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  • 2010-2014  (170)
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  • 1
    Publikationsdatum: 2013-09-26
    Beschreibung: A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
    Schlagwort(e): RNA characterisation and manipulation
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2011-05-06
    Beschreibung: Langmuir DOI: 10.1021/la200961a
    Print ISSN: 0743-7463
    Digitale ISSN: 1520-5827
    Thema: Chemie und Pharmazie
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2012-07-04
    Beschreibung: A numerical modeling of coupled welding arc with weld pool is established using FLUENT software for moving shielded GTA welding to systematically investigate the effects of electrode bevel angle on the argon arc properties as well as the weld shape on SUS304 stainless steel. The calculated results show that the argon arc is constricted and the peak values of heat flux and shear stress on the weld pool decrease with increasing electrode bevel angle, while the radial distribution of heat flux and shear stress varying slightly. The weld shape is controlled by the pool flow patterns driving by the surface tension, gas shear stress, electromagnetic force and buoyancy. The Marangoni convection induced by surface tension plays an important role on weld shapes. All the weld shapes are wide and shallow with low weld metal oxygen content, while the narrow and deep weld shapes form under high weld metal oxygen content, which is related with the oxygen concentration in the shielding gas. Th...
    Print ISSN: 1757-8981
    Digitale ISSN: 1757-899X
    Thema: Maschinenbau
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2011-04-06
    Beschreibung: Methylation on lysine 9 of histone H3 (H3K9me) and DNA methylation play important roles in the transcriptional silencing of specific genes and repetitive elements. Both marks are detected on class I and II endogenous retroviruses (ERVs) in murine embryonic stem cells (mESCs). Recently, we reported that the H3K9-specific lysine methyltransferase (KMTase) Eset/Setdb1/KMT1E is required for H3K9me3 and the maintenance of silencing of ERVs in mESCs. In contrast, G9a/Ehmt2/KMT1C is dispensable, despite the fact that this KMTase is required for H3K9 dimethylation (H3K9me2) and efficient DNA methylation of these retroelements. Transcription of the exogenous retrovirus (XRV) Moloney murine leukemia virus is rapidly extinguished after integration in mESCs, concomitant with de novo DNA methylation. However, the role that H3K9 KMTases play in this process has not been addressed. Here, we demonstrate that G9a, but not Suv39h1 or Suv39h2, is required for silencing of newly integrated Moloney murine leukemia virus–based vectors in mESCs. The silencing defect in G9a−/− cells is accompanied by a reduction of H3K9me2 at the proviral LTR, indicating that XRVs are direct targets of G9a. Furthermore, de novo DNA methylation of newly integrated proviruses is impaired in the G9a−/− line, phenocopying proviral DNA methylation and silencing defects observed in Dnmt3a-deficient mESCs. Once established, however, maintenance of silencing of XRVs, like ERVs, is dependent exclusively on the KMTase Eset. Taken together, these observations reveal that in mESCs, the H3K9 KMTase G9a is required for the establishment, but not for the maintenance, of silencing of newly integrated proviruses.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
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    Unbekannt
    Society of Exploration Geophysicists (SEG)
    Publikationsdatum: 2014-09-05
    Beschreibung: As an inversion-based imaging algorithm, least-squares reverse time migration (LSRTM) refines seismic images toward true-reflectivity earth models. It overcomes the shortcomings of conventional migration algorithms via iterative least-squares inversion to gradually correct migration errors. LSRTM also suppresses side lobes of image wavelets to generate images with high spatial resolution. Recovered weak events and steep dips are enhanced during iterations with balanced illumination. The true-amplitude behavior of LSRTM will greatly benefit quantitative seismic interpretations. LSRTM can be a practical image-domain broadband solution to generate high-resolution images with fine layers as well as accurate complex structures.
    Print ISSN: 1070-485X
    Digitale ISSN: 1938-3789
    Thema: Geologie und Paläontologie
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2011-08-24
    Beschreibung: We describe herein the discovery of a series of panaxytriol (PXT)-derived polyacetylene small molecules with promising cytoprotective activity. In mouse xenograft models, we have demonstrated the capacity of our synthetic analogs to mitigate a range of cancer therapeutic agent-induced toxicities, including body weight loss, lethality, neurotoxicity, and hematotoxicity. Our PXT analogs have also been found to reduce radiation-induced body weight loss and lethality in mouse models. Moreover, several PXT analogs appear to exhibit moderate in vivo antiinflammatory activity as well as in vitro immunoenhancing capabilities. These compounds appear to derive their activity through induction of cancer preventive phase 2 enzymes. The studies described herein suggest that coadministration of a PXT-derived agent with cancer chemotherapeutics or radiation therapy may serve to mitigate a range of therapy-associated toxicities.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    facet.materialart.
