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  1. AU="Matthias Harbers"
  2. AU="Yang, Yuantong"
  3. AU="Carstens, Elma"
  4. AU="Wu, Xiaoxing"
  5. AU="Sato, Marika"
  6. AU="Rautiala, Petri"
  7. AU="Lin, Liqin"
  8. AU="Deborah Jean McClelland"
  9. AU="Brar, Ajit"
  10. AU="Aniyan Kumbalaparambil, Yesoda"
  11. AU=Carolan Michael
  12. AU="Pojskić, Mirza"
  13. AU="Tsujimoto, Sakura"
  14. AU=Di Tano Giuseppe
  15. AU="Khan, Sobia"
  16. AU="Kao, Yu-Yin"
  17. AU="Katerina Demnerova"
  18. AU="Sorrentino, I"
  19. AU="Pogge von Strandmann, Elke"
  20. AU="Lenzi, Kerry A"
  21. AU="Sakakura, Akira"
  22. AU="Nowell, Sian"
  23. AU="Mirko Cortese"
  24. AU="Klein, Steffen"
  25. AU="Koike, Toru"
  26. AU="Hung, Chung-Yu"
  27. AU="Muendlein, Hayley I"
  28. AU="Papavramidis, Theodosios"

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  1. Artikel ; Online: Easy Synthesis of Complex Biomolecular Assemblies

    Marie-Laure Fogeron / Lauriane Lecoq / Laura Cole / Matthias Harbers / Anja Böckmann

    Frontiers in Molecular Biosciences, Vol

    Wheat Germ Cell-Free Protein Expression in Structural Biology

    2021  Band 8

    Abstract: Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic ...

    Abstract Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
    Schlagwörter cell-free protein expression ; wheat germ ; structural biology ; NMR ; labeling ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-03-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: A comparison of non-magnetic and magnetic beads for measuring IgG antibodies against Plasmodium vivax antigens in a multiplexed bead-based assay using Luminex technology (Bio-Plex 200 or MAGPIX).

    Ramin Mazhari / Jessica Brewster / Rich Fong / Caitlin Bourke / Zoe S J Liu / Eizo Takashima / Takafumi Tsuboi / Wai-Hong Tham / Matthias Harbers / Chetan Chitnis / Julie Healer / Maria Ome-Kaius / Jetsumon Sattabongkot / James Kazura / Leanne J Robinson / Christopher King / Ivo Mueller / Rhea J Longley

    PLoS ONE, Vol 15, Iss 12, p e

    2020  Band 0238010

    Abstract: Multiplexed bead-based assays that use Luminex® xMAP® technology have become popular for measuring antibodies against proteins of interest in many fields, including malaria and more recently SARS-CoV-2/COVID-19. There are currently two formats that are ... ...

    Abstract Multiplexed bead-based assays that use Luminex® xMAP® technology have become popular for measuring antibodies against proteins of interest in many fields, including malaria and more recently SARS-CoV-2/COVID-19. There are currently two formats that are widely used: non-magnetic beads or magnetic beads. Data are lacking regarding the comparability of results obtained using these two types of beads, and for assays run on different instruments. Whilst non-magnetic beads can only be run on flow-based instruments (such as the Luminex® 100/200™ or Bio-Plex® 200), magnetic beads can be run on both these and the newer MAGPIX® instruments. In this study we utilized a panel of purified recombinant Plasmodium vivax proteins and samples from malaria-endemic areas to measure P. vivax-specific IgG responses using different combinations of beads and instruments. We directly compared: i) non-magnetic versus magnetic beads run on a Bio-Plex® 200, ii) magnetic beads run on the Bio-Plex® 200 versus MAGPIX® and iii) non-magnetic beads run on a Bio-Plex® 200 versus magnetic beads run on the MAGPIX®. We also performed an external comparison of our optimized assay. We observed that IgG antibody responses, measured against our panel of P. vivax proteins, were moderately-strongly correlated in all three of our comparisons (pearson r>0.5 for 18/19 proteins), however higher amounts of protein were required for coupling to magnetic beads. Our external comparison indicated that results generated in different laboratories using the same coupled beads are also highly comparable (pearson r>0.7), particularly if a reference standard curve is used.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 621
    Sprache Englisch
    Erscheinungsdatum 2020-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Aptamer-dependent full-length cDNA synthesis by overlap extension PCR

