Journal articles: 'Search and recombination'

1

Inbar, Ori, and Martin Kupiec. "Homology Search and Choice of Homologous Partner during Mitotic Recombination." Molecular and Cellular Biology 19, no. 6 (June 1, 1999): 4134–42. http://dx.doi.org/10.1128/mcb.19.6.4134.

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ABSTRACT Homologous recombination is an important DNA repair mechanism in vegetative cells. During the repair of double-strand breaks, genetic information is transferred between the interacting DNA sequences (gene conversion). This event is often accompanied by a reciprocal exchange between the homologous molecules, resulting in crossing over. The repair of DNA damage by homologous recombination with repeated sequences dispersed throughout the genome might result in chromosomal aberrations or in the inactivation of genes. It is therefore important to understand how the suitable homologous partner for recombination is chosen. We have developed a system in the yeast Saccharomyces cerevisiae that can monitor the fate of a chromosomal double-strand break without the need to select for recombinants. The broken chromosome is efficiently repaired by recombination with one of two potential partners located elsewhere in the genome. One of the partners has homology to the broken ends of the chromosome, whereas the other is homologous to sequences distant from the break. Surprisingly, a large proportion of the repair is carried out by recombination involving the sequences distant from the broken ends. This repair is very efficient, despite the fact that it requires the processing of a large chromosomal region flanking the break. Our results imply that the homology search involves extensive regions of the broken chromosome and is not carried out exclusively by sequences adjacent to the double-strand break. We show that the mechanism that governs the choice of homologous partners is affected by the length and sequence divergence of the interacting partners, as well as by mutations in the mismatch repair genes. We present a model to explain how the suitable homologous partner is chosen during recombinational repair. The model provides a mechanism that may guard the integrity of the genome by preventing recombination between dispersed repeated sequences.

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Elf, Johan. "Hypothesis: Homologous Recombination Depends on Parallel Search." Cell Systems 3, no. 4 (October 2016): 325–27. http://dx.doi.org/10.1016/j.cels.2016.10.005.

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You, Xuemei, Yinghong Ma, Zhiyuan Liu, and Mingzhao Xie. "An ABC Algorithm with Recombination." International Journal of Computers Communications & Control 13, no. 4 (July 25, 2018): 590–601. http://dx.doi.org/10.15837/ijccc.2018.4.3275.

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Artificial bee colony (ABC) is an efficient swarm intelligence algorithm, which has shown good exploration ability. However, its exploitation capacity needs to be improved. In this paper, a novel ABC variant with recombination (called RABC) is proposed to enhance the exploitation. RABC firstly employs a new search model inspired by the updating equation of particle swarm optimization (PSO). Then, both the new search model and the original ABC model are recombined to build a hybrid search model. The effectiveness of the proposed RABC is validated on ten famous benchmark optimization problems. Experimental results show RABC can significantly improve the quality of solutions and accelerate the convergence speed.

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Renkawitz, Jörg, Claudio A. Lademann, and Stefan Jentsch. "Mechanisms and principles of homology search during recombination." Nature Reviews Molecular Cell Biology 15, no. 6 (May 14, 2014): 369–83. http://dx.doi.org/10.1038/nrm3805.

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Messeni Petruzzelli, Antonio, and Tommaso Savino. "Search, Recombination, and Innovation: Lessons from Haute Cuisine." Long Range Planning 47, no. 4 (August 2014): 224–38. http://dx.doi.org/10.1016/j.lrp.2012.09.001.

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Miné-Hattab, Judith, and Rodney Rothstein. "Increased chromosome mobility facilitates homology search during recombination." Nature Cell Biology 14, no. 5 (April 8, 2012): 510–17. http://dx.doi.org/10.1038/ncb2472.

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Drugan, Mădălina M., and Dirk Thierens. "Geometrical Recombination Operators for Real-Coded Evolutionary MCMCs." Evolutionary Computation 18, no. 2 (June 2010): 157–98. http://dx.doi.org/10.1162/evco.2010.18.2.18201.

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Markov chain Monte Carlo (MCMC) algorithms are sampling methods for intractable distributions. In this paper, we propose and investigate algorithms that improve the sampling process from multi-dimensional real-coded spaces. We present MCMC algorithms that run a population of samples and apply recombination operators in order to exchange useful information and preserve commonalities in highly probable individual states. We call this class of algorithms Evolutionary MCMCs (EMCMCs). We introduce and analyze various recombination operators which generate new samples by use of linear transformations, for instance, by translation or rotation. These recombination methods discover specific structures in the search space and adapt the population samples to the proposal distribution. We investigate how to integrate recombination in the MCMC framework to sample from a desired distribution. The recombination operators generate individuals with a computational effort that scales linearly in the number of dimensions and the number of parents. We present results from experiments conducted on a mixture of multivariate normal distributions. These results show that the recombinative EMCMCs outperform the standard MCMCs for target distributions that have a nontrivial structural relationship between the dimensions.

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Ellis, S. C., and J. Bland-Hawthorn. "THE SEARCH FOR CELESTIAL POSITRONIUM VIA THE RECOMBINATION SPECTRUM." Astrophysical Journal 707, no. 1 (November 23, 2009): 457–71. http://dx.doi.org/10.1088/0004-637x/707/1/457.

