74 research outputs found

    Distribution of Human Intergenic Regions within Synteny Blocks or within Breakpoint Regions

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    <p>(A) Regions of length ≤1 Mb and (B) length >1 Mb that are within synteny blocks (blue) and within breakpoint regions or across breakpoint regions and synteny blocks (red). Data derived from NCBI Human version 34 and Mouse version 30.</p

    Breakpoint Reuse Rates as a Function of Upstream Regulatory Region Size in Intergenic Breakage Model Simulations

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    <p>Genes from NCBI Human version 34 were each extended by length 0 to 210 kb upstream, thus shortening or eliminating the intergenic regions. In the intergenic breakage model, simulated reversals were performed with breakpoints chosen uniformly among the nucleotides remaining in the shortened intergenic regions, while in the random breakage model, breakpoints were chosen uniformly among all nucleotides in the genome. Then blocks were derived, and the breakpoint reuse rate was computed.</p

    GRIMM-Synteny and ST-Synteny on the Same Simulated Data

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    <p>The genomic dot-plot is shown in thick green. The synteny blocks identified by GRIMM-Synteny are shown as blue rectangles, and the ones from ST-Synteny are dashed red rectangles. When block coordinates coincide, this appears as dashed blue/red. Signs of the blocks are shown as diagonals. Tiny blocks have been artificially enlarged for visibility and do not actually protrude into other blocks. The simulated human genome has anchors 1 through 5,000. The simulated mouse genome was generated as π = Simulation(5000, 15, 500, 5). Blocks were identified via GRIMM-Synteny(π, 8, 3) and ST-Synteny(π, 5, 3).</p

    Nested Inversions Are Always Amalgamated by ST-Synteny

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    <p>The dot-plot of a signed permutation of anchors (green) between two genomes is shown. Since the anchors are signed, they are represented as ±45-degree segments. Blocks were constructed by ST-Synteny (red) and GRIMM-Synteny (blue). ST-Synteny amalgamates everything into one block. GRIMM-Synteny produces the correct blocks. If the genome on the horizontal axis is taken to be the identity permutation 1 2 3 4 5, then the genome on the vertical axis is the signed permutation −3 2 −1 −5 4.</p

    Synteny Blocks between Human and Mouse X Chromosomes

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    <p>Blocks for the X chromosomes were constructed by GRIMM-Synteny (blue) based on anchor coordinates and ST-Synteny (red) based only on anchor permutations. Anchors are shown in green. Small blocks deleted by ST-Synteny are shown in black.</p

    Asymmetric Treatment of Genomes by ST-Synteny

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    <div><p>In comparing two genomes, ST-Synteny may produce different synteny blocks depending on which one is chosen as the reference genome. The synteny blocks produced by ST-Synteny are shown as red boxes around the anchors.</p><p>(A) The genome shown on the <i>y</i>-axis is the reference genome 1, …, 10, and the genome shown on the <i>x</i>-axis is represented as a permutation π of this.</p><p>(B) The exact same anchor arrangement is shown, but the <i>x</i>-axis is taken as the reference genome 1, …, 10 and the <i>y</i>-axis is the permutation π<sup>−1</sup>. Although the anchor arrangements are identical, ST-Synteny with parameters <i>w</i> = 2, Δ = 1 produces different blocks depending on which genome is the reference genome.</p></div

    Breakpoint Reuse Rates in Simulations

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    <div><p>The simulated number of microrearrangements is <i>k,</i> and the microrearrangement size is <i>w.</i> The same simulated rearrangements were analyzed three ways.</p><p>(A) ST-Synteny simulation, with signs of blocks determined using their majority sign rule.</p><p>(B) ST-Synteny simulation, with signs of blocks determined using GRIMM-Synteny's separable permutation rule.</p><p>(C) GRIMM-Synteny simulation. Anchors have length 1 for comparison with ST-Synteny.</p></div

    Room-Temperature Ligand-Free Pd/C-Catalyzed C–S Bond Formation: Synthesis of 2‑Substituted Benzothiazoles

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    The synthesis of 2-substituted benzothiazoles has been achieved via cyclization of <i>o</i>-iodothiobenzanilide derivatives using Pd/C as the catalyst at room temperature. The protocol is ligand-free, additive-free, and high-yielding and involves very mild conditions

    Conjugate Addition vs Heck Reaction: A Theoretical Study on Competitive Coupling Catalyzed by Isoelectronic Metal (Pd(II) and Rh(I))

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    Density functional theory studies have been carried out to investigate the mechanism of the Pd­(II)­(bpy)- and Rh­(I)­(bpy)-catalyzed conjugate additions and their competitive Heck reactions involving α,β-unsaturated carbonyl compounds. The critical steps of the mechanism are insertion and termination. The insertion step favors 1,2-addition of the vinyl-coordinated species to generate a stable <i>C</i>-bound enolate intermediate, which then may isomerize to either an oxa-π-allyl species or an <i>O</i>-bound enolate. The termination step involves a competition between β-hydride elimination, leading to a Heck reaction product, and protonolysis reaction that gives a conjugate addition product. These two pathways are competitive in the Pd­(II)-catalyzed reaction, while a preference for protonolysis has been found in the Rh­(I)-catalyzed reaction. The calculations are in good agreement with the experimental observations. The potential energy surface and the rate-determining step of the β-hydride elimination are similar for both Pd­(II)- and Rh­(I)-catalyzed processes. The rate-determining steps of the Pd­(II)- and Rh­(I)-catalyzed protonolysis are different. Introduction of an N- or P-ligand significantly stabilizes the protonolysis transition state via the O-bound enolate or oxa-π-allyl complex intermediate, resulting in a reduced free energy of activation. However, the barrier of the β-hydride elimination is less sensitive to ligands. For the Rh­(I)-catalyzed reaction, protonolysis is calculated to be more favorable than the β-hydride elimination for all investigated N and P ligands due to the significant ligand stabilization to the protonolysis transition state. For the Pd­(II)-catalyzed reaction, the complex with monodentate pyridine ligands prefers the Heck-type product through β-hydride elimination, while the complex with bidentate N and P ligands favors the protonolysis. The theoretical finding suggests the possibility to control the selectivity between the conjugate addition and the Heck reaction by using proper ligands
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