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  1. AU="Qingbo Shu"
  2. AU=Tang Bufu
  3. AU="Bodas, Moran"
  4. AU="Gaustad, Peter"
  5. AU="Khalil, Suzan O"
  6. AU="Nalbandian, Angele"
  7. AU="Raimondo, Lucia"
  8. AU="Bandeira Filho, Orlando C de S"
  9. AU="Cirino, Raphael Henrique Déa"
  10. AU="Galiano, Michele"
  11. AU="Tarabal, Vinícius S"
  12. AU="Meinke, William"
  13. AU="Wang, Guyu"
  14. AU="Honeyman, Emma M"
  15. AU="di Franco, Rossella"
  16. AU=Yildirim M.
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  1. Article ; Online: Species-specific quantification of circulating ebolavirus burden using VP40-derived peptide variants.

    Qingbo Shu / Tara Kenny / Jia Fan / Christopher J Lyon / Lisa H Cazares / Tony Y Hu

    PLoS Pathogens, Vol 17, Iss 11, p e

    2021  Volume 1010039

    Abstract: Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since ... ...

    Abstract Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since there are differences in the disease severity caused by different species, species identification and viral burden quantification are critical for treating infected patients timely and effectively. Here we developed an immunoprecipitation-coupled mass spectrometry (IP-MS) assay for VP40 antigen detection and quantification. We carefully selected two regions of VP40, designated as peptide 8 and peptide12 from the protein sequence that showed minor variations among Ebolavirus species through MS analysis of tryptic peptides and antigenicity prediction based on available bioinformatic tools, and generated high-quality capture antibodies pan-specific for these variant peptides. We applied this assay to human plasma spiked with recombinant VP40 protein from EBOV, SUDV, and BDBV and virus-like particles (VLP), as well as EBOV infected NHP plasma. Sequence substitutions between EBOV and SUDV, the two species with highest lethality, produced affinity variations of 2.6-fold for p8 and 19-fold for p12. The proposed IP-MS assay differentiates four of the six known EBV species in one assay, through a combination of p8 and p12 data. The IP-MS assay limit of detection (LOD) using multiple reaction monitoring (MRM) as signal readout was determined to be 28 ng/mL and 7 ng/mL for EBOV and SUDV respectively, equivalent to ~1.625-6.5×105 Geq/mL, and comparable to the LOD of lateral flow immunoassays currently used for Ebola surveillance. The two peptides of the IP-MS assay were also identified by their tandem MS spectra using a miniature MALDI-TOF MS instrument, greatly increasing the feasibility of high specificity assay in a decentralized laboratory.
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Species-specific quantification of circulating ebolavirus burden using VP40-derived peptide variants

    Qingbo Shu / Tara Kenny / Jia Fan / Christopher J. Lyon / Lisa H. Cazares / Tony Y. Hu

    PLoS Pathogens, Vol 17, Iss

    2021  Volume 11

    Abstract: Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since ... ...

    Abstract Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since there are differences in the disease severity caused by different species, species identification and viral burden quantification are critical for treating infected patients timely and effectively. Here we developed an immunoprecipitation-coupled mass spectrometry (IP-MS) assay for VP40 antigen detection and quantification. We carefully selected two regions of VP40, designated as peptide 8 and peptide12 from the protein sequence that showed minor variations among Ebolavirus species through MS analysis of tryptic peptides and antigenicity prediction based on available bioinformatic tools, and generated high-quality capture antibodies pan-specific for these variant peptides. We applied this assay to human plasma spiked with recombinant VP40 protein from EBOV, SUDV, and BDBV and virus-like particles (VLP), as well as EBOV infected NHP plasma. Sequence substitutions between EBOV and SUDV, the two species with highest lethality, produced affinity variations of 2.6-fold for p8 and 19-fold for p12. The proposed IP-MS assay differentiates four of the six known EBV species in one assay, through a combination of p8 and p12 data. The IP-MS assay limit of detection (LOD) using multiple reaction monitoring (MRM) as signal readout was determined to be 28 ng/mL and 7 ng/mL for EBOV and SUDV respectively, equivalent to ~1.625–6.5×105 Geq/mL, and comparable to the LOD of lateral flow immunoassays currently used for Ebola surveillance. The two peptides of the IP-MS assay were also identified by their tandem MS spectra using a miniature MALDI-TOF MS instrument, greatly increasing the feasibility of high specificity assay in a decentralized laboratory. Author summary We developed a quantitative assay for carefully selected species-specific VP40 peptide variants by selecting two VP40 ...
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Subject code 540
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Non-Rigid Vehicle-Borne LiDAR-Assisted Aerotriangulation

    Li Zheng / Yuhao Li / Meng Sun / Zheng Ji / Manzhu Yu / Qingbo Shu

    Remote Sensing, Vol 11, Iss 10, p

    2019  Volume 1188

    Abstract: VLS (Vehicle-borne Laser Scanning) can easily scan the road surface in the close range with high density. UAV (Unmanned Aerial Vehicle) can capture a wider range of ground images. Due to the complementary features of platforms of VLS and UAV, combining ... ...

