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1
Hope, Justin C., Lissette Delgado Cruzata, Amit Duvshani, Jun Mitsumoto, Mohamed Maftahi, and Greg A. Freyer. "Mus81-Eme1-Dependent and -Independent Crossovers Form in Mitotic Cells during Double-Strand Break Repair in Schizosaccharomyces pombe." Molecular and Cellular Biology 27, no. 10 (March 12, 2007): 3828–38. http://dx.doi.org/10.1128/mcb.01596-06.
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ABSTRACT During meiosis, double-strand breaks (DSBs) lead to crossovers, thought to arise from the resolution of double Holliday junctions (HJs) by an HJ resolvase. In Schizosaccharomyces pombe, meiotic crossovers are produced primarily through a mechanism requiring the Mus81-Eme1 endonuclease complex. Less is known about the processes that produces crossovers during the repair of DSBs in mitotic cells. We employed an inducible DSB system to determine the role of Rqh1-Top3 and Mus81-Eme1 in mitotic DSB repair and crossover formation in S. pombe. In agreement with the meiotic data, crossovers are suppressed in cells lacking Mus81-Eme1. And relative to the wild type, rqh1Δ cells show a fourfold increase in crossover frequency. This suppression of crossover formation by Rqh1 is dependent on its helicase activity. We found that the synthetic lethality of cells lacking both Rqh1 and Eme1 is suppressed by loss of swi5 +, which allowed us to show that the excess crossovers formed in an rqh1Δ background are independent of Mus81-Eme1. This result suggests that a second process for crossover formation exists in S. pombe and is consistent with our finding that deletion of swi5 + restored meiotic crossovers in eme1Δ cells. Evidence suggesting that Rqh1 also acts downstream of Swi5 in crossover formation was uncovered in these studies. Our results suggest that during Rhp51-dependent repair of DSBs, Rqh1-Top3 suppresses crossovers in the Rhp57-dependent pathway while Mus81-Eme1 and possibly Rqh1 promote crossovers in the Swi5-dependent pathway.
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Meneely, Philip M., Anna F. Farago, and Tate M. Kauffman. "Crossover Distribution and High Interference for Both the X Chromosome and an Autosome During Oogenesis and Spermatogenesis in Caenorhabditis elegans." Genetics 162, no. 3 (November 1, 2002): 1169–77. http://dx.doi.org/10.1093/genetics/162.3.1169.
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Abstract Regulation of both the number and the location of crossovers during meiosis is important for normal chromosome segregation. We used sequence-tagged site polymorphisms to examine the distribution of all crossovers on the X chromosome during oogenesis and on one autosome during both oogenesis and spermatogenesis in Caenorhabditis elegans. The X chromosome has essentially one crossover during oogenesis, with only three possible double crossover exceptions among 220 recombinant X chromosomes. All three had one of the two crossovers in the same chromosomal interval, suggesting that crossovers in that interval do not cause interference. No other interval was associated with double crossovers. Very high interference was also found on an autosome during oogenesis, implying that each chromosome has only one crossover during oogenesis. During spermatogenesis, recombination on this autosome was reduced by ∼30% compared to oogenesis, but the relative distribution of the residual crossovers was only slightly different. In contrast to previous results with other autosomes, no double crossover chromosomes were observed. Despite an increased frequency of nonrecombinant chromosomes, segregation of a nonrecombinant autosome during spermatogenesis appears to occur normally. This indicates that an achiasmate segregation system helps to ensure faithful disjunction of autosomes during spermatogenesis.
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Halldorsson, Bjarni V., Gunnar Palsson, Olafur A. Stefansson, Hakon Jonsson, Marteinn T. Hardarson, Hannes P. Eggertsson, Bjarni Gunnarsson, et al. "Characterizing mutagenic effects of recombination through a sequence-level genetic map." Science 363, no. 6425 (January 24, 2019): eaau1043. http://dx.doi.org/10.1126/science.aau1043.
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Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.
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Pender, Brendan, Graham Currie, Alexa Delbosc, and Yibing Wang. "Proactive Recovery from Rail Disruptions through Provision of Track Crossovers and Bus Bridging." Transportation Research Record: Journal of the Transportation Research Board 2275, no. 1 (January 2012): 68–76. http://dx.doi.org/10.3141/2275-08.
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This paper explores the importance of providing track crossovers in addressing the issue of replacement bus services in response to unplanned rail service disruptions by using a case study in Melbourne, Australia. Crossovers determine the point from which rail replacement bus services can operate and thus are critical in determining the scale, costs, and benefits of rail disruption management. Despite research evidence that provision for crossovers is important in managing rail disruption, the research literature gives little guidance concerning how it can be achieved and what the relative costs and benefits of providing crossovers are. Theoretical modeling evaluated passenger and operator impacts of alternative crossover plans for a case study of unplanned service disruptions on a suburban rail line in Melbourne. Results showed that an additional crossover reduced user rail disruption costs by 78% to 96%, while bus hire costs were reduced by 63% to 93%. Results suggested that only a few rail disruptions annually would make the provision of track crossovers financially viable on the basis of savings in rail replacement bus service costs. Research found that locating crossovers as close as possible to areas of major disruption provided the most benefits for users and operators. Sensitivity tests showed that even with significantly lower ridership and a lower frequency of disruption, the addition of crossovers was financially positive and generated substantial user benefits. All highlighted results are with respect to the one suburban rail line under analysis. Provision of additional track crossovers appears to be a highly positive means of reducing costs and improving services. However, research indicates that crossovers can cause disruption on some rail systems, and this factor needs to be considered in rail planning.
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Serra, Heïdi, Christophe Lambing, Catherine H. Griffin, Stephanie D. Topp, Divyashree C. Nageswaran, Charles J. Underwood, Piotr A. Ziolkowski, et al. "Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis." Proceedings of the National Academy of Sciences 115, no. 10 (February 20, 2018): 2437–42. http://dx.doi.org/10.1073/pnas.1713071115.
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During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100–200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene HEI10 and introduced mutations in the anticrossovers helicase genes RECQ4A and RECQ4B. As HEI10 and recq4a recq4b increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.
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van Kampen, Jacqueline. "Crossover restrictions, A-bar pronouns and discourse antecedents." Linguistics in the Netherlands 32 (December 11, 2015): 88–104. http://dx.doi.org/10.1075/avt.32.07kam.
