GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
    Oxford University Press (OUP) ; 2014
    In:  Bioinformatics Vol. 30, No. 12 ( 2014-06-15), p. 1651-1659
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 30, No. 12 ( 2014-06-15), p. 1651-1659
    Abstract: Motivation: Advances in sequencing technologies and computational algorithms have enabled the study of genomic variants to dissect their functional consequence. Despite this unprecedented progress, current tools fail to reliably detect and characterize more complex allelic variants, such as short tandem repeats (STRs). We developed TSSV as an efficient and sensitive tool to specifically profile all allelic variants present in targeted loci. Based on its design, requiring only two short flanking sequences, TSSV can work without the use of a complete reference sequence to reliably profile highly polymorphic, repetitive or uncharacterized regions. Results: We show that TSSV can accurately determine allelic STR structures in mixtures with 10% representation of minor alleles or complex mixtures in which a single STR allele is shared. Furthermore, we show the universal utility of TSSV in two other independent studies: characterizing de novo mutations introduced by transcription activator-like effector nucleases (TALENs) and profiling the noise and systematic errors in an IonTorrent sequencing experiment. TSSV complements the existing tools by aiding the study of highly polymorphic and complex regions and provides a high-resolution map that can be used in a wide range of applications, from personal genomics to forensic analysis and clinical diagnostics. Availability and implementation: We have implemented TSSV as a Python package that can be installed through the command-line using pip install TSSV command. Its source code and documentation are available at https://pypi.python.org/pypi/tssv and http://www.lgtc.nl/tssv. Contact:  S.Y.Anvar@lumc.nl Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btu068
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    Interleukin-10 Regulates the Tissue Factor Activity of Monocytes in an In Vitro Model of Bacterial Endocarditis
    American Society for Microbiology ; 2001
    In:  Infection and Immunity Vol. 69, No. 5 ( 2001-05), p. 3197-3202
    Details
    In: Infection and Immunity, American Society for Microbiology, Vol. 69, No. 5 ( 2001-05), p. 3197-3202
    Abstract: Monocytes are important effector cells in the pathogenesis of bacterial endocarditis since they provide the tissue factor that activates the coagulation system and maintains established vegetations. Monocytes secrete cytokines that can modulate monocyte tissue factor activity (TFA), thereby affecting the formation and maintenance of vegetations. In this study, we show that monocytes cultured for 4 h on a Streptococcus sanguis -infected fibrin matrix mimicking the in vivo vegetational surface express high levels of TFA. This was accompanied by secretion of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α), interleukin-1α (IL-1α), and IL-1β. After a 24-h incubation period the anti-inflammatory cytokine IL-10 could also be detected. Our data show that, whereas TNF-α and IL-1 have a minor role in the induction of TFA by monocytes cultured on a fibrin matrix, TNF-α but not IL-1 plays an important role in the induction of IL-10 by these cells. In turn, our data show that IL-10 is an important factor in the downregulation of monocyte TFA. In summary, we conclude that IL-10 is an important factor in the control of monocyte TFA in endocardial vegetations.
    Type of Medium: Online Resource
    ISSN: 0019-9567 , 1098-5522
    URL: Article
    DOI: 10.1128/IAI.69.5.3197-3202.2001
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2001
    detail.hit.zdb_id: 1483247-1
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    Altered Gene Expression in Staphylococcus aureus upon Interaction with Human Endothelial Cells
    American Society for Microbiology ; 2000
    In:  Infection and Immunity Vol. 68, No. 4 ( 2000-04), p. 1765-1772
    Details
    In: Infection and Immunity, American Society for Microbiology, Vol. 68, No. 4 ( 2000-04), p. 1765-1772
    Abstract: Staphylococcus aureus is isolated from a substantial number of patients with infective endocarditis who are not known to have predisposing heart abnormalities. It has been suggested that the infection is initiated by the direct binding of S. aureus to human vascular endothelium. To determine the mutual response of the endothelial cells and the bacteria, we studied the interaction between S. aureus and human vascular endothelium. Scanning electron microscopic analyses showed that binding of S. aureus to human umbilical vein endothelial cells (HUVEC) mainly occurred via thread-like protrusions extending from the cell surface. Bound bacteria appeared to be internalized via retraction of the protrusions into newly formed invaginations of the endothelial cell surface. The growth phase of S. aureus had a major impact on the interaction with HUVEC. Logarithmically growing bacteria showed increased binding to, and were more readily internalized by, HUVEC compared to stationary-phase bacteria. To assess the bacterial response to the cellular environment, an expression library of S. aureus was used to identify genes whose expression was induced after 4 h of exposure to HUVEC. The identified genes could be divided into different categories based on the functions of the encoded proteins (transport, catabolism, biosynthesis, and DNA repair). Further analyses of five of the S. aureus transposon clones showed that HUVEC as well as human serum are stimuli for triggering gene expression in S. aureus .