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DEL RÍO, MANUEL BELTRÁN, CHRISTOPHER R. STEPHENS, and DAVID A. ROSENBLUETH. "FITNESS LANDSCAPE EPISTASIS AND RECOMBINATION." Advances in Complex Systems 18, no. 07n08 (November 2015): 1550026. http://dx.doi.org/10.1142/s0219525915500265.

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Homologous recombination is an important operator in the evolution of biological organisms. However, there is still no clear, generally accepted understanding of why it exists and under what circumstances it is useful. In this paper, we consider its utility in the context of an infinite population haploid model with selection and homologous recombination. We define utility in terms of two metrics — the increase in frequency of fit genotypes, and the increase in average population fitness, relative to those associated with selection only. Explicitly, we explore the full parameter space of a two-locus two-allele system, showing, as a function of the landscape and the initial population, that recombination is beneficial in terms of these metrics in two distinct regimes: a relatively landscape independent regime — the search regime — where recombination aids in the search for a fit genotype that is absent or at low frequency in the population; and the modular regime, where recombination allows for the juxtaposition of fit “modules” or Building Blocks (BBs). Thus, we conclude that the ubiquity and utility of recombination is intimately associated with the existence of modularity and redundancy in biological fitness landscapes.

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Alejska, M. "A universal BMV-based RNA recombination system--how to search for general rules in RNA recombination." Nucleic Acids Research 33, no. 12 (July 1, 2005): e105-e105. http://dx.doi.org/10.1093/nar/gni106.

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Lee, Andrew J., Masayuki Endo, Jamie K. Hobbs, A. Giles Davies, and Christoph Wälti. "Micro-homology intermediates: RecA’s transient sampling revealed at the single molecule level." Nucleic Acids Research 49, no. 3 (January 21, 2021): 1426–35. http://dx.doi.org/10.1093/nar/gkaa1258.

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Abstract Recombinase A (RecA) is central to homologous recombination. However, despite significant advances, the mechanism with which RecA is able to orchestrate a search for homology remains elusive. DNA nanostructure-augmented high-speed AFM offers the spatial and temporal resolutions required to study the RecA recombination mechanism directly and at the single molecule level. We present the direct in situ observation of RecA-orchestrated alignment of homologous DNA strands to form a stable recombination product within a supporting DNA nanostructure. We show the existence of subtle and short-lived states in the interaction landscape, which suggests that RecA transiently samples micro-homology at the single RecA monomer-level throughout the search for sequence alignment. These transient interactions form the early steps in the search for sequence homology, prior to the formation of stable pairings at >8 nucleotide seeds. The removal of sequence micro-homology results in the loss of the associated transient sampling at that location.

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Waldman, A. S. "The search for homology does not limit the rate of extrachromosomal homologous recombination in mammalian cells." Genetics 136, no. 2 (February 1, 1994): 597–605. http://dx.doi.org/10.1093/genetics/136.2.597.

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Abstract Mouse LTK- cells were transfected with a pair of defective Herpes simplex virus thymidine kinase (tk) genes. One tk gene had an 8-bp insertion mutation while the second gene had a 100-bp inversion. Extrachromosomal homologous recombination leading to the reconstruction of a functional tk gene was monitored by selecting for tk positive cells using medium supplemented with hypoxanthine/aminopterin/thymidine. To assess whether the search for homology may be a rate-limiting step of recombination, we asked whether the presence of an excess number of copies of a tk gene possessing both the insertion and inversion mutations could inhibit recombination between the singly mutated tk genes. Effective competitive inhibition would require that homology searching (homologous pairing) occur rapidly and efficiently. We cotransfected plasmid constructs containing the singly mutated genes in the presence or absence of competitor sequences in various combinations of linear or circular forms. We observed effective inhibition by the competitor DNA in six of the seven combinations studied. A lack of inhibition was observed only when the insertion mutant gene was cleaved within the insertion mutation and cotransfected with the two other molecules in circular form. Additional experiments suggested that homologous interactions between two DNA sequences may compete in trans with recombination between two other sequences. We conclude that homology searching is not a rate-limiting step of extrachromosomal recombination in mammalian cells. Additionally, we speculate that a limiting factor is involved in a recombination step following homologous pairing and has a high affinity for DNA termini.

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Misevičius, Alfonsas. "TESTING OF CROSSOVER OPERATORS FOR THE GREY PATTERN PROBLEM." Technological and Economic Development of Economy 12, no. 1 (March 31, 2006): 37–43. http://dx.doi.org/10.3846/13928619.2006.9637720.

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Recently genetic algorithms (GAs) are a great success in solving combinatorial optimization problems. In this paper the performance issues related to the genetic search in the context of the grey pattern problem (GPP) are discussed. The main attention is paid to the investigation of the solution recombination, i.e. crossover operators, which play an important role developing robust genetic algorithms. We implemented seven crossover operators within the hybrid genetic algorithm (HGA) framework, and carried out the extensive experiments in order to test the influence of the recombination operators on the genetic search process. The results obtained from the experimentation with GPP test instances (benchmarks) demonstrate promising efficiency of so‐called multiple parent crossover which is based on a special type of recombination of several solutions‐parents.

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Peck, Charles C., and Atam P. Dhawan. "Genetic Algorithms as Global Random Search Methods: An Alternative Perspective." Evolutionary Computation 3, no. 1 (March 1995): 39–80. http://dx.doi.org/10.1162/evco.1995.3.1.39.