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The difference between weak crossovers and weakest crossovers is usually derived from a distinction between quantifiers and non-quantifiers (Lasnik & Stowell 1991). In this paper I will derive crossover restrictions from a new example set, long movement constructions with Dutch A-bar pronouns. Besides question wh-pronouns and relative pronouns, the set of Dutch A-bar pronouns includes topic d-pronouns not available in English. I will argue that A-bar pronouns constitute a uniform set of quantifiers, be it quantifiers with a discourse antecedent. To explain the present analysis, I take Safir (2004) and Ruys (2004) as a starting point. A major difference between these approaches and my own is that my analysis will make a distinction between strong crossovers as binding failures versus weak and weakest crossovers as a matter of discourse dependency, whereas it is more usual to see a related explanation for strong and weak crossovers versus weakest crossovers.
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Sanchez, Aurore, Céline Adam, Felix Rauh, Yann Duroc, Lepakshi Ranjha, Bérangère Lombard, Xiaojing Mu, et al. "Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation." Proceedings of the National Academy of Sciences 117, no. 48 (November 16, 2020): 30577–88. http://dx.doi.org/10.1073/pnas.2013012117.
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Crossovers generated during the repair of programmed meiotic double-strand breaks must be tightly regulated to promote accurate homolog segregation without deleterious outcomes, such as aneuploidy. The Mlh1–Mlh3 (MutLγ) endonuclease complex is critical for crossover resolution, which involves mechanistically unclear interplay between MutLγ and Exo1 and polo kinase Cdc5. Using budding yeast to gain temporal and genetic traction on crossover regulation, we find that MutLγ constitutively interacts with Exo1. Upon commitment to crossover repair, MutLγ–Exo1 associate with recombination intermediates, followed by direct Cdc5 recruitment that triggers MutLγ crossover activity. We propose that Exo1 serves as a central coordinator in this molecular interplay, providing a defined order of interaction that prevents deleterious, premature activation of crossovers. MutLγ associates at a lower frequency near centromeres, indicating that spatial regulation across chromosomal regions reduces risky crossover events. Our data elucidate the temporal and spatial control surrounding a constitutive, potentially harmful, nuclease. We also reveal a critical, noncatalytic role for Exo1, through noncanonical interaction with polo kinase. These mechanisms regulating meiotic crossovers may be conserved across species.
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Zhu, Longfei, Nadia Fernández-Jiménez, Maja Szymanska-Lejman, Alexandre Pelé, Charles J. Underwood, Heïdi Serra, Christophe Lambing, et al. "Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis." Proceedings of the National Academy of Sciences 118, no. 33 (August 12, 2021): e2021970118. http://dx.doi.org/10.1073/pnas.2021970118.
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The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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Baioletti, Marco, Gabriele Di Bari, Alfredo Milani, and Valentino Santucci. "An Experimental Comparison of Algebraic Crossover Operators for Permutation Problems." Fundamenta Informaticae 174, no. 3-4 (September 28, 2020): 201–28. http://dx.doi.org/10.3233/fi-2020-1940.
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Crossover operators are very important components in Evolutionary Computation. Here we are interested in crossovers for the permutation representation that find applications in combinatorial optimization problems such as the permutation flowshop scheduling and the traveling salesman problem. We introduce three families of permutation crossovers based on algebraic properties of the permutation space. In particular, we exploit the group and lattice structures of the space. A total of 34 new crossovers is provided. Algebraic and semantic properties of the operators are discussed, while their performances are investigated by experimentally comparing them with known permutation crossovers on standard benchmarks from four popular permutation problems. Three different experimental scenarios are considered and the results clearly validate our proposals.
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Moraglio, Alberto, Yong-Hyuk Kim, Yourim Yoon, and Byung-Ro Moon. "Geometric Crossovers for Multiway Graph Partitioning." Evolutionary Computation 15, no. 4 (December 2007): 445–74. http://dx.doi.org/10.1162/evco.2007.15.4.445.
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Geometric crossover is a representation-independent generalization of the traditional crossover defined using the distance of the solution space. By choosing a distance firmly rooted in the syntax of the solution representation as a basis for geometric crossover, one can design new crossovers for any representation. Using a distance tailored to the problem at hand, the formal definition of geometric crossover allows us to design new problem-specific crossovers that embed problem-knowledge in the search. The standard encoding for multiway graph partitioning is highly redundant: each solution has a number of representations, one for each way of labeling the represented partition. Traditional crossover does not perform well on redundant encodings. We propose a new geometric crossover for graph partitioning based on a labeling-independent distance that filters out the redundancy of the encoding. A correlation analysis of the fitness landscape based on this distance shows that it is well suited to graph partitioning. A second difficulty with designing a crossover for multiway graph partitioning is that of feasibility: in general recombining feasible partitions does not lead to feasible offspring partitions. We design a new geometric crossover for permutations with repetitions that naturally suits partition problems and we test it on the graph partitioning problem. We then combine it with the labeling-independent crossover and obtain a much superior geometric crossover inheriting both advantages.
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Lambing, Christophe, Pallas C. Kuo, Andrew J. Tock, Stephanie D. Topp, and Ian R. Henderson. "ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference inArabidopsis." Proceedings of the National Academy of Sciences 117, no. 24 (June 4, 2020): 13647–58. http://dx.doi.org/10.1073/pnas.1921055117.
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During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8–cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8–cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly,asy1/+heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases inasy1/+occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal inasy1/+, it is undetectable inasy1mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.
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Franklin, F. C. H., J. D. Higgins, E. Sanchez-Moran, S. J. Armstrong, K. E. Osman, N. Jackson, and G. H. Jones. "Control of meiotic recombination in Arabidopsis: role of the MutL and MutS homologues." Biochemical Society Transactions 34, no. 4 (July 21, 2006): 542–44. http://dx.doi.org/10.1042/bst0340542.
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Immunocytochemistry reveals that the Arabidopsis mismatch repair proteins AtMSH4, AtMLH3 and AtMLH1 are expressed during prophase I of meiosis. Expression of AtMSH4 precedes AtMLH3 and AtMLH1 which co-localize as foci during pachytene. Co-localization between AtMSH4 and AtMLH3 occurs, but appears transient. AtMLH3 foci are not detected in an Atmsh4 mutant. However, localization of AtMSH4 is unaffected in Atmlh3, suggesting that recombination may proceed to dHj (double Holliday junction) formation. Mean chiasma frequency in Atmsh4 is reduced to 1.55 compared with 9.86 in wild-type. In contrast with wild-type, the distribution of residual crossovers in Atmsh4 closely fits a Poisson distribution. This is consistent with a two-pathway model for meiotic crossing-over whereby most crossovers occur via an AtMSH4-dependent pathway that is subject to interference, with the remaining crossovers arising via an interference-independent pathway. Loss of AtMLH3 results in an approx. 60% reduction in crossovers. Results suggest that dHj resolution can occur, but in contrast with wild-type where most or all dHjs are directed to form crossovers, the outcome is biased in favour of a non-crossover outcome. The results are compatible with a model whereby the MutL complex maintains or imposes a dHj conformation that ensures crossover formation.
