several DNA polymerases [Escherichia coli DNA polymerase III holoenzyme, its alpha subunit, DNA polymerase I Klenow fragment proficient (exo+) or deficient (exo-) in its 3' --> 5' exonuclease activity, and Sequenase]. The dGuo-C8-AAF lesion appears to be a strong block for all DNA polymerases: exo+ DNA polymerases stop one nucleotide before encountering the lesion, while partial incorporation opposite the lesion is observed only with enzymes devoid of the exonuclease activity. The efficiency of incorporation across from the adduct depends on both the DNA polymerase and the position of the lesion. When polymerase I Klenow fragment exo- is used, translesion synthesis (TLS) is observed with efficiencies varying according to the position of the adduct (G2 > G1 > G3). Sequencing of the TLS products shows that error-free TLS is observed only when the AAF lesion is bound to G1, while all TLS events occurring at G2- or G3-AAF adducts are mutagenic. The major mutational event is a G deletion (27, 76, and 55% of the events for G1, G2, and G3, respectively), while two-G deletions occur to a lesser extent (17-30%). These results are discussed in view of the slippage model developed for frameshift mutagenesis occurring during translesion synthesis at replication blocking lesions.