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Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

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Schillebeeckx, Simon JD, and Metin Onal Vural. "Search and Interactive Recombination: Does social hierarchy affect team creativity?" Academy of Management Proceedings 2017, no. 1 (August 2017): 11985. http://dx.doi.org/10.5465/ambpp.2017.81.

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16

Lutz, D., R. Genzel, E. Sturm, L. Tacconi, E. Wieprecht, T. Alexander, H. Netzer, et al. "A Search for Broad Infrared Recombination Lines in NGC 1068." Astrophysical Journal 530, no. 2 (February 20, 2000): 733–37. http://dx.doi.org/10.1086/308416.

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Anantharamaiah, K. R., V. Radhakrishnan, D. Morris, M. Vivekanand, D. Downes, and C. S. Shukre. "A Search for Radio Recombination Lines of Positronium Near the Galactic Center." Symposium - International Astronomical Union 136 (1989): 607–16. http://dx.doi.org/10.1017/s0074180900187108.

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Several attempts were made to detect the possible radio recombination lines of positronium near the galactic center. An absorption feature seen at λ6cm, in the D-configuration of the VLA was not confirmed by subsequent observations at λ6cm and λ20cm using the B and C configurations of the VLA. An observation at λ3mm using the IRAM 30m telescope also did not detect any line. On the basis of one recombination line photon for every positron (McClintock 1984), our non-detections imply an upper limit to the positron production rate of < 3.1 × 1043 s−1, within about 2″ of the galactic center.

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Mazina, Olga M., and Alexander V. Mazin. "Human Rad54 Protein Stimulates DNA Strand Exchange Activity of hRad51 Protein in the Presence of Ca2+." Journal of Biological Chemistry 279, no. 50 (October 4, 2004): 52042–51. http://dx.doi.org/10.1074/jbc.m410244200.

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Rad51 and Rad54 proteins play a key role in homologous recombination in eukaryotes. Recently, we reported that Ca2+is requiredin vitrofor human Rad51 protein to form an active nucleoprotein filament that is important for the search of homologous DNA and for DNA strand exchange, two critical steps of homologous recombination. Here we find that Ca2+is also required for hRad54 protein to effectively stimulate DNA strand exchange activity of hRad51 protein. This finding identifies Ca2+as a universal cofactor of DNA strand exchange promoted by mammalian homologous recombination proteinsin vitro. We further investigated the hRad54-dependent stimulation of DNA strand exchange. The mechanism of stimulation appeared to include specific interaction of hRad54 protein with the hRad51 nucleoprotein filament. Our results show that hRad54 protein significantly stimulates homology-independent coaggregation of dsDNA with the filament, which represents an essential step of the search for homologous DNA. The results obtained indicate that hRad54 protein serves as a dsDNA gateway for the hRad51-ssDNA filament, promoting binding and an ATP hydrolysis-dependent translocation of dsDNA during the search for homologous sequences.

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Amin, A. A., and P. D. Sadowski. "Synthesis of an enzymatically active FLP recombinase in vitro: search for a DNA-binding domain." Molecular and Cellular Biology 9, no. 5 (May 1989): 1987–95. http://dx.doi.org/10.1128/mcb.9.5.1987-1995.1989.

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We have used an in vitro transcription and translation system to synthesize an enzymatically active FLP protein. The FLP mRNA synthesized in vitro by SP6 polymerase is translated efficiently in a rabbit reticulocyte lysate to produce enzymatically active FLP. Using this system, we assessed the effect of deletions and tetrapeptide insertions on the ability of the respective variant proteins synthesized in vitro to bind to the FLP recognition target site and to carry out excisive recombination. Deletions of as few as six amino acids from either the carboxy- or amino-terminal region of FLP resulted in loss of binding activity. Likewise, insertions at amino acid positions 79, 203, and 286 abolished DNA-binding activity. On the other hand, a protein with an insertion at amino acid 364 retained significant DNA-binding activity but had no detectable recombination activity. Also, an insertion at amino acid 115 had no measurable effect on DNA binding, but recombination was reduced by 95%. In addition, an insertion at amino acid 411 had no effect on DNA binding and recombination. On the basis of these results, we conclude that this approach fails to define a discrete DNA-binding domain. The possible reasons for this result are discussed.

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Amin, A. A., and P. D. Sadowski. "Synthesis of an enzymatically active FLP recombinase in vitro: search for a DNA-binding domain." Molecular and Cellular Biology 9, no. 5 (May 1989): 1987–95. http://dx.doi.org/10.1128/mcb.9.5.1987.

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We have used an in vitro transcription and translation system to synthesize an enzymatically active FLP protein. The FLP mRNA synthesized in vitro by SP6 polymerase is translated efficiently in a rabbit reticulocyte lysate to produce enzymatically active FLP. Using this system, we assessed the effect of deletions and tetrapeptide insertions on the ability of the respective variant proteins synthesized in vitro to bind to the FLP recognition target site and to carry out excisive recombination. Deletions of as few as six amino acids from either the carboxy- or amino-terminal region of FLP resulted in loss of binding activity. Likewise, insertions at amino acid positions 79, 203, and 286 abolished DNA-binding activity. On the other hand, a protein with an insertion at amino acid 364 retained significant DNA-binding activity but had no detectable recombination activity. Also, an insertion at amino acid 115 had no measurable effect on DNA binding, but recombination was reduced by 95%. In addition, an insertion at amino acid 411 had no effect on DNA binding and recombination. On the basis of these results, we conclude that this approach fails to define a discrete DNA-binding domain. The possible reasons for this result are discussed.