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Otto, Sarah P., and Bret A. Payseur. "Crossover Interference: Shedding Light on the Evolution of Recombination." Annual Review of Genetics 53, no. 1 (December 3, 2019): 19–44. http://dx.doi.org/10.1146/annurev-genet-040119-093957.
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Through recombination, genes are freed to evolve more independently of one another, unleashing genetic variance hidden in the linkage disequilibrium that accumulates through selection combined with drift. Yet crossover numbers are evolutionarily constrained, with at least one and not many more than one crossover per bivalent in most taxa. Crossover interference, whereby a crossover reduces the probability of a neighboring crossover, contributes to this homogeneity. The mechanisms by which interference is achieved and crossovers are regulated are a major current subject of inquiry, facilitated by novel methods to visualize crossovers and to pinpoint recombination events. Here, we review patterns of crossover interference and the models built to describe this process. We then discuss the selective forces that have likely shaped interference and the regulation of crossover numbers.
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Hinch, Anjali Gupta, Gang Zhang, Philipp W. Becker, Daniela Moralli, Robert Hinch, Benjamin Davies, Rory Bowden, and Peter Donnelly. "Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm." Science 363, no. 6433 (March 21, 2019): eaau8861. http://dx.doi.org/10.1126/science.aau8861.
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Recombination is critical to meiosis and evolution, yet many aspects of the physical exchange of DNA via crossovers remain poorly understood. We report an approach for single-cell whole-genome DNA sequencing by which we sequenced 217 individual hybrid mouse sperm, providing a kilobase-resolution genome-wide map of crossovers. Combining this map with molecular assays measuring stages of recombination, we identified factors that affect crossover probability, including PRDM9 binding on the non-initiating template homolog and telomere proximity. These factors also influence the time for sites of recombination-initiating DNA double-strand breaks to find and engage their homologs, with rapidly engaging sites more likely to form crossovers. We show that chromatin environment on the template homolog affects positioning of crossover breakpoints. Our results also offer insights into recombination in the pseudoautosomal region.
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Auger, Donald L., and William F. Sheridan. "Negative Crossover Interference in Maize Translocation Heterozygotes." Genetics 159, no. 4 (December 1, 2001): 1717–26. http://dx.doi.org/10.1093/genetics/159.4.1717.
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Abstract Negative interference describes a situation where two genetic regions have more double crossovers than would be expected considering the crossover rate of each region. We detected negative crossover interference while attempting to genetically map translocation breakpoints in maize. In an attempt to find precedent examples we determined there was negative interference among previously published translocation breakpoint mapping data in maize. It appears that negative interference was greater when the combined map length of the adjacent regions was smaller. Even positive interference appears to have been reduced when the combined lengths of adjacent regions were below 40 cM. Both phenomena can be explained by a reduction in crossovers near the breakpoints or, more specifically, by a failure of regions near breakpoints to become competent for crossovers. A mathematical explanation is provided.
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Jinks-Robertson, Sue, Shariq Sayeed, and Tamara Murphy. "Meiotic Crossing Over Between Nonhomologous Chromosomes Affects Chromosome Segregation in Yeast." Genetics 146, no. 1 (May 1, 1997): 69–78. http://dx.doi.org/10.1093/genetics/146.1.69.
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Meiotic recombination between artificial repeats positioned on nonhomologous chromosomes occurs efficiently in the yeast Saccharomyces cerevisiae. Both gene conversion and crossover eventS have been observed, with crossovers yielding reciprocal translocations. In the current study, 5.5-kb ura3 repeats positioned on chromosomes V and XV were used to examine the effect of ectopic recombination on meiotic chromosome segregation. Ura+ random spores were selected and gene conversion vs. crossover events were distinguished by Southern blot analysis. Approximately 15% of the crossover events between chromosomes V and XV were associated with missegregation of one of these chromosomes. The missegregation was manifest as hyperploid spores containing either both translocations plus a normal chromosome, or both normal chromosomes plus one of the translocations. In those cases where it could be analyzed, missegregation occurred at the first meiotic division. These data are discussed in terms of a model in which ectopic crossovers compete efficiently with normal allelic crossovers in directing meiotic chromosome segregation.
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Parpia, Sameer, Jim A. Julian, Lehana Thabane, Chushu Gu, Timothy J. Whelan, and Mark N. Levine. "Treatment crossovers in time-to-event non-inferiority randomised trials of radiotherapy in patients with breast cancer." BMJ Open 4, no. 10 (October 2014): e006531. http://dx.doi.org/10.1136/bmjopen-2014-006531.
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BackgroundIn non-inferiority trials of radiotherapy in patients with early stage breast cancer, it is inevitable that some patients will cross over from the experimental arm to the standard arm prior to initiation of any treatment due to complexities in treatment planning or subject preference. Although the intention-to-treat (ITT) analysis is the preferred approach for superiority trials, its role in non-inferiority trials is still under debate. This has led to the use of alternative approaches such as the per-protocol (PP) analysis or the as-treated (AT) analysis, despite the inherent biases of such approaches.MethodsUsing simulations, we investigate the effect of 2%, 5% and 10% random and non-random crossovers prior to radiotherapy initiation on the ITT, PP, AT and the combination of ITT and PP analyses with respect to type I error in trials with time-to-event outcomes. We also evaluate bias and SE of the estimates from the ITT, PP and AT approaches.ResultsThe AT approach had the best performance in terms of type I error, but was anticonservative as non-random crossover increased. The ITT and PP approaches were anticonservative under all percentages of random and non-random crossover. Similarly, lowest bias was seen with the AT approach; however, bias increased as the percentage of non-random crossover increased. The ITT and PP had poor performance in terms of bias as crossovers increased.ConclusionsIf minimal crossovers were to occur, we have shown that the AT approach has the lowest type I error rates and smallest opportunity for bias. Results of trials with a high number of crossovers should be interpreted with caution, especially when crossover is non-random. Attempts to prevent crossovers should be maximised.
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Veller, Carl, Nancy Kleckner, and Martin A. Nowak. "A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel’s second law." Proceedings of the National Academy of Sciences 116, no. 5 (January 11, 2019): 1659–68. http://dx.doi.org/10.1073/pnas.1817482116.
