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Nina V. Fedoroff - One of the best experts on this subject based on the ideXlab platform.

  • BARBARA McClintock's remarkable life spanned the history of genetics in the 20th
    2017
    Co-Authors: Nina V. Fedoroff
    Abstract:

    century. Though technically rooted in Mendel's experiments carried out decades earlier, the science of genetics began with the rediscovery of his work at the turn of the century. In 1902, the year of McClintock's birth, William Bateson wrote prophetically that 'an exact determination of the laws of heredity will probably work more change in man's outlook on the world, and in his power over nature, than any other advance in natural knowledge that can be clearly foreseen'. Indeed, the science of genetics, to which McClintock made seminal contributions, both experimental and conceptual, has come to dominate all of the biological sciences, from molecular biology, through cell and developmental biology, to medicine and agriculture. And Bateson's immodest guess was arguably an underestimate of the impact of genetic knowledge on humanity. The chromosomal basis of heredity was already well-established by the time McClintock began her graduate training in the Botany Department at Cornell University. McClintock made her first significant contribution as a graduate student, developing cytological techniques that allowed her to identify each of the 10 maize chromosomes. These early experiments laid the groundwork for a remarkable series of cytogenetic discoveries by the Cornell maize genetics group between 1929 and 1935. By all accounts, McClintock was the intellectual driving force of this talented group and either contributed substantially to or was exclusively responsible for many of the discoveries. These include the identification of maize linkage groups with individual chromosomes, the well-known cytological proof of genetic crossing over, evidence of chromatid crossing over, the cytological determination of the physical location of genes within chromosomes, identification of the genetic consequences of non-homologous pairing, establishment of the causal relationship between the instability of ring-shaped chromosomes and phenotypic variegation, the discovery that the centromere is divisible, and the identification of a chromosomal site essential for the formation of the nucleolus.

  • McClintock's challenge in the 21st century.
    Proceedings of the National Academy of Sciences of the United States of America, 2012
    Co-Authors: Nina V. Fedoroff
    Abstract:

    In 1950, Barbara McClintock published a Classic PNAS article, “The origin and behavior of mutable loci in maize,” which summarized the evidence leading to her discovery of transposition. The article described a number of genome alterations revealed through her studies of the Dissociation locus, the first mobile genetic element she identified. McClintock described the suite of nuclear events, including transposon activation and various chromosome aberrations and rearrangements, that unfolded in the wake of genetic crosses that brought together two broken chromosomes 9. McClintock left future generations with the challenge of understanding how genomes respond to genetic and environmental stresses by mounting adaptive responses that frequently include genome restructuring.

  • Epigenetic Regulation of the Maize Spm Transposable Element
    Cold Spring Harbor Monograph Archive, 1996
    Co-Authors: Nina V. Fedoroff
    Abstract:

    Maize transposons, the mobile genes discovered by Barbara McClintock half a century ago, were the first plant genes known to be epigenetically silenced. Early in the study of the Suppressor-mutator ( Spm ) transposable element, McClintock recognized that the transposable element could be silenced heritably but not irreversibly, an odd and important observation (McClintock 1957McClintock 1958). A silent Spm transposon showed none of its usual genetic activities. It could neither itself move or cause another transposable element to move, nor could it change the expression of genes with Spm insertions, as could an active transposable element (McClintock 1956). However, a silent transposable element was different from a mutant transposable element because it could return to a genetically active form, reacquiring all of its activities simultaneously. McClintock explored the ability of the Spm element to alternate between active and silent phases in considerable genetic detail over the subsequent decade, noting that an unrelated transposon, the Activator ( Ac ) element, could be similarly silenced (McClintock 1959McClintock 1961McClintock 1962McClintock 1964McClintock 1965a,b, 1971). McClintock’s most striking deduction was that an active Spm could reactivate an inactive one (McClintock 1971). We now know that both transcription and transposition of the Spm element are subject to negative epigenetic control by a molecular mechanism that involves methylation of transposable element regulatory sequences (Fedoroff 1994). The transposable element itself encodes an autoregulatory protein that promotes the reactivation of an epigenetically silenced transposable element. I review the early genetic clues in McClintock’s work pointing to the existence of both epigenetic and autoregulatory...