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Rudin, N., and J. E. Haber. "Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences." Molecular and Cellular Biology 8, no. 9 (September 1988): 3918–28. http://dx.doi.org/10.1128/mcb.8.9.3918-3928.1988.

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Novel recombinational repair of a site-specific double-strand break (DSB) in a yeast chromosome was investigated. When the recognition site for the HO endonuclease enzyme is embedded in nonyeast sequences and placed between two regions of homology, expression of HO endonuclease stimulates recombination between the homologous flanking regions to yield a deletion, the apparent product of an intrachromosomal exchange between direct repeats. This deletion-repair event is very efficient, thus preventing essentially all the potential lethality due to the persistence of a DSB. Interestingly, unlike previous studies involving spontaneous recombination between chromosomal repeats, the recombination events stimulated by HO-induced DSBs are accompanied by loss of the sequences separating the homologous regions greater than 99.5% of the time. Repair is dependent on the RAD52 gene. The deletion-repair event provides an in vivo assay for the sensitivity of any particular recognition site to HO cleavage. By taking advantage of a galactose-inducible HO gene, it has been possible to follow the kinetics of this event at the DNA level and to search for intermediates in this reaction. Deletion-repair requires approximately 45 min and is inhibited when cycloheximide is added after HO endonuclease cleavage.

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Rudin, N., and J. E. Haber. "Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences." Molecular and Cellular Biology 8, no. 9 (September 1988): 3918–28. http://dx.doi.org/10.1128/mcb.8.9.3918.

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Novel recombinational repair of a site-specific double-strand break (DSB) in a yeast chromosome was investigated. When the recognition site for the HO endonuclease enzyme is embedded in nonyeast sequences and placed between two regions of homology, expression of HO endonuclease stimulates recombination between the homologous flanking regions to yield a deletion, the apparent product of an intrachromosomal exchange between direct repeats. This deletion-repair event is very efficient, thus preventing essentially all the potential lethality due to the persistence of a DSB. Interestingly, unlike previous studies involving spontaneous recombination between chromosomal repeats, the recombination events stimulated by HO-induced DSBs are accompanied by loss of the sequences separating the homologous regions greater than 99.5% of the time. Repair is dependent on the RAD52 gene. The deletion-repair event provides an in vivo assay for the sensitivity of any particular recognition site to HO cleavage. By taking advantage of a galactose-inducible HO gene, it has been possible to follow the kinetics of this event at the DNA level and to search for intermediates in this reaction. Deletion-repair requires approximately 45 min and is inhibited when cycloheximide is added after HO endonuclease cleavage.

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Toribio, M. C., L. K. Morabito, J. B. R. Oonk, F. Salgado, A. G. G. M. Tielens, and H. J. A. Röttgering. "Radio Recombination Line studies on M82 from LOFAR HBA observations." Proceedings of the International Astronomical Union 10, S309 (July 2014): 350. http://dx.doi.org/10.1017/s1743921314010412.

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AbstractWe continue our search for extragalactic Carbon Radio Recombination Lines (CRRL) in M82 with the LOw Frequency ARray (LOFAR; van Haarlem et al.2013). The goal of our project is to determine the physical conditions of the cold neutral gas in this object, for which low frequency radio recombination lines can provide a sensitive probe.

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Dahliah, Diana, Guillaume Brunin, Janine George, Viet-Anh Ha, Gian-Marco Rignanese, and Geoffroy Hautier. "High-throughput computational search for high carrier lifetime, defect-tolerant solar absorbers." Energy & Environmental Science 14, no. 9 (2021): 5057–73. http://dx.doi.org/10.1039/d1ee00801c.

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Feng, Lijie, Yilang Li, Zhenfeng Liu, and Jinfeng Wang. "Idea Generation and New Direction for Exploitation Technologies of Coal-Seam Gas through Recombinative Innovation and Patent Analysis." International Journal of Environmental Research and Public Health 17, no. 8 (April 23, 2020): 2928. http://dx.doi.org/10.3390/ijerph17082928.

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Coal-seam gas (CSG), as an alternative energy, has the characteristics of resource scarcity and technological exploitation complexity. The generation of ideas is vital to develop more efficient exploitation technologies for CSG. Innovative ideas originate from the recombination of existing knowledge elements according to recombinative innovation. The previous literature has focused on exploring an abundance of combinations, which leads to blindness towards idea generation. For this reason, it is critical to search for more valuable matching patterns among the redundant combinations of elements. In line with this concept, this paper proposes a method that consists of three phases: the collection of knowledge elements, the analysis of knowledge element depth and diversity, and the analysis of knowledge element relationships. In this process, we take the patent document as the carrier of knowledge recombination and identify the optimization method in the reorganization process by means of latent Dirichlet allocation (LDA) and association rules. This method is expected to assist in sparking better ideas for CSG exploitation technologies.

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Mohan, N. R., K. R. Anantharamaiah, and W. M. Goss. "Search for Radio Recombination Lines towards the Gravitational Lens PKS1830-211." Symposium - International Astronomical Union 199 (2002): 116–17. http://dx.doi.org/10.1017/s0074180900168676.

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A search for radio recombination lines near 20 cm at z=0.193 and z=0.886 towards the gravitational lens system PKS1830-211 has yielded upper limits of |τL| ≤ 5 × 10−5 and ≤ 5 × 10−4 at the two redshifts respectively. Based on the non-detections, we derive upper limits to the emission measure of the ionized gas in the absorbing systems. We also present continuum flux density measurements over the frequency range 0.3—45 GHz made at a single epoch.