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Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel’s second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter r¯ as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that r¯ is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of r¯ is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) r¯ in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.
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Lloyd, Andrew, and Eric Jenczewski. "Modelling Sex-Specific Crossover Patterning in Arabidopsis." Genetics 211, no. 3 (January 22, 2019): 847–59. http://dx.doi.org/10.1534/genetics.118.301838.
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“Interference” is a major force governing the patterning of meiotic crossovers. A leading model describing how interference influences crossover patterning is the beam-film model, a mechanical model based on the accumulation and redistribution of crossover-promoting “stress” along the chromosome axis. We use the beam-film model in conjunction with a large Arabidopsis reciprocal backcross data set to gain “mechanistic” insights into the differences between male and female meiosis, and crossover patterning. Beam-film modeling suggests that the underlying mechanics of crossover patterning and interference are identical in the two sexes, with the large difference in recombination rates and distributions able to be entirely explained by the shorter chromosome axes in females. The modeling supports previous indications that fewer crossovers occur via the class II pathway in female meiosis and that this could be explained by reduced DNA double-strand breaks in female meiosis, paralleling the observed reduction in synaptonemal complex length between the two sexes. We also demonstrate that changes in the strength of suppression of neighboring class I crossovers can have opposite effects on “effective” interference depending on the distance between two genetic intervals.
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Castronovo, Salvatore, Paul W. Dorothy, and Thomas L. Maleck. "Investigation of the Effectiveness of Boulevard Roadways." Transportation Research Record: Journal of the Transportation Research Board 1635, no. 1 (January 1998): 147–54. http://dx.doi.org/10.3141/1635-20.
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The state of Michigan has been constructing directional crossovers in the medians of boulevard roadways since the 1960s to alleviate the congestion and interlocking that were occurring at bidirectional crossover locations. The objective of this research is to investigate the safety benefits of divided roadway and directional crossover median designs. An investigation of the mean accident rates of roadways with boulevards compared to the mean accident rates of roadways with continuous center left-turn lanes revealed that there is a significant difference, with boulevard roadways having a lower mean accident rate for those Michigan roadways investigated. Investigation into the difference of the mean accident rates for boulevard roadways with medians of different widths indicated that roadways with medians greater than 9.15 m (30 ft) but less than 18.30 m (60 ft) had the lowest mean accident rate of the three median categories investigated. The difference was significant for most accident types when compared to roadways with medians less than or equal to 9.15 m (30 ft) and greater or equal to 18.30 m (60 ft). The investigation of the accident rates for boulevard roadways with directional and bidirectional signalized crossovers, while not conclusive, indicated that boulevard roadways with direction crossovers had a lower mean accident rate than boulevard roadways with bidirectional crossovers for signalized roadways.
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Satya Krishna, Idury, Rusan Kumar Barik, and S. S. Karthikeyan. "A dual-band crossover using cross-shaped microstrip line for small and large band ratios." International Journal of Microwave and Wireless Technologies 9, no. 8 (April 17, 2017): 1629–35. http://dx.doi.org/10.1017/s1759078717000290.
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A novel design of planar dual-band microstrip crossover operating at small and large frequency ratios is presented. These features of the proposed dual-band crossover are achieved by a cross-shaped transmission line. To obtain the dual-band characteristics, the required closed form design formulas are computed using the ABCD matrix method. Based on the design formulas, the realizable small and large band ratios are calculated as 1.65–2.14 and 4.1–8.76, respectively. To validate the computed band ratios, three examples of dual-band crossovers are presented. Finally, two prototypes of dual-band crossover working at smaller and larger frequency ratios are fabricated and tested. The fabricated dual-band crossovers exhibit good return loss and isolation of over 20 dB with minimal insertion loss.
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Whitby, M. C. "Making crossovers during meiosis." Biochemical Society Transactions 33, no. 6 (October 26, 2005): 1451–55. http://dx.doi.org/10.1042/bst0331451.
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Homologous recombination (HR) is required to promote both correct chromosome segregation and genetic variation during meiosis. For this to be successful recombination intermediates must be resolved to generate reciprocal exchanges or ‘crossovers’ between the homologous chromosomes (homologues) during the first meiotic division. Crossover recombination promotes faithful chromosome segregation by establishing connections (chiasmata) between the homologues, which help guide their proper bipolar alignment on the meiotic spindle. Recent studies of meiotic recombination in both the budding and fission yeasts have established that there are at least two pathways for generating crossovers. One pathway involves the resolution of fully ligated four-way DNA junctions [HJs (Holliday junctions)] by an as yet unidentified endonuclease. The second pathway appears to involve the cleavage of the precursors of ligated HJs, namely displacement (D) loops and unligated/nicked HJs, by the Mus81-Eme1/Mms4 endonuclease.
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Yue, Jianhai, Xiaojun Zhao, and Pengjian Shang. "Effect of Trends on Detrended Fluctuation Analysis of Precipitation Series." Mathematical Problems in Engineering 2010 (2010): 1–15. http://dx.doi.org/10.1155/2010/749894.
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We use detrended fluctuation analysis (DFA) method to detect the long-range correlation and scaling properties of daily precipitation series of Beijing from 1973 to 2004 before and after adding diverse trends to the original series. The correlation and scaling properties of the original series are difficult to analyze due to existing crossovers. The effects of the coefficient and the power of the added trends on the scaling exponents and crossovers of the series are tested. A crossover is found to be independent of the added trends, which arises from the intrinsic periodic trend of the precipitation series. However, another crossover caused by the multifractal vanishes with the increasing power of added trends.
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Kelly, Karen O., Abby F. Dernburg, Gillian M. Stanfield, and Anne M. Villeneuve. "Caenorhabditis elegans msh-5 Is Required for Both Normal and Radiation-Induced Meiotic Crossing Over but Not for Completion of Meiosis." Genetics 156, no. 2 (October 1, 2000): 617–30. http://dx.doi.org/10.1093/genetics/156.2.617.
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Abstract Crossing over and chiasma formation during Caenorhabditis elegans meiosis require msh-5, which encodes a conserved germline-specific MutS family member. msh-5 mutant oocytes lack chiasmata between homologous chromosomes, and crossover frequencies are severely reduced in both oocyte and spermatocyte meiosis. Artificially induced DNA breaks do not bypass the requirement for msh-5, suggesting that msh-5 functions after the initiation step of meiotic recombination. msh-5 mutants are apparently competent to repair breaks induced during meiosis, but accomplish repair in a way that does not lead to crossovers between homologs. These results combine with data from budding yeast to establish a conserved role for Msh5 proteins in promoting the crossover outcome of meiotic recombination events. Apart from the crossover deficit, progression through meiotic prophase is largely unperturbed in msh-5 mutants. Homologous chromosomes are fully aligned at the pachytene stage, and germ cells survive to complete meiosis and gametogenesis with high efficiency. Our demonstration that artificially induced breaks generate crossovers and chiasmata using the normal meiotic recombination machinery suggests (1) that association of breaks with a preinitiation complex is not a prerequisite for entering the meiotic recombination pathway and (2) that the decision for a subset of recombination events to become crossovers is made after the initiation step.
