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  • 1
    Electronic Resource
    Electronic Resource
    Duplicated chromosome segments in maize (Zea mays L.): further evidence from hexokinase isozymes (1986)
    Springer
    Theoretical and applied genetics 72 (1986), S. 178-185 
    Details
    ISSN: 1432-2242
    Keywords: Hexokinase (HEX) ; Zea mays L. ; Isozymes ; Gene duplication ; Genetic linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The genetic control of hexokinase isozymes (ATP: d-hexose-6-phosphotransferase, E.C. 2.7.7.1, HEX) in maize (Zea mays L.) was studied by starch gel electrophoresis. Genetic analysis of a large number of inbred lines and crosses indicates that the major isozymes observed are encoded by two nuclear loci, designated Hex1 and Hex2. Five active allozymes and one null variant are associated with Hex1, while Hex2 has nine active alleles in addition to a null variant. Alleles at both loci govern the presence of single bands, with no intragenic or intergenic heteromers visible, suggesting that maize HEX's are active as monomers. Organelle preparations demonstrate that the products of both loci are cytosolic. All alleles, including the nulls, segregate normally in crosses. Vigorous and fertile plants were synthesized that were homozygous for null alleles at both loci, suggesting that other hexosephosphorylating enzymes exist in maize that are undetected with our assay conditions. Linkage analyses and crosses with B-A translocation stocks place Hex1 on the short arm of chromosome 3, 27 centimorgans from Pgd2 (phosphogluconate dehydrogenase) and Hex2 on the long arm of chromosome 6, approximately 45 centimorgans from Pgd1. It is suggested that the parallel linkages among these two pairs of duplicated genes reflects an evolutionary history involving chromosome segment duplication or polyploidy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00266990
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  • 2
    Electronic Resource
    Electronic Resource
    Evaluation of marker-assisted selection through computer simulation (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 376-382 
    Details
    ISSN: 1432-2242
    Keywords: Recurrent selection ; Restriction fragment length polymorphisms ; Marker-assisted selection ; Computer simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Computer simulation was used to evaluate responses to marker-assisted selection (MAS) and to compare MAS responses with those typical of phenotypic recurrent selection (PRS) in an allogamous annual crop species such as maize (Zea mays L.). Relative to PRS, MAS produced rapid responses early in the selection process; however, the rate of these responses diminished greatly within three to five cycles. The gains from MAS ranged from 44.7 to 99.5% of the maximum potential, depending on the genetic model considered. Linkage distance between markers and quantitative trait loci (QTLs) was the factor which most limited the responses from MAS. When averaged across all models considered, flanking QTLs within two marker loci produced 38% more gain than did selection based on single markers if markers were loosely-linked to a QTL (20% recombination). Flanking markers were much less advantageous when markers were closely-linked to a QTL (5% recombination), producing an advantage over single markers of only 11%. Markers were most effective in fully exploiting the genetic potential when fewer QTLs controlled the trait. Large QTL numbers exacerbated the problem of marker-QTL recombination by requiring more generations for fixation. In annual crop species, MAS may offer a primary advantage of enabling two selection cycles per year versus the 2 years per cycle required by most PRS schemes for the evaluation of testcross progeny. MAS thus appears to allow very rapid gains for the first 2–3 years of recurrent selection, after which time conventional methods might replace MAS to achieve further responses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223648
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular-marker-facilitated investigations of quantitative trait loci in maize (1992)
    Springer
    Theoretical and applied genetics 83 (1992), S. 765-774 
    Details
    ISSN: 1432-2242
    Keywords: Restriction fragment length polymorphisms(RFLPs) ; Isozymes ; Quantitative trait loci (QTLs) ; Mapping ; Zea mays L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Restriction fragment length polymorphisms have become powerful tools for genetic investigations in plant species. They allow a much greater degree of genome saturation with neutral markers than has been possible with isozymes or morphological loci. A previous investigation employed isozymes as genetic markers to infer the location of genetic factors influencing the expression of quantitative traits in the maize population: (CO159×Tx303)F2. This investigation was conducted to examine the inferences that might be derived using a highly saturated map of RFLP markers and isozymes to detect quantitative trait loci (QTLs) in the same maize F2 population. Marker loci that were associated with QTL effects in this investigation generally corresponded well with previous information where such comparisons were possible. Additionally, a number of previously unmarked genomic regions were found to contain factors with large effects on some plant traits. Availability of numerous marker loci in some genomic regions allowed: more accurate localization of QTLs, resolution of linkage between QTLs affecting the same traits, and determination that some chromsome regions previously found to affect a number of traits are likely to be due to linkage of QTLs affecting different traits. Many of the factors that affected plant height quantitatively in this investigation were found to map to regions also including known sites of major genes influencing plant height. Although the data are not conclusive, they suggest that some of the identified QTLs may be allelic to known major genes affecting plant height.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00226696