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Schippers, S., T. Bartsch, C. Brandau, A. Müller, J. Linkemann, A. A. Saghiri, and A. Wolf. "Experimental search for interference effects in the totale−+Sc3+recombination rate." Physical Review A 59, no. 4 (April 1, 1999): 3092–94. http://dx.doi.org/10.1103/physreva.59.3092.

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Landoni, Matteo, and dt ogilvie. "In Search of the Spin-Out Entrepreneur." Journal of Open Innovation: Technology, Market, and Complexity 8, no. 3 (June 22, 2022): 106. http://dx.doi.org/10.3390/joitmc8030106.

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A spin-out happens when an employee quits a company to start a new venture; however, theories do not agree on whether the ‘spin-out entrepreneur’ will start the company in the same or in a different industry. We investigated a sample of 250 entrepreneurs and 120 spin-out companies to understand what led an entrepreneur or a group of founders to enter a new industry. Our results contribute to theory, suggesting that spin-out entrepreneurs usually move to different and innovative industries owing to recombination of knowledge in founding teams. Our evidence supports the positive effect of different experiences within the team.

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Lewis, L. Kevin, G. Karthikeyan, James W. Westmoreland, and Michael A. Resnick. "Differential Suppression of DNA Repair Deficiencies of Yeast rad50, mre11 and xrs2 Mutants by EXO1 and TLC1 (the RNA Component of Telomerase)." Genetics 160, no. 1 (January 1, 2002): 49–62. http://dx.doi.org/10.1093/genetics/160.1.49.

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Abstract Rad50, Mre11, and Xrs2 form a nuclease complex that functions in both nonhomologous end-joining (NHEJ) and recombinational repair of DNA double-strand breaks (DSBs). A search for highly expressed cDNAs that suppress the DNA repair deficiency of rad50 mutants yielded multiple isolates of two genes: EXO1 and TLC1. Overexpression of EXO1 or TLC1 increased the resistance of rad50, mre11, and xrs2 mutants to ionizing radiation and MMS, but did not increase resistance in strains defective in recombination (rad51, rad52, rad54, rad59) or NHEJ only (yku70, sir4). Increased Exo1 or TLC1 RNA did not alter checkpoint responses or restore NHEJ proficiency, but DNA repair defects of yku70 and rad27 (fen) mutants were differentially suppressed by the two genes. Overexpression of Exo1, but not mutant proteins containing substitutions in the conserved nuclease domain, increased recombination and suppressed HO and EcoRI endonuclease-induced killing of rad50 strains. exo1 rad50 mutants lacking both nuclease activities exhibited a high proportion of enlarged, G2-arrested cells and displayed a synergistic decrease in DSB-induced plasmid:chromosome recombination. These results support a model in which the nuclease activity of the Rad50/Mre11/Xrs2 complex is required for recombinational repair, but not NHEJ. We suggest that the 5′–3′ exo activity of Exo1 is able to substitute for Rad50/Mre11/Xrs2 in rescission of specific classes of DSB end structures. Gene-specific suppression by TLC1, which encodes the RNA subunit of the yeast telomerase complex, demonstrates that components of telomerase can also impact on DSB repair pathways.

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Surendranath, Vineeth, Janet Chusainow, Joachim Hauber, Frank Buchholz, and Bianca H. Habermann. "SeLOX—a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems." Nucleic Acids Research 38, suppl_2 (June 5, 2010): W293—W298. http://dx.doi.org/10.1093/nar/gkq523.

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Lardeux, Frédéric, Frédéric Saubion, and Jin-Kao Hao. "GASAT: A Genetic Local Search Algorithm for the Satisfiability Problem." Evolutionary Computation 14, no. 2 (June 2006): 223–53. http://dx.doi.org/10.1162/evco.2006.14.2.223.

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This paper presents GASAT, a hybrid algorithm for the satisfiability problem (SAT). The main feature of GASAT is that it includes a recombination stage based on a specific crossover and a tabu search stage. We have conducted experiments to evaluate the different components of GASAT and to compare its overall performance with state-of-the-art SAT algorithms. These experiments show that GASAT provides very competitive results.

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Halim, Felix, Panagiotis Karras, and Roland Yap. "Local Search in Histogram Construction." Proceedings of the AAAI Conference on Artificial Intelligence 24, no. 1 (July 5, 2010): 1680–85. http://dx.doi.org/10.1609/aaai.v24i1.7713.

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The problem of dividing a sequence of values into segments occurs in database systems, information retrieval, and knowledge management. The challenge is to select a finite number of boundaries for the segments so as to optimize an objective error function defined over those segments. Although this optimization problem can be solved in polynomial time, the algorithm which achieves the minimum error does not scale well, hence it is not practical for applications with massive data sets. There is considerable research with numerous approximation and heuristic algorithms. Still, none of those approaches has resolved the quality-efficiency tradeoff in a satisfactory manner. In (Halim, Karras, and Yap 2009), we obtain near linear time algorithms which achieve both the desired scalability and near-optimal quality, thus dominating earlier approaches. In this paper, we show how two ideas from artificial intelligence, an efficient local search and recombination of multiple solutions reminiscent of genetic algorithms, are combined in a novel way to obtain state of the art histogram construction algorithms.