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Mitavskiy, Boris. "Crossover Invariant Subsets of the Search Space for Evolutionary Algorithms." Evolutionary Computation 12, no. 1 (March 2004): 19–46. http://dx.doi.org/10.1162/evco.2004.12.1.19.
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This paper addresses the relationship between schemata and crossover operators. In Appendix A a general mathematical framework is developed which reveals an interesting correspondence between the families of reproduction transformations and the corresponding collections of invariant subsets of the search space. On the basis of this mathematical apparatus it is proved that the family of masked crossovers is, for all practical purposes, the largest family of transformations whose corresponding collection of invariant subsets is the family of Antonisse's schemata. In the process, a number of other interesting facts are shown. It is proved that the full dynastic span of a given subset of the search space under either one of the traditional families of crossover transformations (one-point crossovers or masked crossovers) is obtained after [log2n] iterations where n is the dimension of the search space. The generalized notion of invariance introduced in the current paper unifies Radcliffe's notions of firespectfl and figene transmissionfl. Besides providing basic tools for the theoretical analysis carried out in the current paper, the general facts established in Appendix A provide a way to extend Radcliffe's notion of figenetic representation functionfl to compare various evolutionary computation techniques via their representation.
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Cherry, Todd L., and Jason F. Shogren. "Rationality crossovers." Journal of Economic Psychology 28, no. 2 (April 2007): 261–77. http://dx.doi.org/10.1016/j.joep.2006.12.002.
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Zalevsky, Jonathan, Amy J. MacQueen, Joseph B. Duffy, Kenneth J. Kemphues, and Anne M. Villeneuve. "Crossing Over During Caenorhabditis elegans Meiosis Requires a Conserved MutS-Based Pathway That Is Partially Dispensable in Budding Yeast." Genetics 153, no. 3 (November 1, 1999): 1271–83. http://dx.doi.org/10.1093/genetics/153.3.1271.
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Abstract Formation of crossovers between homologous chromosomes during Caenorhabditis elegans meiosis requires the him-14 gene. Loss of him-14 function severely reduces crossing over, resulting in lack of chiasmata between homologs and consequent missegregation. Cytological analysis showing that homologs are paired and aligned in him-14 pachytene nuclei, together with temperature-shift experiments showing that him-14 functions during the pachytene stage, indicate that him-14 is not needed to establish pairing or synapsis and likely has a more direct role in crossover formation. him-14 encodes a germline-specific member of the MutS family of DNA mismatch repair (MMR) proteins. him-14 has no apparent role in MMR, but like its Saccharomyces cerevisiae ortholog MSH4, has a specialized role in promoting crossing over during meiosis. Despite this conservation, worms and yeast differ significantly in their reliance on this pathway: whereas worms use this pathway to generate most, if not all, crossovers, yeast still form 30–50% of their normal number of crossovers when this pathway is absent. This differential reliance may reflect differential stability of crossover-competent recombination intermediates, or alternatively, the presence of two different pathways for crossover formation in yeast, only one of which predominates during nematode meiosis. We discuss a model in which HIM-14 promotes crossing over by interfering with Holliday junction branch migration.
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Fernandes, Joiselle Blanche, Mathilde Séguéla-Arnaud, Cécile Larchevêque, Andrew H. Lloyd, and Raphael Mercier. "Unleashing meiotic crossovers in hybrid plants." Proceedings of the National Academy of Sciences 115, no. 10 (November 28, 2017): 2431–36. http://dx.doi.org/10.1073/pnas.1713078114.
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Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana that rely on the activity of FANCM [Crismani W, et al. (2012) Science 336:1588–1590], RECQ4 [Séguéla-Arnaud M, et al. (2015) Proc Natl Acad Sci USA 112:4713–4718], and FIGL1 [Girard C, et al. (2015) PLoS Genet 11:e1005369]. Here we analyzed recombination in plants in which one, two, or all three of these pathways were disrupted in both pure line and hybrid contexts. The greatest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3,037 cM. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways did not further increase recombination, suggesting that some upper limit had been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, although in wild type recombination is much higher in male meiosis than in female meiosis (490 cM vs. 290 cM), female recombination is higher than male recombination in recq4 figl1 (3,200 cM vs. 2,720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase in recombination observed in recq4 figl1 hybrids opens the possibility of manipulating recombination to enhance plant breeding efficiency.
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Santos, Teresa de los, Neil Hunter, Cindy Lee, Brittany Larkin, Josef Loidl, and Nancy M. Hollingsworth. "The Mus81/Mms4 Endonuclease Acts Independently of Double-Holliday Junction Resolution to Promote a Distinct Subset of Crossovers During Meiosis in Budding Yeast." Genetics 164, no. 1 (May 1, 2003): 81–94. http://dx.doi.org/10.1093/genetics/164.1.81.
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Abstract Current models for meiotic recombination require that crossovers derive from the resolution of a double-Holliday junction (dHJ) intermediate. In prokaryotes, enzymes responsible for HJ resolution are well characterized but the identification of a eukaryotic nuclear HJ resolvase has been elusive. Indirect evidence suggests that MUS81 from humans and fission yeast encodes a HJ resolvase. We provide three lines of evidence that Mus81/Mms4 is not the major meiotic HJ resolvase in S. cerevisiae: (1) MUS81/MMS4 is required to form only a distinct subset of crossovers; (2) rather than accumulating, dHJ intermediates are reduced in an mms4 mutant; and (3) expression of a bacterial HJ resolvase has no suppressive effect on mus81 meiotic phenotypes. Our analysis also reveals the existence of two distinct classes of crossovers in budding yeast. Class I is dependent upon MSH4/MSH5 and exhibits crossover interference, while class II is dependent upon MUS81/MMS4 and exhibits no interference. mms4 specifically reduces crossing over on small chromosomes, which are known to undergo less interference. The correlation between recombination rate and degree of interference to chromosome size may therefore be achieved by modulating the balance between class I/class II crossovers.
