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  • Articles  (52)
  • Nucleic Acids Research  (17)
  • Applied Physics Letters  (8)
  • Acta Crystallographica Section E  (3)
  • 103079
  • 60967
  • 622
  • 1
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    Template-free synthesis of Nd0.1Bi0.9FeO3 nanotubes with large inner diameter and wasp-waisted hysteresis loop (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-08-12
    Description: One-dimensional (1D) nanotubes of Nd 0.1 Bi 0.9 FeO 3 (NBFO) with an inner diameter of ∼50 nm were synthesized via sol-gel based electrospinning without template assistant. The phases, morphologies, crystalline structures, and magnetic properties of these 1D nanostructures were characterized by means of X-ray diffraction, scanning electron microscopy, transmission electron microscopy and SQUID, respectively. It was found that the calcination condition plays a crucial role in determining the morphologies and the magnetic properties. Interestingly, these 1D NBFO nanotubes exhibit wasp-waisted magnetic hysteresis with a lower coercivity and larger saturation magnetization, which were prevalent in natural rocks and artificial composite materials. The origin of these wasp-waisted hysteresis loops was discussed.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    Conducting mechanisms of forming-free TiW/Cu2O/Cu memristive devices (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-08-26
    Description: P-type Cu 2 O is a promising CMOS-compatible candidate to fabricate memristive devices for next-generation memory, logic and neuromorphic computing. In this letter, the microscopic switching and conducting mechanisms in TiW/Cu 2 O/Cu memristive devices have been thoroughly investigated. The bipolar resistive switching behaviors without an electro-forming process are ascribed to the formation and rupture of the conducting filaments composed of copper vacancies. In the low resistive state, the transport of electrons in the filaments follows Mott's variable range hopping theory. When the devices switch back to high resistive state, the coexistence of Schottky emission at the Cu/Cu 2 O interface and electron hopping between the residual filaments is found to dominate the conducting process. Our results will contribute to the further understanding and optimization of p-type memristive materials.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    Description: tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called ‘tRFinCancer’ was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called ‘tRFBrowser’ shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Broadening the versatility of lentiviral vectors as a tool in nucleic acid research via genetic code expansion (2015)
    Oxford University Press
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    Publication Date: 2015-06-24
    Description: With the aim of broadening the versatility of lentiviral vectors as a tool in nucleic acid research, we expanded the genetic code in the propagation of lentiviral vectors for site-specific incorporation of chemical moieties with unique properties. Through systematic exploration of the structure–function relationship of lentiviral VSVg envelope by site-specific mutagenesis and incorporation of residues displaying azide- and diazirine-moieties, the modifiable sites on the vector surface were identified, with most at the PH domain that neither affects the expression of envelope protein nor propagation or infectivity of the progeny virus. Furthermore, via the incorporation of such chemical moieties, a variety of fluorescence probes, ligands, PEG and other functional molecules are conjugated, orthogonally and stoichiometrically, to the lentiviral vector. Using this methodology, a facile platform is established that is useful for tracking virus movement, targeting gene delivery and detecting virus–host interactions. This study may provide a new direction for rational design of lentiviral vectors, with significant impact on both basic research and therapeutic applications.
    Keywords: Cell biology, DNA-Mediated Cell Transformation and Nucleic Acids Transfer
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    A systematic survey of the Cys2His2 zinc finger DNA-binding landscape (2015)
    Oxford University Press
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    Publication Date: 2015-02-18
    Description: Cys 2 His 2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of 〉160 000 unique domain–DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain–DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Local order origin of thermal stability enhancement in amorphous Ag doping GeTe (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-01-22
    Description: We demonstrate the impacts of Ag doping on the local atomic structure of amorphous GeTe phase-change material. The variations of phonon vibrational modes, boding nature, and atomic structure are shown by Raman, X-ray photoelectron spectroscopy, and ab initio calculation. Combining the experiments and simulations, we observe that the number of Ge atoms in octahedral site decreases and that in tetrahedral site increases. This modification in local order of GeTe originating from the low valence element will affect the crystallization behavior of amorphous GeTe, which is verified by differential scanning calorimetry and transmission electron microscope results. This work not only gives the analysis on the structural change of GeTe with Ag dopants but also provides a method to enhance the thermal stability of amorphous phase-change materials for memory and brain-inspired computing applications.
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    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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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.
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    Topics: Biology
    Published by Oxford University Press
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  • 8
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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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    Topics: Biology
    Published by Oxford University Press
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  • 9
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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.
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    Topics: Biology
    Published by Oxford University Press
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  • 10
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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
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    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.
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    Topics: Biology
    Published by Oxford University Press
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