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Eremeev, Anton, and Julia Kovalenko. "Optimal recombination in genetic algorithms for combinatorial optimization problems: Part I." Yugoslav Journal of Operations Research 24, no. 1 (2014): 1–20. http://dx.doi.org/10.2298/yjor130731040e.

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This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We consider efficient reductions of the ORPs, allowing to establish polynomial solvability or NP-hardness of the ORPs, as well as direct proofs of hardness results. Part I presents the basic principles of optimal recombination with a survey of results on Boolean Linear Programming Problems. Part II (to appear in a subsequent issue) is devoted to the ORPs for problems which are naturally formulated in terms of search for an optimal permutation.

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Dighe, Rahul, and Mark J. Jakiela. "Solving Pattern Nesting Problems with Genetic Algorithms Employing Task Decomposition and Contact Detection." Evolutionary Computation 3, no. 3 (September 1995): 239–66. http://dx.doi.org/10.1162/evco.1995.3.3.239.

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A hierarchical approach for nesting two-dimensional shapes based on genetic algorithms is described. For the higher-level search, a representation that facilitates genetic search based on recombination is developed. An alternatiye to overlap computation based on assembly of polygons is used at the lower level of search. Two implementations to find minimum-area enclosures for polygons, with and without a cohstraint on the width of stock, are discussed. Sample output illustrating the effectiveness of the approach is provided.

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Smirnov, G. T., S. Poppi, S. Cortiglioni, S. Montebugnoli, and G. Maccaferri. "Search for radio recombination lines at 408 MHz with the northern cross." Astronomical & Astrophysical Transactions 20, no. 2 (August 2001): 203–6. http://dx.doi.org/10.1080/10556790108229698.

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Hintz, D., B. Fuhrmeister, S. Czesla, J. H. M. M. Schmitt, A. Schweitzer, E. Nagel, E. N. Johnson, et al. "The CARMENES search for exoplanets around M dwarfs." Astronomy & Astrophysics 638 (June 2020): A115. http://dx.doi.org/10.1051/0004-6361/202037596.

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The He I infrared (IR) line at a vacuum wavelength of 10 833 Å is a diagnostic for the investigation of atmospheres of stars and planets orbiting them. For the first time, we study the behavior of the He I IR line in a set of chromospheric models for M-dwarf stars, whose much denser chromospheres may favor collisions for the level population over photoionization and recombination, which are believed to be dominant in solar-type stars. For this purpose, we use published PHOENIX models for stars of spectral types M2 V and M3 V and also compute new series of models with different levels of activity following an ansatz developed for the case of the Sun. We perform a detailed analysis of the behavior of the He I IR line within these models. We evaluate the line in relation to other chromospheric lines and also the influence of the extreme ultraviolet (EUV) radiation field. The analysis of the He I IR line strengths as a function of the respective EUV radiation field strengths suggests that the mechanism of photoionization and recombination is necessary to form the line for inactive models, while collisions start to play a role in our most active models. Moreover, the published model set, which is optimized in the ranges of the Na I D2, Hα, and the bluest Ca II IR triplet line, gives an adequate prediction of the He I IR line for most stars of the stellar sample. Because especially the most inactive stars with weak He I IR lines are fit worst by our models, it seems that our assumption of a 100% filling factor of a single inactive component no longer holds for these stars.

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Engebrecht, J., and G. S. Roeder. "Yeast mer1 mutants display reduced levels of meiotic recombination." Genetics 121, no. 2 (February 1, 1989): 237–47. http://dx.doi.org/10.1093/genetics/121.2.237.

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Abstract Mutations at the MER1 locus were identified in a search for meiotic mutants defective in chromosome segregation. mer1 strains show decreased levels of inter- and intrachromosomal meiotic recombination and produce inviable spores. The MER1 gene was cloned by complementation of the spore inviability phenotype. Strains carrying disruptions of the MER1 gene are mitotically viable. The epistatic relationships between MER1 and previously characterized meiotic genes are described.

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Gallardo, Mercedes, and Andrés Aguilera. "A New Hyperrecombination Mutation Identifies a Novel Yeast Gene, THP1, Connecting Transcription Elongation With Mitotic Recombination." Genetics 157, no. 1 (January 1, 2001): 79–89. http://dx.doi.org/10.1093/genetics/157.1.79.

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Abstract Given the importance of the incidence of recombination in genomic instability, it is of great interest to know the elements or processes controlling recombination in mitosis. One such process is transcription, which has been shown to induce recombination in bacteria, yeast, and mammals. To further investigate the genetic control of the incidence of recombination and genetic instability and, in particular, its connection with transcription, we have undertaken a search for hyperrecombination mutants among a large number of strains deleted in genes of unknown function. We have identified a new gene, THP1 (YOL072w), whose deletion mutation strongly stimulates recombination between repeats. In addition, thp1Δ impairs transcription, a defect that is particularly strong at the level of elongation through particular DNA sequences such as lacZ. The hyperrecombination phenotype of thp1Δ cells is fully dependent on transcription elongation of the repeat construct. When transcription is impeded either by shutting off the promoter or by using a premature transcription terminator, hyperrecombination between repeats is abolished, providing new evidence that transcription-elongation impairment may be a source of recombinogenic substrates in mitosis. We show that Thp1p and two other proteins previously shown to control transcription-associated recombination, Hpr1p and Tho2p, act in the same “pathway” connecting transcription elongation with the incidence of mitotic recombination.