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MUÑOZ-DIOSDADO, A., L. GUZMÁN-VARGAS, A. RAMÍREZ-ROJAS, J. L. DEL RÍO-CORREA, and F. ANGULO-BROWN. "SOME CASES OF CROSSOVER BEHAVIOR IN HEART INTERBEAT AND ELECTROSEISMIC TIME SERIES." Fractals 13, no. 04 (December 2005): 253–63. http://dx.doi.org/10.1142/s0218348x05002970.
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Fractal time series with scaling properties expressed through power laws appear in many contexts. These properties are very important from several viewpoints. For instance, they reveal the nature of the correlations present in the fractal signals. It is common that the scaling properties characterized by means of invariant quantities suffer changes along with the dynamical evolution of the studied systems. One of these changes is a crossover in the scaling properties reflecting an important change in the system dynamical behavior. In this article, we present two cases of crossover behavior corresponding to interbeat and electroseismic time series, we observe the crossovers in time series of experimental data and their corresponding simulation with simple models. We suggest a possible explanation of the observed crossovers in terms of the models considered.
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Tock, Andrew J., Daniel M. Holland, Wei Jiang, Kim Osman, Eugenio Sanchez-Moran, James D. Higgins, Keith J. Edwards, Cristobal Uauy, F. Chris H. Franklin, and Ian R. Henderson. "Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation." Genome Research 31, no. 9 (August 23, 2021): 1614–28. http://dx.doi.org/10.1101/gr.273672.120.
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The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.
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Lo, Yi-Chen, Kimberly S. Paffett, Or Amit, Jennifer A. Clikeman, Rosa Sterk, Mark A. Brenneman, and Jac A. Nickoloff. "Sgs1 Regulates Gene Conversion Tract Lengths and Crossovers Independently of Its Helicase Activity." Molecular and Cellular Biology 26, no. 11 (June 1, 2006): 4086–94. http://dx.doi.org/10.1128/mcb.00136-06.
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ABSTRACT RecQ helicases maintain genome stability and suppress tumors in higher eukaryotes through roles in replication and DNA repair. The yeast RecQ homolog Sgs1 interacts with Top3 topoisomerase and Rmi1. In vitro, Sgs1 binds to and branch migrates Holliday junctions (HJs) and the human RecQ homolog BLM, with Top3α, resolves synthetic double HJs in a noncrossover sense. Sgs1 suppresses crossovers during the homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Crossovers are associated with long gene conversion tracts, suggesting a model in which Sgs1 helicase catalyzes reverse branch migration and convergence of double HJs for noncrossover resolution by Top3. Consistent with this model, we show that allelic crossovers and gene conversion tract lengths are increased in sgs1Δ. However, crossover and tract length suppression was independent of Sgs1 helicase activity, which argues against helicase-dependent HJ convergence. HJs may converge passively by a “random walk,” and Sgs1 may play a structural role in stimulating Top3-dependent resolution. In addition to the new helicase-independent functions for Sgs1 in crossover and tract length control, we define three new helicase-dependent functions, including the suppression of chromosome loss, chromosome missegregation, and synthetic lethality in srs2Δ. We propose that Sgs1 has helicase-dependent functions in replication and helicase-independent functions in DSB repair by HR.
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Copenhaver, G. P., E. A. Housworth, and F. W. Stahl. "Crossover Interference in Arabidopsis." Genetics 160, no. 4 (April 1, 2002): 1631–39. http://dx.doi.org/10.1093/genetics/160.4.1631.
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AbstractThe crossover distribution in meiotic tetrads of Arabidopsis thaliana differs from those previously described for Drosophila and Neurospora. Whereas a chi-square distribution with an even number of degrees of freedom provides a good fit for the latter organisms, the fit for Arabidopsis was substantially improved by assuming an additional set of crossovers sprinkled, at random, among those distributed as per chi square. This result is compatible with the view that Arabidopsis has two pathways for meiotic crossing over, only one of which is subject to interference. The results further suggest that Arabidopsis meiosis has >10 times as many double-strand breaks as crossovers.
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Nabeshima, Kentaro, Anne M. Villeneuve, and Monica P. Colaiácovo. "Crossing over is coupled to late meiotic prophase bivalent differentiation through asymmetric disassembly of the SC." Journal of Cell Biology 168, no. 5 (February 28, 2005): 683–89. http://dx.doi.org/10.1083/jcb.200410144.
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Homologous chromosome pairs (bivalents) undergo restructuring during meiotic prophase to convert a configuration that promotes crossover recombination into one that promotes bipolar spindle attachment and localized cohesion loss. We have imaged remodeling of meiotic chromosome structures after pachytene exit in Caenorhabditis elegans. Chromosome shortening during diplonema is accompanied by coiling of chromosome axes and highly asymmetric departure of synaptonemal complex (SC) central region proteins SYP-1 and SYP-2, which diminish over most of the length of each desynapsing bivalent while becoming concentrated on axis segments distal to the single emerging chiasma. This and other manifestations of asymmetry along chromosomes are lost in synapsis-proficient crossover-defective mutants, which often retain SYP-1,2 along the full lengths of coiled diplotene axes. Moreover, a γ-irradiation treatment that restores crossovers in the spo-11 mutant also restores asymmetry of SYP-1 localization. We propose that crossovers or crossover precursors serve as symmetry-breaking events that promote differentiation of subregions of the bivalent by triggering asymmetric disassembly of the SC.
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Liu, Haoxuan, Calum J. Maclean, and Jianzhi Zhang. "Evolution of the Yeast Recombination Landscape." Molecular Biology and Evolution 36, no. 2 (December 7, 2018): 412–22. http://dx.doi.org/10.1093/molbev/msy233.
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Abstract Meiotic recombination comprises crossovers and noncrossovers. Recombination, crossover in particular, shuffles mutations and impacts both the level of genetic polymorphism and the speed of adaptation. In many species, the recombination rate varies across the genome with hot and cold spots. The hotspot paradox hypothesis asserts that recombination hotspots are evolutionarily unstable due to self-destruction. However, the genomic landscape of double-strand breaks (DSBs), which initiate recombination, is evolutionarily conserved among divergent yeast species, casting doubt on the hotspot paradox hypothesis. Nonetheless, because only a subset of DSBs are associated with crossovers, the evolutionary conservation of the crossover landscape could differ from that of DSBs. Here, we investigate this possibility by generating a high-resolution recombination map of the budding yeast Saccharomyces paradoxus through whole-genome sequencing of 50 meiotic tetrads and by comparing this recombination map with that of S. cerevisiae. We observe a 40% lower recombination rate in S. paradoxus than in S. cerevisiae. Compared with the DSB landscape, the crossover landscape is even more conserved. Further analyses indicate that the elevated conservation of the crossover landscape is explained by a near-subtelomeric crossover preference in both yeasts, which we find to be attributable at least in part to crossover interference. We conclude that the yeast crossover landscape is highly conserved and that the evolutionary conservation of this landscape can differ from that of the DSB landscape.
