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Conly L Rieder - One of the best experts on this subject based on the ideXlab platform.
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microtubules do not promote mitotic Slippage when the spindle assembly checkpoint cannot be satisfied
Journal of Cell Biology, 2008Co-Authors: Daniela A Brito, Zhenye Yang, Conly L RiederAbstract:When the spindle assembly checkpoint (SAC) cannot be satisfied, cells exit mitosis via mitotic Slippage. In microtubule (MT) poisons, Slippage requires cyclin B proteolysis, and it appears to be accelerated in drug concentrations that allow some MT assembly. To determine if MTs accelerate Slippage, we followed mitosis in human RPE-1 cells exposed to various spindle poisons. At 37°C, the duration of mitosis in nocodazole, colcemid, or vinblastine concentrations that inhibit MT assembly varied from 20 to 30 h, revealing that different MT poisons differentially depress the cyclin B destruction rate during Slippage. The duration of mitosis in Eg5 inhibitors, which induce monopolar spindles without disrupting MT dynamics, was the same as in cells lacking MTs. Thus, in the presence of numerous unattached kinetochores, MTs do not accelerate Slippage. Finally, compared with cells lacking MTs, exit from mitosis is accelerated over a range of spindle poison concentrations that allow MT assembly because the SAC becomes satisfied on abnormal spindles and not because Slippage is accelerated.
John F Atkins - One of the best experts on this subject based on the ideXlab platform.
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productive mrna stem loop mediated transcriptional Slippage crucial features in common with intrinsic terminators
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Christophe Penno, Virag Sharma, Arthur Coakley, Mary Oconnell Motherway, Douwe Van Sinderen, Lucyna Lubkowska, Maria L Kireeva, Mikhail Kashlev, Pavel V Baranov, John F AtkinsAbstract:Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional Slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the Slippage site, the length and composition of the Slippage site motif, and the identity of its 3′ adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this Slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the Slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the Slippage sequence and the 3′ nt context. The only previous proposal of stem loop mediated Slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical Slippage model involving the RNAP translocation state as the main motor in Slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription Slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
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Transcriptional Slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression
Genome Biology, 2005Co-Authors: Pavel V Baranov, Andrew W Hammer, Jiadong Zhou, Raymond F Gesteland, John F AtkinsAbstract:Background Transcription Slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mRNAs. Individual mRNA molecules within this population differ in the number of nucleotides they contain that are not specified by the template. When transcriptional Slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein product. Except where the products of the resulting mRNAs have distinct functions, transcription Slippage occurring in a coding region is expected to be disadvantageous. This probably leads to selection against most Slippage-prone sequences in coding regions. Results To find a length at which such selection is evident, we analyzed the distribution of repetitive runs of A and T of different lengths in 108 bacterial genomes. This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine nucleotides. Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional Slippage-prone sequences used for gene expression. Conclusions IS element genes are the largest group found to exploit this phenomenon. A number of genes with disrupted open reading frames (ORFs) have Slippage-prone sequences at which transcriptional Slippage would result in uninterrupted ORF restoration at the mRNA level. The ability of such genes to encode functional full-length protein products brings into question their annotation as pseudogenes and in these cases is pertinent to the significance of the term 'authentic frameshift' frequently assigned to such genes.
Rimvydas Milašius - One of the best experts on this subject based on the ideXlab platform.
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Influence of Fabric Structure Parameters on Seam Slippage
Fibres & Textiles in Eastern Europe, 2012Co-Authors: E. Malciauskiene, A. Milasius, Rimvydas MilašiusAbstract:*JSC „Drobė co“, Draugystės str. 14, LT-51259, Kaunas, Lithuania Abstract The Slippage resistance of yarns at the seam in woven fabrics is a very important factor and very strict claims are made with respect to this property. It is necessary to know how the fabric structure influences seam Slippage quality before manufacturing a fabric. The purpose of this work was to establish which of the fabric structure parameters influence seam Slippage. Our previous work investigated the influence of weave on the seam Slippage characteristics of a fabric, and a new weave factor was proposed which best characterises the weave from the thread Slippage point of view. It was found that the seam Slippage influences not only the weave factor in the slip direction but also in the normal direction. In the paper, by means of the design of experiments, the influence of weave, warp density and weft density on seam Slippage was investigated. It was found that the warp density has a very low influence on seam Slippage characteristics. Only the weft density and weave influence seam Slippage.
