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  • Articles  (20)
  • 2010-2014  (20)
  • Physical Review B  (9)
  • Nucleic Acids Research  (9)
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  • Articles  (20)
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  • 1
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    Bias-controlled single-electron charging of a self-assembled quantum dot in a two-dimensional-electron-gas-based n-i-Schottky diode (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-02-15
    Description: Author(s): J. D. Mar, X. L. Xu, J. J. Baumberg, F. S. F. Brossard, A. C. Irvine, C. Stanley, and D. A. Williams We present bias-dependent micro-photoluminescence (μ-PL) spectroscopy of the neutral (X^{0} ) and singly negatively-charged (X^{-} ) excitons in single InAs/GaAs self-assembled quantum dots (QDs) embedded in the intrinsic region of an n-i-Schottky diode based on a two-dimensional electron gas (2DEG... [Phys. Rev. B 83, 075306] Published Mon Feb 14, 2011
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    Theory of laser-induced demagnetization at high temperatures (2012)
    American Physical Society (APS)
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    Publication Date: 2012-02-18
    Description: Author(s): A. Manchon, Q. Li, L. Xu, and S. Zhang Laser-induced demagnetization is theoretically studied by explicitly taking into account interactions among electrons, spins, and lattice. Assuming that the demagnetization processes take place during the thermalization of the subsystems, the temperature dynamics is given by the energy transfer betw... [Phys. Rev. B 85, 064408] Published Fri Feb 17, 2012
    Keywords: Magnetism
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Tumor-targeted in vivo gene silencing via systemic delivery of cRGD-conjugated siRNA (2014)
    Oxford University Press
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    Publication Date: 2014-10-10
    Description: RNAi technology is taking strong position among the key therapeutic modalities, with dozens of siRNA-based programs entering and successfully progressing through clinical stages of drug development. To further explore potentials of RNAi technology as therapeutics, we engineered and tested VEGFR2 siRNA molecules specifically targeted to tumors through covalently conjugated cyclo(Arg-Gly-Asp- d -Phe-Lys[PEG-MAL]) (cRGD) peptide, known to bind αvβ3 integrin receptors. cRGD-siRNAs were demonstrated to specifically enter and silence targeted genes in cultured αvβ3 positive human cells (HUVEC). Microinjection of zebrafish blastocysts with VEGFR2 cRGD-siRNA resulted in specific inhibition of blood vessel growth. In tumor-bearing mice, intravenously injected cRGD-siRNA molecules generated no innate immune response and bio-distributed to tumor tissues. Continuous systemic delivery of two different VEGFR2 cRGD-siRNAs resulted in down-regulation of corresponding mRNA (55 and 45%) and protein (65 and 45%) in tumors, as well as in overall reduction of tumor volume (90 and 70%). These findings demonstrate strong potential of cRGD-siRNA molecules as anti-tumor therapy.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    An intensity ratio of interlocking loops determines circadian period length (2014)
    Oxford University Press
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    Publication Date: 2014-09-17
    Description: Circadian clocks allow organisms to orchestrate the daily rhythms in physiology and behaviors, and disruption of circadian rhythmicity can profoundly affect fitness. The mammalian circadian oscillator consists of a negative primary feedback loop and is associated with some ‘auxiliary’ loops. This raises the questions of how these interlocking loops coordinate to regulate the period and maintain its robustness. Here, we focused on the REV-ERBα/ Cry1 auxiliary loop, consisting of Rev-Erbα/ROR-binding elements (RORE) mediated Cry1 transcription, coordinates with the negative primary feedback loop to modulate the mammalian circadian period. The silicon simulation revealed an unexpected rule: the intensity ratio of the primary loop to the auxiliary loop is inversely related to the period length, even when post-translational feedback is fixed. Then we measured the mRNA levels from two loops in 10-mutant mice and observed the similar monotonic relationship. Additionally, our simulation and the experimental results in human osteosarcoma cells suggest that a coupling effect between the numerator and denominator of this intensity ratio ensures the robustness of circadian period and, therefore, provides an efficient means of correcting circadian disorders. This ratio rule highlights the contribution of the transcriptional architecture to the period dynamics and might be helpful in the construction of synthetic oscillators.