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Berns, Roy S., and Rolf G. Kuehni. "What determines crossover wavelengths of metameric pairs with three crossovers?" Color Research & Application 15, no. 1 (February 1990): 23–28. http://dx.doi.org/10.1002/col.5080150107.
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Neuwirth, Efrem A. H., Masamitsu Honma, and Andrew J. Grosovsky. "Interchromosomal Crossover in Human Cells Is Associated with Long Gene Conversion Tracts." Molecular and Cellular Biology 27, no. 15 (May 21, 2007): 5261–74. http://dx.doi.org/10.1128/mcb.01852-06.
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ABSTRACT Crossovers have rarely been observed in specific association with interchromosomal gene conversion in mammalian cells. In this investigation two isogenic human B-lymphoblastoid cell lines, TI-112 and TSCER2, were used to select for I-SceI-induced gene conversions that restored function at the selectable thymidine kinase locus. Additionally, a haplotype linkage analysis methodology enabled the rigorous detection of all crossover-associated convertants, whether or not they exhibited loss of heterozygosity. This methodology also permitted characterization of conversion tract length and structure. In TI-112, gene conversion tracts were required to be complex in tract structure and at least 7.0 kb in order to be selectable. The results demonstrated that 85% (39/46) of TI-112 convertants extended more than 11.2 kb and 48% also exhibited a crossover, suggesting a mechanistic link between long tracts and crossover. In contrast, continuous tracts as short as 98 bp are selectable in TSCER2, although selectable gene conversion tracts could include a wide range of lengths. Indeed, only 16% (14/95) of TSCER2 convertants were crossover associated, further suggesting a link between long tracts and crossover. Overall, these results demonstrate that gene conversion tracts can be long in human cells and that crossovers are observable when long tracts are recoverable.
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Urbanowicz, Anna, Magdalena Alejska, Piotr Formanowicz, Jacek Błażewicz, Marek Figlerowicz, and Jozef J. Bujarski. "Homologous Crossovers among Molecules of Brome Mosaic Bromovirus RNA1 or RNA2 Segments In Vivo." Journal of Virology 79, no. 9 (May 1, 2005): 5732–42. http://dx.doi.org/10.1128/jvi.79.9.5732-5742.2005.
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ABSTRACT Previously we demonstrated frequent homologous crossovers among molecules of the RNA3 segment in the tripartite brome mosaic bromovirus (BMV) RNA genome (A. Bruyere, M. Wantroba, S. Flasinski, A. Dzianott, and J. J. Bujarski, J. Virol. 74:4214-4219, 2000). To further our knowledge about mechanisms of viral RNA genome variability, in this paper we have studied homologous recombination in BMV RNA1 and RNA2 components during infection. We have found that basal RNA-RNA crossovers could occur within coding regions of both RNAs, although recombination frequencies slightly varied at different RNA sections. In all cases, the frequencies were much lower than the rate observed for the intercistronic recombination hot spot in BMV RNA3. Probability calculations accounted for at least one homologous crossover per RNA molecule per replication cycle. In addition, we have demonstrated an efficient repair of mutations within the conserved 3′ and 5′ noncoding regions, most likely due to error-prone BMV RNA replication. Overall, our data verify that homologous crossovers are common events a during virus life cycle, and we discuss their importance for viral RNA genetics.
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Riezebos, Jan. "Inventory order crossovers." International Journal of Production Economics 104, no. 2 (December 2006): 666–75. http://dx.doi.org/10.1016/j.ijpe.2004.11.011.
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Batlogg, B., and V. J. Emery. "Crossovers in cuprates." Nature 382, no. 6586 (July 1996): 20–21. http://dx.doi.org/10.1038/382020a0.
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Devadoss, R., K. Paul, and M. Balakrishnan. "Coplanar QCA crossovers." Electronics Letters 45, no. 24 (2009): 1234. http://dx.doi.org/10.1049/el.2009.2819.
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Zahn, L. M. "Crossovers and Cancer." Science 338, no. 6114 (December 20, 2012): 1513. http://dx.doi.org/10.1126/science.338.6114.1513-b.
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Hassold, Terry, and Patricia Hunt. "Rescuing distal crossovers." Nature Genetics 39, no. 10 (October 2007): 1187–88. http://dx.doi.org/10.1038/ng1007-1187.
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Kim, Hye Young, and Ji Soo Ha. "Korean fashion crossovers." International Journal of Fashion Design, Technology and Education 3, no. 1 (March 2010): 33–41. http://dx.doi.org/10.1080/17543261003641855.
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Metzenberg, A. B., G. Wurzer, T. H. Huisman, and O. Smithies. "Homology requirements for unequal crossing over in humans." Genetics 128, no. 1 (May 1, 1991): 143–61. http://dx.doi.org/10.1093/genetics/128.1.143.
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Abstract To gain insight into mechanisms of unequal homologous recombination in vivo, genes generated by homologous unequal crossovers in the human beta-globin gene cluster were examined by nucleotide sequencing and hybridization experiments. The naturally occurring genes studied included one delta-beta Lepore-Baltimore fusion gene, one delta-beta Lepore-Hollandia fusion gene, 12 delta-beta Lepore-Boston genes, one A gamma-beta fusion Kenya gene, one A gamma-G gamma fusion (the central gene of a triplication) and one G gamma-A gamma fusion. A comparison of the nucleotide sequences of three Lepore-Boston genes indicates that they were derived from at least two independent homologous but unequal crossover events, although the crossovers occurred within the same 58-bp region. Nine additional Lepore-Boston genes from individuals of various ethnic origins were shown, by hybridization to specific oligonucleotide probes, to have been generated by a crossover in the same region as the sequenced genes. Evidence for gene conversion accompanying a homologous unequal crossover event was found in only one case (although some of the single nucleotide differences observed in other genes in this study may be related to the crossover events in ways that we do not presently understand). Thus, as judged by this limited sample, concurrent gene conversions are not commonly associated with homologous but unequal exchange in humans in vivo. Classification of the recombinant chromosomes by their polymorphic restriction sites in the beta-globin gene cluster indicated that the Lepore-Boston genes are found in at least six different haplotype backgrounds. Therefore the total number of independent examples in this study is at least 6, and at most 12. We have shown that in at least six cases of genes that have arisen by homologous but unequal crossing over in vivo, each event occurred in a relatively extensive region of uninterrupted identity between the parental genes. This preference cannot be explained by a mechanism whereby crossovers occur at random within misaligned related but not identical genes. In general, crossovers occur in regions that are among the largest available stretches of identity for a particular pair of mismatched genes. Our data are in agreement with those of other types of studies of homologous recombination, and support the idea that sequence identity, rather than general homology, is a critical factor in homologous recombination.
