Heterozygous diploid and interspecies SCRaMbLEing

Shen, Michael; Wu, Yi; Yang, Kun; Li, Yunxiang; Xu, Hui; Zhang, Haoran; Li, Bing Zhi; Li, Xia; Xiao, Wen; Zhou, Xiao Dong; Mitchell, Leslie A.; Bader, Joel S.; Yuan, Ying‐Jin; Boeke, Jef D.

doi:10.1038/s41467-018-04157-0

Cited by 86 publications

(81 citation statements)

References 29 publications

(29 reference statements)

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“…Returning to experiment, we next investigate MZM hybridization, which can be measured using the spacing of Coulomb blockade conductance peaks in Coulomb islands as a function of island length [10,37,59,60]. The exponential length dependence of hybridization energy is a signature of MZMs localized at the opposite ends of the nanowire [61][62][63].…”

Section: Coulomb Blockade Spectroscopymentioning

confidence: 99%

Flux-induced topological superconductivity in full-shell nanowires

Vaitiekėnas

Winkler

Heck

et al. 2020

Science

200

232

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We present a novel route to realizing topological superconductivity using magnetic flux applied to a full superconducting shell surrounding a semiconducting nanowire core. In the destructive Little-Parks regime, reentrant regions of superconductivity are associated with integer number of phase windings in the shell. Tunneling into the core reveals a hard induced gap near zero applied flux, corresponding to zero phase winding, and a gapped region with a discrete zero-energy state around one applied flux quantum, Φ0 = h/2e, corresponding to 2π phase winding. Theoretical analysis indicates that in the presence of radial spin-orbit coupling in the semiconductor, the winding of the superconducting phase can induce a transition to a topological phase supporting Majorana zero modes. Realistic modeling shows a topological phase persisting over a wide range of parameters, and reproduces experimental tunneling conductance data. Further measurements of Coulomb blockade peak spacing around one flux quantum in full-shell nanowire islands shows exponentially decreasing deviation from 1e periodicity with device length, consistent with Majorana modes at the ends of the nanowire. arXiv:2003.13177v1 [cond-mat.mes-hall]

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Section: Coulomb Blockade Spectroscopymentioning

confidence: 99%

Flux-induced topological superconductivity in full-shell nanowires

Vaitiekėnas

Winkler

Heck

et al. 2020

Science

200

232

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“…An even better approach might be to create hybrids with segmental monosomy and test their fitness directly. Such strains could be engineered using chromosome fragmentation vectors or recombinase-based approaches such as the Sc2.0 shuffle system (Morrow et al 1997;Dymond et al 2011;Shen et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Fitness Benefits of Loss of Heterozygosity in SaccharomycesHybrids

Lancaster

Payen

Heil

et al. 2018

Preprint

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With two genomes in the same organism, interspecific hybrids have unique opportunities and costs. In both plants and yeasts, wild, pathogenic, and domesticated hybrids may eliminate portions of one parental genome, a phenomenon known as loss of heterozygosity (LOH).Laboratory evolution of hybrid yeast recapitulates these results, with LOH occurring in just a few hundred generations of propagation. In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be, and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids, such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness effects of hemizygosity are dependent on the species context, the selective environment, and the species origin of the deleted allele. Further, we found that hybrids have a larger distribution of fitness consequences vs. matched S. cerevisiae hemizygous diploids. Our results suggest that LOH can be a successful strategy for adaptation of hybrids to new environments, and we identify candidate loci that drive the chromosomal rearrangements observed in evolution of yeast hybrids.

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“…More recently, researchers have developed several new methods based on SCRaMbLE, including Reporter of SCRaMbLEd cells using Efficient Selection, Multiplex SCRaMbLE Iterative Cycling, diploid SCRaMbLE, SCRaMbLE‐in, in vitro SCRaMbLE, and L‐SCRaMbLE, which explore the SCRaMbLE system in various applications. However, due to the limited number of completed synthetic chromosomes, SCRaMbLE has only been applied in strains with one or two synthetic chromosomes.…”

Section: Recombinase‐based Genome Engineeringmentioning

confidence: 99%

Whole‐Genome Regulation for Yeast Metabolic Engineering

Jiang

Dai

2019

Small Methods

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As the most thoroughly investigated eukaryotic microorganism, Saccharomyces cerevisiae is widely used as a cell factory for producing valuable compounds. Currently, strain construction and optimization still cost a vast amount of capital and time to achieve industrially relevant parameters. To efficiently excavate the genetic factors required for desired traits, many high‐throughput genome engineering tools are developed. This review focuses on the genome‐wide approaches that are applied in yeast. Through multiplex genome editing and/or transcription regulation, these tools generate cell populations with great genetic diversity, enabling identification of the critical factors and synergistic interactions in a short time.

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Heterozygous diploid and interspecies SCRaMbLEing

Cited by 86 publications

References 29 publications

Flux-induced topological superconductivity in full-shell nanowires

Flux-induced topological superconductivity in full-shell nanowires

Fitness Benefits of Loss of Heterozygosity in SaccharomycesHybrids

Whole‐Genome Regulation for Yeast Metabolic Engineering

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