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  1. Abstract

    Genomes sometimes undergo large-scale rearrangements. Programmed genome rearrangements in ciliates offer an extreme example, making them a compelling model system to study DNA rearrangements. Currently, available methods for genome annotation are not adequate for highly scrambled genomes. We present a theoretical framework and software implementation for the systematic extraction and analysis of DNA rearrangement annotations from pairs of genome assemblies corresponding to precursor and product versions. The software makes no assumptions about the structure of the rearrangements, and permits the user to select parameters to suit the data. Compared to previous approaches, this work achieves more complete precursor-product mappings, allows for full transparency and reproducibility, and can be adapted to genomic data from different sources.

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  2. Free, publicly-accessible full text available July 1, 2024
  3. Abstract

    This study investigates the effect of adding oligomers on the rheological properties of polymer nanocomposite melts with the goal of enhancing the processability of nanocomposites. The scaling analysis of plateau modulus (GN) is used in understanding the complex mechanical behavior of entangled poly(methyl acrylate) (PMA) melts upon oligomer addition. Increasing the oligomer amount led to a decrease inGNand an apparent degree of entanglement (Z) in the neat polymer melt. The particle dispersion states at two particle loadings with oligomer addition are examined in transmission electron microscopy (TEM) and small‐angle X‐ray scattering (SAXS). The dilution exponent is found unchanged at 7 and 17 vol% particle loadings for the well‐dispersed PMA‐SiO2nanocomposites compared to the neat PMA solution. These findings suggest that attractive particles with strong interfacial layers do not influence the tube dilution scaling of the polymer with the oligomer. To the contrary, composites with weak polymer‐particle interfaces demonstrate phase separation of particles when oligomers are introduced and its exponent for tube dilution scaling reaches 4 at a particle loading of 17 vol%, potentially indicating that network‐forming clusters influence chain entanglements in this scenario.

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  4. Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax , Tetrahymena thermophila and Paramecium tetraurelia , but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precise programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi , Tetmemena sp. , and the model ciliate Oxytricha trifallax . To complement existing data, we sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi , which provides an outgroup, and the germline genome of Tetmemena sp.. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's : 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier-diverged spirotrich, E. woodruffi , also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay. 
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  5. Abstract High-sensitivity interstellar scintillation and polarization observations of PSR B0656+14 made at three epochs over a year using the Five-hundred-meter Aperture Spherical radio Telescope (FAST) show that the scattering is dominated by two different compact regions. We identify the one nearer to the pulsar with the shell of the Monogem Ring, thereby confirming the association. The other is probably associated with the Local Bubble. We find that the observed position angles of the pulsar spin axis and the spatial velocity are significantly different, with a separation of 19.°3 ± 0.°8, inconsistent with a previously published near-perfect alignment of 1° ± 2°. The two independent scattering regions are clearly defined in the secondary spectra, which show two strong forward parabolic arcs. The arc curvatures imply that the scattering screens corresponding to the outer and inner arcs are located approximately 28 pc from PSR B0656+14 and 185 pc from the Earth, respectively. Comparison of the observed Doppler profiles with electromagnetic simulations shows that both scattering regions are mildly anisotropic. For the outer arc, we estimate the anisotropy A R to be approximately 1.3, with the scattering irregularities aligned parallel to the pulsar velocity. For the outer arc, we compare the observed delay profiles with delay profiles computed from a theoretical strong-scattering model. Our results suggest that the spatial spectrum of the scattering irregularities in the Monogem Ring is flatter than Kolmogorov, but further observations are required to confirm this. 
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  6. null (Ed.)