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Rattray, A. J., and L. S. Symington. "Use of a chromosomal inverted repeat to demonstrate that the RAD51 and RAD52 genes of Saccharomyces cerevisiae have different roles in mitotic recombination." Genetics 138, no. 3 (November 1, 1994): 587–95. http://dx.doi.org/10.1093/genetics/138.3.587.
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Abstract An intrachromosomal recombination assay that monitors events between alleles of the ade2 gene oriented as inverted repeats was developed. Recombination to adenine prototrophy occurred at a rate of 9.3 x 10(-5)/cell/generation. Of the total recombinants, 50% occurred by gene conversion without crossing over, 35% by crossover and 15% by crossover associated with conversion. The rate of recombination was reduced 3,000-fold in a rad52 mutant, but the distribution of residual recombination events remained similar to that seen in the wild type strain. In rad51 mutants the rate of recombination was reduced only 4-fold. In this case, gene conversion events unassociated with a crossover were reduced 18-fold, whereas crossover events were reduced only 2.5-fold. A rad51 rad52 double mutant strain showed the same reduction in the rate of recombination as the rad52 mutant, but the distribution of events resembled that seen in rad51. From these observations it is concluded that (i) RAD52 is required for high levels of both gene conversions and reciprocal crossovers, (ii) that RAD51 is not required for intrachromosomal crossovers, and (iii) that RAD51 and RAD52 have different functions, or that RAD52 has functions in addition to those of the Rad51/Rad52 protein complex.
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Lin, Yao Tang, and Jia Li Hou. "A Genetic Algorithm with Weight-Based Encoding for One-Dimensional Bin Packing Problem." Applied Mechanics and Materials 182-183 (June 2012): 2100–2104. http://dx.doi.org/10.4028/www.scientific.net/amm.182-183.2100.
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This paper proposes a specialized genetic algorithm (GA) based on an expended relational representation named weight-based encoding for solving one-dimensional bin packing problem (BPP-1). The encoding provides a totally constraint-handling scheme to address general and specific constraints, while naturally eliminates redundancy and infeasibility of previous representations for BPP-1. The current study performs experiments for solving some problem instances from a benchmark data set by our specific coded genetic algorithm with one-point, two-point and grouping crossovers. Experimental results show that the proposed methodology works well for solving BPP-1 and performs well on experimented benchmark instances. In addition, the results also show that two-point and grouping crossovers work better than one-point crossover in our experiments.
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Berlyn, M. B., and S. Letovsky. "COTRANS: a program for cotransduction analysis." Genetics 131, no. 1 (May 1, 1992): 235–41. http://dx.doi.org/10.1093/genetics/131.1.235.
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Abstract COTRANS is a program for analyzing cotransduction data. It calculates distances from pairwise cotransduction frequencies, computes crossovers required to obtain each observed recombinant class, and applies rules to draw conclusions about order. The rules are based on the correlation between the frequency of the classes and the number of required crossovers for each possible ordering compatible with the distance calculations. The procedure emulates a geneticist's stepwise analysis of the data by first calculating distances, then looking for obvious three-point ordering conclusions, and finally proceeding to a complete crossover analysis. It reports results from each step of the analysis and an overall conclusion. COTRANS provides significant gains in speed and convenience over hand analysis, particularly for multipoint crosses with several recombinant classes.
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Aguilera, A., and H. L. Klein. "Genetic and molecular analysis of recombination events in Saccharomyces cerevisiae occurring in the presence of the hyper-recombination mutation hpr1." Genetics 122, no. 3 (July 1, 1989): 503–17. http://dx.doi.org/10.1093/genetics/122.3.503.
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Abstract The hyper-recombination mutation hpr1 specifically increases mitotic intrachromatid crossovers, with no effect on other mitotic recombination events such as unequal sister chromatid exchange and plasmid-chromosome recombination, and no effect on meiotic recombination and a lesser effect on intrachromosomal gene conversion. The excision repair RAD1 gene is partially required for the expression on the hpr1 phenotype. The simplest hypothesis to account for some of the hpr1 stimulated recombination events is that a heteroduplex DNA intermediate and localized gene conversion are involved. hpr1 stimulated crossover events are independent of intrachromosomal gene conversion events stimulated by the hyper-gene conversion mutation hpr5. This result suggests that different intrachromosomal recombination processes are affected in each mutant strain. We propose that HPR1 may function to inhibit intrachromatid crossovers.
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Santoyo, Gustavo, Jaime M. Martínez-Salazar, César Rodríguez, and David Romero. "Gene Conversion Tracts Associated with Crossovers in Rhizobium etli." Journal of Bacteriology 187, no. 12 (June 15, 2005): 4116–26. http://dx.doi.org/10.1128/jb.187.12.4116-4126.2005.
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ABSTRACT Gene conversion has been defined as the nonreciprocal transfer of information between homologous sequences. Despite its broad interest for genome evolution, the occurrence of this mechanism in bacteria has been difficult to ascertain due to the possible occurrence of multiple crossover events that would mimic gene conversion. In this work, we employ a novel system, based on cointegrate formation, to isolate gene conversion events associated with crossovers in the nitrogen-fixing bacterium Rhizobium etli. In this system, selection is applied only for cointegrate formation, with gene conversions being detected as unselected events. This minimizes the likelihood of multiple crossovers. To track the extent and architecture of gene conversions, evenly spaced nucleotide changes were made in one of the nitrogenase structural genes (nifH), introducing unique sites for different restriction endonucleases. Our results show that (i) crossover events were almost invariably accompanied by a gene conversion event occurring nearby; (ii) gene conversion events ranged in size from 150 bp to 800 bp; (iii) gene conversion events displayed a strong bias, favoring the preservation of incoming sequences; (iv) even small amounts of sequence divergence had a strong effect on recombination frequency; and (v) the MutS mismatch repair system plays an important role in determining the length of gene conversion segments. A detailed analysis of the architecture of the conversion events suggests that multiple crossovers are an unlikely alternative for their generation. Our results are better explained as the product of true gene conversions occurring under the double-strand break repair model for recombination.