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Stadler, Peter F., and Günter P. Wagner. "Algebraic Theory of Recombination Spaces." Evolutionary Computation 5, no. 3 (September 1997): 241–75. http://dx.doi.org/10.1162/evco.1997.5.3.241.

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A new mathematical representation is proposed for the configuration space structure induced by recombination, which we call “P-structure.” It consists of a mapping of pairs of objects to the power set of all objects in the search space. The mapping assigns to each pair of parental “genotypes” the set of all recombinant genotypes obtainable from the parental ones. It is shown that this construction allows a Fourier decomposition of fitness landscapes into a superposition of “elementary landscapes.” This decomposition is analogous to the Fourier decomposition of fitness landscapes on mutation spaces. The elementary landscapes are obtained as eigenfunctions of a Laplacian operator defined for P-structures. For binary string recombination, the elementary landscapes are exactly the p-spin functions (Walsh functions), that is, the same as the elementary landscapes of the string point mutation spaces (i.e., the hypercube). This supports the notion of a strong homomorphism between string mutation and recombination spaces. However, the effective nearest neighbor correlations on these elementary landscapes differ between mutation and recombination and among different recombination operators. On average, the nearest neighbor correlation is higher for one-point recombination than for uniform recombination. For one-point recombination, the correlations are higher for elementary landscapes with fewer interacting sites as well as for sites that have closer linkage, confirming the qualitative predictions of the Schema Theorem. We conclude that the algebraic approach to fitness landscape analysis can be extended to recombination spaces and provides an effective way to analyze the relative hardness of a landscape for a given recombination operator.

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Eiben, Agoston E., and Thomas Bäck. "Empirical Investigation of Multiparent Recombination Operators in Evolution Strategies." Evolutionary Computation 5, no. 3 (September 1997): 347–65. http://dx.doi.org/10.1162/evco.1997.5.3.347.

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An extension of evolution strategies to multiparent recombination involving a variable number ϱ of parents to create an offspring individual is proposed. The extension is experimentally evaluated on a test suite of functions differing in their modality and separability and the regular/irregular arrangement of their local optima. Multiparent diagonal crossover and uniform scanning crossover and a multiparent version of intermediary recombination are considered in the experiments. The performance of the algorithm is observed to depend on the particular combination of recombination operator and objective function. In most of the cases a significant increase in performance is observed as the number of parents increases. However, there might also be no significant impact of recombination at all, and for one of the unimodal objective functions, the performance is observed to deteriorate over the course of evolution for certain choices of the recombination operator and the number of parents. Additional experiments with a skewed initialization of the population clarify that intermediary recombination does not cause a search bias toward the origin of the coordinate system in the case of domains of variables that are symmetric around zero.

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Zhang, Weiwei, Jingjing Lin, Honglei Jing, and Qiuwen Zhang. "A Novel Hybrid Clonal Selection Algorithm with Combinatorial Recombination and Modified Hypermutation Operators for Global Optimization." Computational Intelligence and Neuroscience 2016 (2016): 1–14. http://dx.doi.org/10.1155/2016/6204728.

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Artificial immune system is one of the most recently introduced intelligence methods which was inspired by biological immune system. Most immune system inspired algorithms are based on the clonal selection principle, known as clonal selection algorithms (CSAs). When coping with complex optimization problems with the characteristics of multimodality, high dimension, rotation, and composition, the traditional CSAs often suffer from the premature convergence and unsatisfied accuracy. To address these concerning issues, a recombination operator inspired by the biological combinatorial recombination is proposed at first. The recombination operator could generate the promising candidate solution to enhance search ability of the CSA by fusing the information from random chosen parents. Furthermore, a modified hypermutation operator is introduced to construct more promising and efficient candidate solutions. A set of 16 common used benchmark functions are adopted to test the effectiveness and efficiency of the recombination and hypermutation operators. The comparisons with classic CSA, CSA with recombination operator (RCSA), and CSA with recombination and modified hypermutation operator (RHCSA) demonstrate that the proposed algorithm significantly improves the performance of classic CSA. Moreover, comparison with the state-of-the-art algorithms shows that the proposed algorithm is quite competitive.

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Chittela, Rajani Kant, and Jayashree K. Sainis. "Plant DNA Recombinases: A Long Way to Go." Journal of Nucleic Acids 2010 (2010): 1–10. http://dx.doi.org/10.4061/2010/646109.

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DNA homologous recombination is fundamental process by which two homologous DNA molecules exchange the genetic information for the generation of genetic diversity and maintain the genomic integrity. DNA recombinases, a special group of proteins bind to single stranded DNA (ssDNA) nonspecifically and search the double stranded DNA (dsDNA) molecule for a stretch of DNA that is homologous with the bound ssDNA. Recombinase A (RecA) has been well characterized at genetic, biochemical, as well as structural level from prokaryotes. Two homologues of RecA called Rad51 and Dmc1 have been detected in yeast and higher eukaryotes and are known to mediate the homologous recombination in eukaryotes. The biochemistry and mechanism of action of recombinase is important in understanding the process of homologous recombination. Even though considerable progress has been made in yeast and human recombinases, understanding of the plant recombination and recombinases is at nascent stage. Since crop plants are subjected to different breeding techniques, it is important to know the homologous recombination process. This paper focuses on the properties of eukaryotes recombinases and recent developments in the field of plant recombinases Dmc1 and Rad51.