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    High-resolution photocurrent spectroscopy of the positive trion state in a single quantum dot (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-05-01
    Description: Author(s): J. D. Mar, J. J. Baumberg, X. L. Xu, A. C. Irvine, C. R. Stanley, and D. A. Williams We demonstrate high-resolution photocurrent spectroscopy of the positive trion state (X + ) in a single InAs/GaAs self-assembled quantum dot (QD). Exploiting a Coulomb-mediated renormalization of the X + transition energy, our approach allows for a sub-μeV resolution, which is more than four orders of ... [Phys. Rev. B 87, 155315] Published Tue Apr 30, 2013
    Keywords: Semiconductors II: surfaces, interfaces, microstructures, and related topics
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Error removal in microchip-synthesized DNA using immobilized MutS (2014)
    Oxford University Press
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    Publication Date: 2014-07-04
    Description: The development of economical de novo gene synthesis methods using microchip-synthesized oligonucleotides has been limited by their high error rates. In this study, a low-cost, effective and improved-throughput (up to 32 oligos per run) error-removal method using an immobilized cellulose column containing the mismatch binding protein MutS was produced to generate high-quality DNA from oligos, particularly microchip-synthesized oligonucleotides. Error-containing DNA in the initial material was specifically retained on the MutS-immobilized cellulose column (MICC), and error-depleted DNA in the eluate was collected for downstream gene assembly. Significantly, this method improved a population of synthetic enhanced green fluorescent protein (720 bp) clones from 0.93% to 83.22%, corresponding to a decrease in the error frequency of synthetic gene from 11.44/kb to 0.46/kb. In addition, a parallel multiplex MICC error-removal strategy was also evaluated in assembling 11 genes encoding ~21 kb of DNA from 893 oligos. The error frequency was reduced by 21.59-fold (from 14.25/kb to 0.66/kb), resulting in a 24.48-fold increase in the percentage of error-free assembled fragments (from 3.23% to 79.07%). Furthermore, the standard MICC error-removal process could be completed within 1.5 h at a cost as low as $0.374 per MICC.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: Human infertility affects 10–15% of couples, half of which is attributed to the male partner. Abnormal spermatogenesis is a major cause of male infertility. Characterizing the genes involved in spermatogenesis is fundamental to understand the mechanisms underlying this biological process and in developing treatments for male infertility. Although many genes have been implicated in spermatogenesis, no dedicated bioinformatic resource for spermatogenesis is available. We have developed such a database, SpermatogenesisOnline 1.0 ( http://mcg.ustc.edu.cn/sdap1/spermgenes/ ), using manual curation from 30 233 articles published before 1 May 2012. It provides detailed information for 1666 genes reported to participate in spermatogenesis in 37 organisms. Based on the analysis of these genes, we developed an algorithm, Greed AUC Stepwise (GAS) model, which predicted 762 genes to participate in spermatogenesis (GAS probability 〉0.5) based on genome-wide transcriptional data in Mus musculus testis from the ArrayExpress database. These predicted and experimentally verified genes were annotated, with several identical spermatogenesis-related GO terms being enriched for both classes. Furthermore, protein–protein interaction analysis indicates direct interactions of predicted genes with the experimentally verified ones, which supports the reliability of GAS. The strategy (manual curation and data mining) used to develop SpermatogenesisOnline 1.0 can be easily extended to other biological processes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Probing DNA clamps with single-molecule force spectroscopy (2013)
    Oxford University Press
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    Publication Date: 2013-09-06
    Description: Detailed mechanisms of DNA clamps in prokaryotic and eukaryotic systems were investigated by probing their mechanics with single-molecule force spectroscopy. Specifically, the mechanical forces required for the Escherichia coli and Saccharomyces cerevisiae clamp opening were measured at the single-molecule level by optical tweezers. Steered molecular dynamics simulations further examined the forces involved in DNA clamp opening from the perspective of the interface binding energies associated with the clamp opening processes. In combination with additional molecular dynamics simulations, we identified the contact networks between the clamp subunits that contribute significantly to the interface stability of the S.cerevisiae and E. coli clamps. These studies provide a vivid picture of the mechanics and energy landscape of clamp opening and reveal how the prokaryotic and eukaryotic clamps function through different mechanisms.
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    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-14
    Description: The genome-wide distribution patterns of the ‘6th base’ 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arrays. However, it has been challenging to directly compare different data sets and samples using data generated by this method. Here, we report a new comparative hMeDIP-seq method, which involves barcoding different input DNA samples at the start and then performing hMeDIP-seq for multiple samples in one hMeDIP reaction. This approach extends the barcode technology from simply multiplexing the DNA deep sequencing outcome and provides significant advantages for quantitative control of all experimental steps, from unbiased hMeDIP to deep sequencing data analysis. Using this improved method, we profiled and compared the DNA hydroxymethylomes of mouse ES cells (ESCs) and mouse ESC-derived neural progenitor cells (NPCs). We identified differentially hydroxymethylated regions (DHMRs) between ESCs and NPCs and uncovered an intricate relationship between the alteration of DNA hydroxymethylation and changes in gene expression during neural lineage commitment of ESCs. Presumably, the DHMRs between ESCs and NPCs uncovered by this approach may provide new insight into the function of 5hmC in gene regulation and neural differentiation. Thus, this newly developed comparative hMeDIP-seq method provides a cost-effective and user-friendly strategy for direct genome-wide comparison of DNA hydroxymethylation across multiple samples, lending significant biological, physiological and clinical implications.
    Keywords: Massively Parallel (Deep) Sequencing, Chromatin and Epigenetics
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    Topics: Biology
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  • 10
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    Topological surface states and Dirac point tuning in ternary topological insulators (2012)
    American Physical Society (APS)
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    Publication Date: 2012-06-05
    Description: Author(s): M. Neupane, S.-Y. Xu, L. A. Wray, A. Petersen, R. Shankar, N. Alidoust, Chang Liu, A. Fedorov, H. Ji, J. M. Allred, Y. S. Hor, T.-R. Chang, H.-T. Jeng, H. Lin, A. Bansil, R. J. Cava, and M. Z. Hasan Using angle-resolved photoemission spectroscopy, we report electronic structure for representative members of ternary topological insulators. We show that several members of this family, such as Bi 2 Se 2 Te, Bi 2 Te 2 Se, and GeBi 2 Te 4 , exhibit a singly degenerate Dirac-like surface state, while Bi 2 Se 2 S is ... [Phys. Rev. B 85, 235406] Published Mon Jun 04, 2012
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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