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  • 1
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    A Meiotic Drive Element in the Maize Pathogen Fusarium verticillioides Is Located Within a 102 kb Region of Chromosome V (2016)
    Genetics Society of America (GSA)
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    Publication Date: 2016-08-10
    Description: Fusarium verticillioides is an agriculturally important fungus because of its association with maize and its propensity to contaminate grain with toxic compounds. Some isolates of the fungus harbor a meiotic drive element known as Spore killer ( Sk K ) that causes nearly all surviving meiotic progeny from an Sk K x Spore killer -susceptible ( Sk S ) cross to inherit the Sk K allele. Sk K has been mapped to chromosome V but the genetic element responsible for meiotic drive has yet to be identified. In this study, we used cleaved amplified polymorphic sequence markers to genotype individual progeny from an Sk K x Sk S mapping population. We also sequenced the genomes of three progeny from the mapping population to determine their single nucleotide polymorphisms. These techniques allowed us to refine the location of Sk K to a contiguous 102 kb interval of chromosome V, herein referred to as the Sk region. Relative to Sk S genotypes, Sk K genotypes have one extra gene within this region for a total of 42 genes. The additional gene in Sk K genotypes, herein named SKC1 for Spore Killer Candidate 1 , is the most highly expressed gene from the Sk region during early stages of sexual development. The Sk region also has three hyper-variable regions, the longest of which includes SKC1 . The possibility that SKC1 , or another gene from the Sk region, is an essential component of meiotic drive and spore killing is discussed.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 2
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    Co-incident insertion enables high efficiency genome engineering in mouse embryonic stem cells (2016)
    Oxford University Press
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    Publication Date: 2016-09-20
    Description: CRISPR/Cas9 nucleases have enabled powerful, new genome editing capabilities; however, the preponderance of non-homologous end joining (NHEJ) mediated repair events over homology directed repair (HDR) in most cell types limits the ability to engineer precise changes in mammalian genomes. Here, we increase the efficiency of isolating precise HDR-mediated events in mouse embryonic stem (ES) cells by more than 20-fold through the use of co -incidental in sertion (COIN) of independent donor DNA sequences. Analysis of on:off-target frequencies at the Lef1 gene revealed that bi-allelic insertion of a PGK-Neo cassette occurred more frequently than expected. Using various selection cassettes targeting multiple loci, we show that the insertion of a selectable marker at one control site frequently coincided with an insertion at an unlinked, independently targeted site, suggesting enrichment of a sub-population of HDR-proficient cells. When individual cell events were tracked using flow cytometry and fluorescent protein markers, individual cells frequently performed either a homology-dependent insertion event or a homology-independent event, but rarely both types of insertions in a single cell. Thus, when HDR-dependent selection donors are used, COIN enriches for HDR-proficient cells among heterogeneous cell populations. When combined with a self-excising selection cassette, COIN provides highly efficient and scarless genome editing.
    Keywords: Synthetic Biology and Assembly Cloning, Targeted gene modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Performance evaluation of data-limited, length-based stock assessment methods (2019)
    Oxford University Press
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    Publication Date: 2019-11-11
    Description: Performance evaluation of data-limited, length-based methods is instrumental in determining and quantifying their accuracy under various scenarios and in providing guidance about model applicability and limitations. We conducted a simulation–estimation analysis to compare the performance of four length-based stock assessment methods: length-based Thompson and Bell (TB), length-based spawning potential ratio (LBSPR), length-based integrated mixed effects (LIME), and length-based risk analysis (LBRA), under varying life history, exploitation status, and recruitment error scenarios. Across all scenarios, TB and LBSPR were the most consistent and accurate assessment methods. LBRA is highly biased, but precautionary, and LIME is more suitable for assessments with time-series longer than a year. All methods have difficulties when assessing short-lived species. The methods are less accurate in estimating the degree of recruitment overfishing when the stocks are severely overexploited, and inconsistent in determining growth overfishing when the stocks are underexploited. Increased recruitment error reduces precision but can decrease bias in estimations. This study highlights the importance of quantifying the accuracy of stock assessment methods and testing methods under different scenarios to determine their strengths and weaknesses and provides guidance on which methods to employ in various situations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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  • 4
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    Ensemble models for data-poor assessment: accounting for uncertainty in life-history information (2019)
    Oxford University Press
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    Publication Date: 2019-02-11
    Description: Length measurements from fishery catch can be used in data-limited assessments to estimate important population parameters to guide management, but results are highly sensitive to assumptions about biological information. Ideally, local life history studies inform biological parameters. In the absence of reliable local estimates, scientists and managers face the difficult task of agreeing on fixed values for life-history parameters, often leading to additional uncertainty unquantified in the assessment or indecision defaulting to status-quo management. We propose an ensemble approach for incorporating life history uncertainty into data-limited stock assessments. We develop multivariate distributions of growth, mortality, and maturity parameter values, then use bivariate interpolation and stacking as an ensemble learning algorithm to propagate uncertainty into length-based, data-limited stock assessment models. Simulation testing demonstrated that stacking across life history parameter values leads to improved interval coverage over simple model averaging or assuming the parameter distribution means when the true life-history parameter values are unknown. We then applied the stacking approach for a U.S. Caribbean stock where the Scientific and Statistical Committee did not accept the assessment due to uncertainty in life history parameters. Stacking can better characterize uncertainty in stock status whenever life-history parameters are unknown but likely parameter distributions are available.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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  • 5
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    Performance of length-based data-limited methods in a multifleet context: application to small tunas, mackerels, and bonitos in the Atlantic Ocean (2019)
    Oxford University Press
    Details
    Publication Date: 2019-02-06
    Description: Large scombrids, commercial tuna species, are regularly assessed and managed. However, most of the small scombrids, many mackerels and bonitos, lack accurate catch data to implement traditional stock assessments despite their economic importance in many small-scale fisheries. In this study, we analysed different approaches using length composition data from multiple fleets with different gear selectivity to assess small scombrids in the Atlantic Ocean. Using simulated populations, we compared two length-based methods (length-based spawning potential ratio and length-based integrated mixed effects ), under different length data grouping scenarios. We found that using length data from the fleet targeting the broadest range of sizes resulted in the lowest bias in spawning potential ratio of all options tested. Based on these results, we used biological and length data to estimate a quantitative proxy of current stock status for ten small scombrid stocks in the Atlantic Ocean. We found that some stocks are likely to be overfished, such as little tunny (Euthynnus alletteratus) in the Southeast Atlantic and wahoo (Acanthocybium solandri) in the Northwest Atlantic. This is a starting point in the estimation of stock status for these species, but should not be thought of as a replacement for other more data-intensive assessments.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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