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West, Stephen C. "The search for a human Holliday junction resolvase." Biochemical Society Transactions 37, no. 3 (May 20, 2009): 519–26. http://dx.doi.org/10.1042/bst0370519.

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Four-way DNA intermediates, known as Holliday junctions, are formed during mitotic and meiotic recombination, and their efficient resolution is essential for proper chromosome segregation. Bacteria, bacteriophages and archaea promote Holliday junction resolution by the introduction of symmetrically related nicks across the junction, in reactions mediated by Holliday junction resolvases. In 2008, after a search that lasted almost 20 years, a Holliday junction resolvase was identified in humans. The protein, GEN1, was identified using MS following the brute-force fractionation of extracts prepared from human cells grown in tissue culture. GEN1 fits the paradigm developed from studies of prokaryotic Holliday junction resolvases, in that it specifically recognizes junctions and resolves them using a mechanism similar to that exhibited by the Escherichia coli RuvC protein.

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Shang, Yongliang, Tao Huang, Hongbin Liu, Yanlei Liu, Heng Liang, Xiaoxia Yu, Mengjing Li, et al. "MEIOK21: a new component of meiotic recombination bridges required for spermatogenesis." Nucleic Acids Research 48, no. 12 (May 28, 2020): 6624–39. http://dx.doi.org/10.1093/nar/gkaa406.

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Abstract Repair of DNA double-strand breaks (DSBs) with homologous chromosomes is a hallmark of meiosis that is mediated by recombination ‘bridges’ between homolog axes. This process requires cooperation of DMC1 and RAD51 to promote homology search and strand exchange. The mechanism(s) regulating DMC1/RAD51-ssDNA nucleoprotein filament and the components of ‘bridges’ remain to be investigated. Here we show that MEIOK21 is a newly identified component of meiotic recombination bridges and is required for efficient formation of DMC1/RAD51 foci. MEIOK21 dynamically localizes on chromosomes from on-axis foci to ‘hanging foci’, then to ‘bridges’, and finally to ‘fused foci’ between homolog axes. Its chromosome localization depends on DSBs. Knockout of Meiok21 decreases the numbers of HSF2BP and DMC1/RAD51 foci, disrupting DSB repair, synapsis and crossover recombination and finally causing male infertility. Therefore, MEIOK21 is a novel recombination factor and probably mediates DMC1/RAD51 recruitment to ssDNA or their stability on chromosomes through physical interaction with HSF2BP.

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Smith, Michael J., Eric E. Bryant, Fraulin J. Joseph, and Rodney Rothstein. "DNA damage triggers increased mobility of chromosomes in G1-phase cells." Molecular Biology of the Cell 30, no. 21 (October 1, 2019): 2620–25. http://dx.doi.org/10.1091/mbc.e19-08-0469.

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During S phase in Saccharomyces cerevisiae, chromosomal loci become mobile in response to DNA double-strand breaks both at the break site (local mobility) and throughout the nucleus (global mobility). Increased nuclear exploration is regulated by the recombination machinery and the DNA damage checkpoint and is likely an important aspect of homology search. While mobility in response to DNA damage has been studied extensively in S phase, the response in interphase has not, and the question of whether homologous recombination proceeds to completion in G1 phase remains controversial. Here, we find that global mobility is triggered in G1 phase. As in S phase, global mobility in G1 phase is controlled by the DNA damage checkpoint and the Rad51 recombinase. Interestingly, despite the restriction of Rad52 mediator foci to S phase, Rad51 foci form at high levels in G1 phase. Together, these observations indicate that the recombination and checkpoint machineries promote global mobility in G1 phase, supporting the notion that recombination can occur in interphase diploids.

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Yang, Haijuan, and Nikola P. Pavletich. "Insights into homology search from cryo-EM structures of RecA-DNA recombination intermediates." Current Opinion in Genetics & Development 71 (December 2021): 188–94. http://dx.doi.org/10.1016/j.gde.2021.09.002.

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Jaszkiewicz, Andrzej, and Paweł Kominek. "Genetic local search with distance preserving recombination operator for a vehicle routing problem." European Journal of Operational Research 151, no. 2 (December 2003): 352–64. http://dx.doi.org/10.1016/s0377-2217(02)00830-5.

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Ziesel, Andrew, Qixuan Weng, Jasvinder S. Ahuja, Abhishek Bhattacharya, Raunak Dutta, Evan Cheng, G. Valentin Börner, Michael Lichten, and Nancy M. Hollingsworth. "Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase." PLOS Genetics 18, no. 12 (December 12, 2022): e1010407. http://dx.doi.org/10.1371/journal.pgen.1010407.

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During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5’ end resection of the DSBs creates 3’ single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to involve a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5’-3’ helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, and (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates.

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del Val, Elsa, William Nasser, Hafid Abaibou, and Sylvie Reverchon. "RecA and DNA recombination: a review of molecular mechanisms." Biochemical Society Transactions 47, no. 5 (October 18, 2019): 1511–31. http://dx.doi.org/10.1042/bst20190558.

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Abstract Recombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson–Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg2+, two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8–20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer–monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics.

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Boni, Maciej F., Yang Zhou, Jeffery K. Taubenberger, and Edward C. Holmes. "Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus." Journal of Virology 82, no. 10 (March 19, 2008): 4807–11. http://dx.doi.org/10.1128/jvi.02683-07.

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ABSTRACT To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (∼2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (>100 nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus.

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Journal articles on the topic 'Search and recombination'

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