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Influence of Weave into Slippage of Yarns in Woven Fabric
Materials Science, 2011Co-Authors: Edita Malčiauskienė, A. Milasius, Ginta Laureckienė, Rimvydas MilašiusAbstract:Slippage resistance of yarns at a seam in woven fabrics is a very important factor and very strict claims are raised for this property. It is necessary to know how fabric structure influences on seam Slippage quality before manufacturing the fabric. The purpose of this work was to establish which of the weave factor is most suitable to describe balanced weave fabrics seam Slippage. It was investigated seam Slippage characteristics in the fabric and the factor was offered, which characterizes best fabric structure from the thread Slippage point of view. Fifteen wool fabrics, which differ only on weave were weaved for investigations. The test was carried out according to LST EN ISO 13936-1standard. First of all, the well known factors such as fabric structure factor P and average float F were investigated and then a new fabric structure factor was offered, which the best characterizes the weave from thread Slippage point of view. The proposed model shows good correlation between experimental and theoretical values of the new weave factor. http://dx.doi.org/10.5755/j01.ms.17.1.248
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Weave Factor for Seam Slippage Prediction of Unbalance Fabrics
Fibres & Textiles in Eastern Europe, 2011Co-Authors: E. Malciauskiene, A. Milasius, Rimvydas MilašiusAbstract:*JSC „Drobė Co“, Draugystės str. 14, LT-51259, Kaunas, Lithuania Abstract In this article the seam Slippage characteristics of unbalanced weave fabrics are analysed. The Slippage resistance of yarns at a seam in woven fabrics is a very important factor, and strong claims have been made about this property. Preliminary investigations showed that balanced and unbalanced woven fabrics must be estimated differently. Well-known factors such as the fabric structure factor P and average float F were investigated, and then a new fabric structure factor, NPR, was proposed, which best characterises the weave from a thread Slippage point of view. According to the coefficient of determination, it was found that the power equation of the new weave factor for balanced fabrics shows good correlation between experimental and theoretical values. It was proved that seam Slippage influences not only the weave factor in the slip direction but also in the normal direction. The weave factor in the slip direction influences seam Slippage by 81%, the weave factor in opposite direction – 19%. However, this new model is unsuitable for describing warp and weft ribs from a thread Slippage point of view because they comprise a separate group of weaves, with particular theories applying to them.
Mikhail Kashlev - One of the best experts on this subject based on the ideXlab platform.
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productive mrna stem loop mediated transcriptional Slippage crucial features in common with intrinsic terminators
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Christophe Penno, Virag Sharma, Arthur Coakley, Mary Oconnell Motherway, Douwe Van Sinderen, Lucyna Lubkowska, Maria L Kireeva, Mikhail Kashlev, Pavel V Baranov, John F AtkinsAbstract:Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional Slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the Slippage site, the length and composition of the Slippage site motif, and the identity of its 3′ adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this Slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the Slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the Slippage sequence and the 3′ nt context. The only previous proposal of stem loop mediated Slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical Slippage model involving the RNAP translocation state as the main motor in Slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription Slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
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isolation and characterization of rna polymerase rpob mutations that alter transcription Slippage during elongation in escherichia coli
Journal of Biological Chemistry, 2013Co-Authors: Yan Ning Zhou, Lucyna Lubkowska, Carolyn Court, Shuo Chen, Donald L Court, Jeffrey N Strathern, Mikhail KashlevAbstract:Transcription fidelity is critical for maintaining the accurate flow of genetic information. The study of transcription fidelity has been limited because the intrinsic error rate of transcription is obscured by the higher error rate of translation, making identification of phenotypes associated with transcription infidelity challenging. Slippage of elongating RNA polymerase (RNAP) on homopolymeric A/T tracts in DNA represents a special type of transcription error leading to disruption of open reading frames in Escherichia coli mRNA. However, the regions in RNAP involved in elongation Slippage and its molecular mechanism are unknown. We constructed an A/T tract that is out of frame relative to a downstream lacZ gene on the chromosome to examine transcriptional Slippage during elongation. Further, we developed a genetic system that enabled us for the first time to isolate and characterize E. coli RNAP mutants with altered transcriptional Slippage in vivo. We identified several amino acid residues in the β subunit of RNAP that affect Slippage in vivo and in vitro. Interestingly, these highly clustered residues are located near the RNA strand of the RNA-DNA hybrid in the elongation complex. Our E. coli study complements an accompanying study of Slippage by yeast RNAP II and provides the basis for future studies on the mechanism of transcription fidelity.
Pavel V Baranov - One of the best experts on this subject based on the ideXlab platform.
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productive mrna stem loop mediated transcriptional Slippage crucial features in common with intrinsic terminators
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Christophe Penno, Virag Sharma, Arthur Coakley, Mary Oconnell Motherway, Douwe Van Sinderen, Lucyna Lubkowska, Maria L Kireeva, Mikhail Kashlev, Pavel V Baranov, John F AtkinsAbstract:Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional Slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the Slippage site, the length and composition of the Slippage site motif, and the identity of its 3′ adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this Slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the Slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the Slippage sequence and the 3′ nt context. The only previous proposal of stem loop mediated Slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical Slippage model involving the RNAP translocation state as the main motor in Slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription Slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.
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Transcriptional Slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression
Genome Biology, 2005Co-Authors: Pavel V Baranov, Andrew W Hammer, Jiadong Zhou, Raymond F Gesteland, John F AtkinsAbstract:Background Transcription Slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mRNAs. Individual mRNA molecules within this population differ in the number of nucleotides they contain that are not specified by the template. When transcriptional Slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein product. Except where the products of the resulting mRNAs have distinct functions, transcription Slippage occurring in a coding region is expected to be disadvantageous. This probably leads to selection against most Slippage-prone sequences in coding regions. Results To find a length at which such selection is evident, we analyzed the distribution of repetitive runs of A and T of different lengths in 108 bacterial genomes. This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine nucleotides. Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional Slippage-prone sequences used for gene expression. Conclusions IS element genes are the largest group found to exploit this phenomenon. A number of genes with disrupted open reading frames (ORFs) have Slippage-prone sequences at which transcriptional Slippage would result in uninterrupted ORF restoration at the mRNA level. The ability of such genes to encode functional full-length protein products brings into question their annotation as pseudogenes and in these cases is pertinent to the significance of the term 'authentic frameshift' frequently assigned to such genes.