    Type of Medium: Online Resource
    ISSN: 0019-9567 , 1098-5522
    URL: Article
    DOI: 10.1128/IAI.68.4.1765-1772.2000
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2000
    detail.hit.zdb_id: 1483247-1
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    Role of Monocytes and Bacteria in Staphylococcus epidermidis Endocarditis
    American Society for Microbiology ; 1998
    In:  Infection and Immunity Vol. 66, No. 2 ( 1998-02), p. 448-450
    Details
    In: Infection and Immunity, American Society for Microbiology, Vol. 66, No. 2 ( 1998-02), p. 448-450
    Abstract: The endocardial vegetation which is formed in the course of bacterial endocarditis (BE) contains tissue factor (TF)-dependent procoagulant activity. Earlier studies showed that monocytes are the main source of TF in the vegetations. The TF activity (TFA) of vegetations isolated from Streptococcus sanguis -infected rabbits depended on the numbers of bacteria as well as monocytes in the vegetation. In this study, we investigated whether for Staphylococcus epidermidis , a frequent pathogen in BE, an effect similar to that found for S. sanguis could be shown. In vitro, S. epidermidis was found to stimulate TFA of fibrin adherent monocytes significantly. This stimulation was maximal at a bacterium-to-monocyte ratio of 7. In vivo, TFA was found to be significantly higher in S. epidermidis -infected than in sterile catheter-induced vegetations. Reduction of vegetational bacterial numbers by teicoplanin treatment lead to a small but significant decrease of TFA. Reduction of monocyte numbers by etoposide did not affect vegetational TFA. Comparison of data for S. epidermidis and S. sanguis revealed that at equivalent bacterial numbers, vegetational TFAs were approximately the same for both microorganisms. Combining the results of the present study with those of a previous study using S. sanguis , we conclude that the main factor determining monocyte-dependent vegetational TFA is the number of vegetation-associated bacteria. The lower TFA found for S. epidermidis -infected than for S. sanguis -infected vegetations can be explained by the significantly lower bacterial numbers in the infected vegetations and consequently a lower stimulation of vegetation-associated monocytes.
    Type of Medium: Online Resource
    ISSN: 0019-9567 , 1098-5522
    URL: Article
    DOI: 10.1128/IAI.66.2.448-450.1998
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 1998
    detail.hit.zdb_id: 1483247-1
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 5
    Online Resource
    Online Resource
    Role of Monocytes in Experimental Staphylococcus aureus Endocarditis
    American Society for Microbiology ; 2000
    In:  Infection and Immunity Vol. 68, No. 8 ( 2000-08), p. 4818-4821
    Details
    In: Infection and Immunity, American Society for Microbiology, Vol. 68, No. 8 ( 2000-08), p. 4818-4821
    Abstract: In the pathogenesis of bacterial endocarditis (BE), the clotting system plays a cardinal role in the formation and maintenance of the endocardial vegetations. The extrinsic pathway is involved in the activation of the coagulation pathway with tissue factor (TF) as the key protein. Staphylococcus aureus is a frequently isolated bacterium from patients with BE. We therefore investigated whether S. aureus can induce TF activity (TFA) on fibrin-adherent monocytes, used as an in vitro model of BE. We also assessed in vivo in rabbits with catheter induced vegetations, the effect of S. aureus infection on vegetational TFA. In vitro experiments showed that adherent S. aureus induced TFA on fibrin-adherent monocytes which was optimal at a bacterium/monocyte ratio of 1 to 1. Monocyte damage occurred when this ratio exceeded 4 to 1 (visually) or 6 to 1 (propidium iodide influx) Consequently, TFA decreased. In vivo S. aureus led to very high bacterial numbers in the vegetations and a significant increase of their weight. However, TFA of infected vegetations was the same as of sterile ones. This may be due to the high bacteria to monocyte ratio as well as bacterium-induced monocyte damage. Teicoplanin treatment of infected rabbits reduced bacterial numbers in the blood and in the vegetations. Two-day treatment resulted in an increase of vegetational TFA, but after four-day treatment vegetational TFA dropped, most probably due to a suboptimal bacterium/monocyte ratio. S. aureus endocarditis in etoposide (Vepesid)-treated rabbits, leading to a selective monocytopenia, caused a rapid death of the animals. In these rabbits no vegetations were found at all. We conclude that, like Streptococcus sanguis and Staphylococcus epidermidis , S. aureus is able to induce TFA in fibrin-adherent blood monocytes. In addition, monocytes have a protective effect during the course of S. aureus endocarditis.
    Type of Medium: Online Resource
    ISSN: 0019-9567 , 1098-5522
    URL: Article
    DOI: 10.1128/IAI.68.8.4818-4821.2000
    RVK:
    XA 10000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2000
    detail.hit.zdb_id: 1483247-1
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 6
    Online Resource
    Online Resource
    Monocytes Maintain Tissue Factor Activity after Cytolysis of Bacteria‐Infected Endothelial Cells in an In Vitro Model of Bacterial Endocarditis
    Oxford University Press (OUP) ; 2002
    In:  The Journal of Infectious Diseases Vol. 186, No. 8 ( 2002-10-15), p. 1145-1154
    Details
    In: The Journal of Infectious Diseases, Oxford University Press (OUP), Vol. 186, No. 8 ( 2002-10-15), p. 1145-1154
    Type of Medium: Online Resource
    ISSN: 0022-1899 , 1537-6613
    URL: Issue
    URL: Article
    DOI: 10.1086/jid.2002.186.issue-8
    DOI: 10.1086/344231
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2002
    detail.hit.zdb_id: 1473843-0
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...