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  • 4
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    Control of SCN circadian rhythms by cryptochromes [Neuroscience] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-03-09
    Description: Circadian rhythms in mammals are coordinated by the suprachiasmatic nucleus (SCN). SCN neurons define circadian time using transcriptional/posttranslational feedback loops (TTFL) in which expression of Cryptochrome (Cry) and Period (Per) genes is inhibited by their protein products. Loss of Cry1 and Cry2 stops the SCN clock, whereas individual deletions accelerate...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Interactions between chromosomal and nonchromosomal elements reveal missing heritability (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-05-13
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Convolutional neural network architectures for predicting DNA-protein binding (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-16
    Description: Motivation: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA–protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth understanding of how to match CNN architecture to a given task is needed to fully harness the power of CNNs for computational biology applications. Results: We present a systematic exploration of CNN architectures for predicting DNA sequence binding using a large compendium of transcription factor datasets. We identify the best-performing architectures by varying CNN width, depth and pooling designs. We find that adding convolutional kernels to a network is important for motif-based tasks. We show the benefits of CNNs in learning rich higher-order sequence features, such as secondary motifs and local sequence context, by comparing network performance on multiple modeling tasks ranging in difficulty. We also demonstrate how careful construction of sequence benchmark datasets, using approaches that control potentially confounding effects like positional or motif strength bias, is critical in making fair comparisons between competing methods. We explore how to establish the sufficiency of training data for these learning tasks, and we have created a flexible cloud-based framework that permits the rapid exploration of alternative neural network architectures for problems in computational biology. Availability and Implementation: All the models analyzed are available at http://cnn.csail.mit.edu . Contact: gifford@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Control of Magnetic Fluctuations by Spin Current (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-09-03
    Description: Author(s): V. E. Demidov, S. Urazhdin, E. R. J. Edwards, M. D. Stiles, R. D. McMichael, and S. O. Demokritov We use microfocus Brillouin light scattering spectroscopy to study the interaction of spin current with magnetic fluctuations in a Permalloy microdisk located on top of a Pt strip carrying an electric current. We show that the fluctuations can be efficiently suppressed or enhanced by different direc... [Phys. Rev. Lett. 107, 107204] Published Fri Sep 02, 2011
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Shift from coral to macroalgae dominance on a volcanically acidified reef (2015)
    Springer Nature
    Details
    Publication Date: 2015-11-26
    Description: A shift from coral to macroalgae dominance of reef systems affected by volcanically acidified waters around Maug (Mariana Islands, North Pacific Ocean) increases fears that reef corals will be displaced by algae as a result of ocean acidification. Nature Climate Change 5 1083 doi: 10.1038/nclimate2758
    Print ISSN: 1758-678X
    Electronic ISSN: 1758-6798
    Topics: Geosciences
    Published by Springer Nature
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  • 9
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    Cell-autonomous clock of astrocytes drives circadian behavior in mammals (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Circadian (~24-hour) rhythms depend on intracellular transcription-translation negative feedback loops (TTFLs). How these self-sustained cellular clocks achieve multicellular integration and thereby direct daily rhythms of behavior in animals is largely obscure. The suprachiasmatic nucleus (SCN) is the fulcrum of this pathway from gene to cell to circuit to behavior in mammals. We describe cell type–specific, functionally distinct TTFLs in neurons and astrocytes of the SCN and show that, in the absence of other cellular clocks, the cell-autonomous astrocytic TTFL alone can drive molecular oscillations in the SCN and circadian behavior in mice. Astrocytic clocks achieve this by reinstating clock gene expression and circadian function of SCN neurons via glutamatergic signals. Our results demonstrate that astrocytes can autonomously initiate and sustain complex mammalian behavior.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Circadian mCry1 expression in SCN [Neuroscience] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-06-05
    Description: The suprachiasmatic nucleus (SCN) coordinates circadian rhythms that adapt the individual to solar time. SCN pacemaking revolves around feedback loops in which expression of Period (Per) and Cryptochrome (Cry) genes is periodically suppressed by their protein products. Specifically, PER/CRY complexes act at E-box sequences in Per and Cry to inhibit...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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