  • DNA Methylation and Activity of the Maize Spm Transposable Element
    Current topics in microbiology and immunology, 1995
    Co-Authors: Nina V. Fedoroff
    Abstract:

    Maize transposons were the first plant genes known to undergo reversible heritable inactivation. Early in the study of the Suppressor-mutator (Spm) trans-posable element McClintock recognized that certain isolates of the element either cycled between inactive and active phases during development or underwent an inactivation event of longer duration and sufficient stability to be heritable, but which was nonetheless occasionally reversed (McClintock 1957, 1958). In subsequent studies, McClintock developed a deeper understanding of the ways in which the Spm element alternated between active and inactive phases (McClintock 1959, 1961, 1962, 1971). She later reported that theActivator element is also subject to a similar type of reversible inactivation, although the she did not study the Activator element’s inactivation mechanism in as great detail as that of Spm (McClintock 1964, 1965a,b).

  • Inactivation of Maize Transposable Elements
    Homologous Recombination and Gene Silencing in Plants, 1994
    Co-Authors: Nina V. Fedoroff, Vicki Chandler
    Abstract:

    Maize transposons were the first genetic elements in plants known to be subject to reversible inactivation. Early in the study of the Suppressor-mutator trans-posable element, McClintock identified cultures in which the “suppressor” and the “mutator” components of the element had a tendency to disappear and reappear simultaneously (McClintock 1957, McClintock 1958). In 1958 she wrote: The Spm element originally present in the a 2 m-1 cultures… did not always effect suppression of gene action in all parts of a plant or kernel. Mutations, however, occurred only in those parts of the plant or kernel in which gene expression was suppressed.

William B. Carey - One of the best experts on this subject based on the ideXlab platform.

  • Reformatting the 9-month Health Supervision Visit to enhance developmental, behavioral and family concerns.
    Journal of Developmental and Behavioral Pediatrics, 2010
    Co-Authors: Martin T. Stein, Carl Plonsky, Barry Zuckerman, William B. Carey
    Abstract:

    CASE. Dr. McClintock reviewed her schedule for the following week when she observed there were eight health supervision visits in 9 month old children. She recalled that these healthy children, whom she followed since birth, were up-to-date on their immunizations. As she reflected on the visits, it occurred to Dr. McClintock that this might be an ideal opportunity to use the time to assess developmental status and behavioral interactions. She could also ask questions about the families, including childcare arrangements, satisfaction with parenting and marriage relationships. Dr. McClintock considered the best use of the time available in order to have the most meaning to the children and their families. What lines of questioning or what screening tests might be most useful during the 9-month office visit?

  • Reformatting the 9-month health supervision visit to enhance developmental, behavioral and family concerns.
    Journal of developmental and behavioral pediatrics : JDBP, 2010
    Co-Authors: Martin T. Stein, Carl Plonsky, Barry Zuckerman, William B. Carey
    Abstract:

    Dr. McClintock reviewed her schedule for the following week when she observed there were eight health supervision visits in 9 month old children. She recalled that these healthy children, whom she followed since birth, were up-to-date on their immunizations. As she reflected on the visits, it occurred to Dr. McClintock that this might be an ideal opportunity to use the time to assess developmental status and behavioral interactions. She could also ask questions about the families, including childcare arrangements, satisfaction with parenting and marriage relationships. Dr. McClintock considered the best use of the time available in order to have the most meaning to the children and their families. What lines of questioning or what screening tests might be most useful during the 9-month office visit?

Casey M Bergman - One of the best experts on this subject based on the ideXlab platform.