    Unbekannt
    Oxford University Press
    Publikationsdatum: 2014-05-22
    Beschreibung: : The studies of chromatin 3D structure help us to understand its formation and function. Techniques combining chromosome conformation capture and next generation sequencing can capture chromatin structure information and has been applied to several different species and cell lines. We built 3DGD (3D Genome Database), a database that currently collected Hi-C data on four species, for easy accessing and visualization of chromatin 3D structure data. With the integration of other omics data such as genome-wide protein–DNA-binding data, this data source would be useful for researchers interested in chromatin structure and its biological functions. Availability and implementation: The 3DGD v1.1, data browser, downloadable files and documentation are available at: http://3dgd.biosino.org/ . Contact: cwang@sibs.ac.cn ; gwding@sibs.ac.cn ; yxli@sibs.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2014-11-18
    Beschreibung: Metallic alloys show complex chemistries that are not yet understood so far. It has been widely accepted that behind the composition selection lies a short-range-order mechanism for solid solutions. The present paper addresses this fundamental question by examining the face-centered-cubic Cu-Zn α-brasses. A new structural approach, the cluster-plus-glue-atom model, is introduced, which suits specifically for the description of short-range-order structures in disordered systems. Two types of formulas are pointed out, [Zn-Cu12]Zn1~6 and [Zn-Cu12](Zn,Cu)6, which explain the α-brasses listed in the American Society for Testing and Materials (ASTM) specifications. In these formulas, the bracketed parts represent the 1st-neighbor cluster, and each cluster is matched with one to six 2nd-neighbor Zn atoms or with six mixed (Zn,Cu) atoms. Such a cluster-based formulism describes the 1st- and 2nd-neighbor local atomic units where the solute and solvent interactions are ideally satisfied. The Cu-Ni industrial alloys are also explained, thus proving the universality of the cluster-formula approach in understanding the alloy selections. The revelation of the composition formulas for the Cu-(Zn,Ni) industrial alloys points to the common existence of simple composition rules behind seemingly complex chemistries of industrial alloys, thus offering a fundamental and practical method towards composition interpretations of all kinds of alloys. Scientific Reports 4 doi: 10.1038/srep07065
    Digitale ISSN: 2045-2322
    Thema: Allgemeine Naturwissenschaft
    Publiziert von Springer Nature
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2013-06-07
    Beschreibung: Visualizing individual molecules with chemical recognition is a longstanding target in catalysis, molecular nanotechnology and biotechnology. Molecular vibrations provide a valuable 'fingerprint' for such identification. Vibrational spectroscopy based on tip-enhanced Raman scattering allows us to access the spectral signals of molecular species very efficiently via the strong localized plasmonic fields produced at the tip apex. However, the best spatial resolution of the tip-enhanced Raman scattering imaging is still limited to 3-15 nanometres, which is not adequate for resolving a single molecule chemically. Here we demonstrate Raman spectral imaging with spatial resolution below one nanometre, resolving the inner structure and surface configuration of a single molecule. This is achieved by spectrally matching the resonance of the nanocavity plasmon to the molecular vibronic transitions, particularly the downward transition responsible for the emission of Raman photons. This matching is made possible by the extremely precise tuning capability provided by scanning tunnelling microscopy. Experimental evidence suggests that the highly confined and broadband nature of the nanocavity plasmon field in the tunnelling gap is essential for ultrahigh-resolution imaging through the generation of an efficient double-resonance enhancement for both Raman excitation and Raman emission. Our technique not only allows for chemical imaging at the single-molecule level, but also offers a new way to study the optical processes and photochemistry of a single molecule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, R -- Zhang, Y -- Dong, Z C -- Jiang, S -- Zhang, C -- Chen, L G -- Zhang, L -- Liao, Y -- Aizpurua, J -- Luo, Y -- Yang, J L -- Hou, J G -- England -- Nature. 2013 Jun 6;498(7452):82-6. doi: 10.1038/nature12151.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23739426" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2014-07-06
    Beschreibung: Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. Seven LPS transport proteins (that is, LptA-LptG) form a trans-envelope protein complex responsible for the transport of LPS from the inner membrane to the outer membrane, the mechanism for which is poorly understood. Here we report the first crystal structure of the unique integral membrane LPS translocon LptD-LptE complex. LptD forms a novel 26-stranded beta-barrel, which is to our knowledge the largest beta-barrel reported so far. LptE adopts a roll-like structure located inside the barrel of LptD to form an unprecedented two-protein 'barrel and plug' architecture. The structure, molecular dynamics simulations and functional assays suggest that the hydrophilic O-antigen and the core oligosaccharide of the LPS may pass through the barrel and the lipid A of the LPS may be inserted into the outer leaflet of the outer membrane through a lateral opening between strands beta1 and beta26 of LptD. These findings not only help us to understand important aspects of bacterial outer membrane biogenesis, but also have significant potential for the development of novel drugs against multi-drug resistant pathogenic bacteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Haohao -- Xiang, Quanju -- Gu, Yinghong -- Wang, Zhongshan -- Paterson, Neil G -- Stansfeld, Phillip J -- He, Chuan -- Zhang, Yizheng -- Wang, Wenjian -- Dong, Changjiang -- 083501/Z/07/Z/Wellcome Trust/United Kingdom -- England -- Nature. 2014 Jul 3;511(7507):52-6. doi: 10.1038/nature13464. Epub 2014 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK [2] Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK. ; 1] Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK [2] Department of Microbiology, College of Resource and Environment Science, Sichuan Agriculture University, Yaan 625000, China. ; Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK. ; 1] Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK [2] Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK [3] College of Life Sciences, Sichuan University, Chengdu 610065, China. ; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK. ; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. ; 1] Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK [2] School of Electronics and Information, Wuhan Technical College of Communications, No.6 Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065, China. ; College of Life Sciences, Sichuan University, Chengdu 610065, China. ; Laboratory of Department of Surgery, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24990744" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Bacterial Outer Membrane Proteins/*chemistry/*metabolism ; Cell Membrane/chemistry/metabolism ; Cell Wall/chemistry/metabolism ; Crystallography, X-Ray ; Lipopolysaccharides/chemistry/*metabolism ; Models, Molecular ; Multiprotein Complexes/*chemistry/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Salmonella typhimurium/*chemistry/cytology ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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