    Abstract VLS (Vehicle-borne Laser Scanning) can easily scan the road surface in the close range with high density. UAV (Unmanned Aerial Vehicle) can capture a wider range of ground images. Due to the complementary features of platforms of VLS and UAV, combining the two methods becomes a more effective method of data acquisition. In this paper, a non-rigid method for the aerotriangulation of UAV images assisted by a vehicle-borne light detection and ranging (LiDAR) point cloud is proposed, which greatly reduces the number of control points and improves the automation. We convert the LiDAR point cloud-assisted aerotriangulation into a registration problem between two point clouds, which does not require complicated feature extraction and match between point cloud and images. Compared with the iterative closest point (ICP) algorithm, this method can address the non-rigid image distortion with a more rigorous adjustment model and a higher accuracy of aerotriangulation. The experimental results show that the constraint of the LiDAR point cloud ensures the high accuracy of the aerotriangulation, even in the absence of control points. The root-mean-square error (RMSE) of the checkpoints on the x, y, and z axes are 0.118 m, 0.163 m, and 0.084m, respectively, which verifies the reliability of the proposed method. As a necessary condition for joint mapping, the research based on VLS and UAV images in uncontrolled circumstances will greatly improve the efficiency of joint mapping and reduce its cost.
    Keywords vehicle-borne laser point cloud ; UAV images ; aerial triangulation ; non-rigid methods ; point cloud registration ; Science ; Q
    Subject code 629
    Language English
    Publishing date 2019-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

    Zhiwu An / Qingbo Shu / Hao Lv / Lian Shu / Jifeng Wang / Fuquan Yang / Yan Fu

    BioMed Research International, Vol

    2018  Volume 2018

    Abstract: Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral ... ...

    Abstract Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.
    Keywords Medicine ; R
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Antigen 85B peptidomic analysis allows species-specific mycobacterial identification

    Wei Zhang / Qingbo Shu / Zhen Zhao / Jia Fan / Christopher J. Lyon / Adrian M. Zelazny / Ye Hu

    Clinical Proteomics, Vol 15, Iss 1, Pp 1-

    2018  Volume 10

    Abstract: Abstract Background Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined ... ...

    Abstract Abstract Background Nontuberculous mycobacteria (NTM)-mediated infections are a growing cause of worldwide morbidity, but lack of rapid diagnostics for specific NTM species can delay the initiation of appropriate treatment regimens. We thus examined whether mass spectrometry analysis of an abundantly secreted mycobacterial antigen could identify specific NTM species. Methods We analyzed predicted tryptic peptides of the major mycobacterial antigen Ag85B for their capacity to distinguish Mycobacterium tuberculosis and three NTM species responsible for the majority of pulmonary infections caused by slow-growing mycobacterial species. Next, we analyzed trypsin-digested culture supernatants of these four mycobacterial species by liquid chromatography–tandem mass spectrometry (LC–MS/MS) to detect candidate species-specific Ag85B peptides, the identity of which were validated by LC–MS/MS performed in parallel reaction monitoring mode. Results Theoretical tryptic digests of the Ag85B proteins of four common mycobacterial species produced peptides with distinct sequences, including two peptides that could each identify the species origin of each Ag85B protein. LC–MS/MS analysis of trypsinized culture supernatants of these four species detected one of these species-specific signature peptides in each sample. Subsequent LC–MS/MS analyses confirmed these results by targeting these species-specific Ag85B peptides. Conclusions LC–MS/MS analysis of Ag85B peptides from trypsin-digested mycobacterial culture supernatants can rapidly detect and identify common mycobacteria responsible for most pulmonary infections caused by slow-growing mycobacteria, and has the potential to rapidly diagnose pulmonary infections caused by these mycobacteria through direct analysis of clinical specimens.
    Keywords Tuberculosis ; Nontuberculous mycobacteria ; Antigen 85B ; Diagnosis ; Liquid chromatography–tandem mass spectrometry ; Medicine ; R
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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