  • McClintock an integrated pipeline for detecting transposable element insertions in whole genome shotgun sequencing data
    G3: Genes Genomes Genetics, 2017
    Co-Authors: Michael G Nelson, Raquel S Linheiro, Casey M Bergman
    Abstract:

    Transposable element (TE) insertions are among the most challenging types of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication . Nevertheless, the recent availability of large resequencing data sets has spurred the development of many new methods to detect TE insertions in whole-genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/McClintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae We find substantial variation among McClintock component methods in their ability to detect nonreference TEs in the yeast genome, but show that nonreference TEs at nearly all biologically realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer nonreference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, target preferences, and target site duplication structure, albeit with varying levels of accuracy. Our work provides a general framework for integrating and analyzing results from multiple TE detection methods, as well as useful guidance for researchers studying TEs in yeast resequencing data.

  • McClintock an integrated pipeline for detecting transposable element insertions in whole genome shotgun sequencing data
    bioRxiv, 2017
    Co-Authors: Michael G Nelson, Raquel S Linheiro, Casey M Bergman
    Abstract:

    Background: Transposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred the development of many new methods to detect TE insertions in whole genome shotgun sequences. These methods generate output in diverse formats and have a large number of software and data dependencies, making their comparative evaluation challenging for potential users. Results: Here we develop an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/McClintock), that automatically runs and generates standardized output for multiple TE detection methods. We demonstrate the utility of the McClintock system by performing comparative evaluation of six TE detection methods using simulated and real genome data from the model microbal eukaryote, Saccharomyces cerevisiae. We find substantial variation among McClintock component methods in their ability to detect non-reference insertions in the yeast genome, but show that non-reference TEs at nearly all biologically-realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer non-reference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most, but not all, McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, tRNA gene target preferences, and target site duplication structure, albeit with varying levels of positional accuracy. Conclusions: Our results suggest that no single TE detection method currently provides comprehensive detection of non-reference TEs, even in the context of a simplified model eukaryotic genome like S. cerevisiae. In spite of these limitations, the McClintock system provides a framework for testing, developing and integrating results from multiple TE detection methods to achieve this ultimate aim, as well as useful guidance for yeast researchers to select appropriate TE detection tools.

Martin T. Stein - One of the best experts on this subject based on the ideXlab platform.

  • Reformatting the 9-month Health Supervision Visit to enhance developmental, behavioral and family concerns.
    Journal of Developmental and Behavioral Pediatrics, 2010
    Co-Authors: Martin T. Stein, Carl Plonsky, Barry Zuckerman, William B. Carey
    Abstract:

    CASE. Dr. McClintock reviewed her schedule for the following week when she observed there were eight health supervision visits in 9 month old children. She recalled that these healthy children, whom she followed since birth, were up-to-date on their immunizations. As she reflected on the visits, it occurred to Dr. McClintock that this might be an ideal opportunity to use the time to assess developmental status and behavioral interactions. She could also ask questions about the families, including childcare arrangements, satisfaction with parenting and marriage relationships. Dr. McClintock considered the best use of the time available in order to have the most meaning to the children and their families. What lines of questioning or what screening tests might be most useful during the 9-month office visit?

  • Reformatting the 9-month health supervision visit to enhance developmental, behavioral and family concerns.
    Journal of developmental and behavioral pediatrics : JDBP, 2010
    Co-Authors: Martin T. Stein, Carl Plonsky, Barry Zuckerman, William B. Carey
    Abstract:

    Dr. McClintock reviewed her schedule for the following week when she observed there were eight health supervision visits in 9 month old children. She recalled that these healthy children, whom she followed since birth, were up-to-date on their immunizations. As she reflected on the visits, it occurred to Dr. McClintock that this might be an ideal opportunity to use the time to assess developmental status and behavioral interactions. She could also ask questions about the families, including childcare arrangements, satisfaction with parenting and marriage relationships. Dr. McClintock considered the best use of the time available in order to have the most meaning to the children and their families. What lines of questioning or what screening tests might be most useful during the 9-month office visit?

Tamara Mcclintock Greenberg - One of the best experts on this subject based on the ideXlab platform.