    Yasumasa Mitani / Takayuki Nakayama / Matthias Harbers / Yoshihide Hayashizaki

    BioTechniques, Vol 37, Iss 1, Pp 124-

    2004  Band 129

    Abstract: Sequencing of the human genome in combination with computational annotation has provided tremendous data on predicted genes. However, for most of them, no corresponding cDNAs are available yet. Furthermore, even where cDNA clones were obtained, gene ... ...

    Abstract Sequencing of the human genome in combination with computational annotation has provided tremendous data on predicted genes. However, for most of them, no corresponding cDNAs are available yet. Furthermore, even where cDNA clones were obtained, gene transcripts often have many different splice variants that are not covered by current gene collections. For direct synthesis of cDNA clones corresponding to predicted genes, new splice variants, or any other gene of interest, we established optimal PCR conditions for the direct amplification of exons from genomic DNA, which require a specific Taq aptamer. PCR products comprising differently tagged exons were concatenated by overlap extension into full-length cDNAs. To prove the effectiveness of the approach, the 1900-bp full-length open reading frame of the human mitochondrial aldehyde dehydrogenase (ALDH2) gene was synthesized in a two-step reaction comprising all 13 exons. Thus, our conditions are of general value for in vitro synthesis of cDNAs and alternative splice variants from genomic DNA.
    Schlagwörter Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2004-07-01T00:00:00Z
    Verlag Future Science Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Eprobe mediated real-time PCR monitoring and melting curve analysis.

    Takeshi Hanami / Diane Delobel / Hajime Kanamori / Yuki Tanaka / Yasumasa Kimura / Ayako Nakasone / Takahiro Soma / Yoshihide Hayashizaki / Kengo Usui / Matthias Harbers

    PLoS ONE, Vol 8, Iss 8, p e

    2013  Band 70942

    Abstract: Real-time monitoring of PCR is one of the most important methods for DNA and RNA detection widely used in research and medical diagnostics. Here we describe a new approach for combined real-time PCR monitoring and melting curve analysis using a 3' end- ... ...

    Abstract Real-time monitoring of PCR is one of the most important methods for DNA and RNA detection widely used in research and medical diagnostics. Here we describe a new approach for combined real-time PCR monitoring and melting curve analysis using a 3' end-blocked Exciton-Controlled Hybridization-sensitive fluorescent Oligonucleotide (ECHO) called Eprobe. Eprobes contain two dye moieties attached to the same nucleotide and their fluorescent signal is strongly suppressed as single-stranded oligonucleotides by an excitonic interaction between the dyes. Upon hybridization to a complementary DNA strand, the dyes are separated and intercalate into the double-strand leading to strong fluorescence signals. Intercalation of dyes can further stabilize the DNA/DNA hybrid and increase the melting temperature compared to standard DNA oligonucleotides. Eprobes allow for specific real-time monitoring of amplification reactions by hybridizing to the amplicon in a sequence-dependent manner. Similarly, Eprobes allow for analysis of reaction products by melting curve analysis. The function of different Eprobes was studied using the L858R mutation in the human epidermal growth factor receptor (EGFR) gene, and multiplex detection was demonstrated for the human EGFR and KRAS genes using Eprobes with two different dyes. Combining amplification and melting curve analysis in a single-tube reaction provides powerful means for new mutation detection assays. Functioning as "sequence-specific dyes", Eprobes hold great promises for future applications not only in PCR but also as hybridization probes in other applications.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2013-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Edesign

    Yasumasa Kimura / Takahiro Soma / Naoko Kasahara / Diane Delobel / Takeshi Hanami / Yuki Tanaka / Michiel J L de Hoon / Yoshihide Hayashizaki / Kengo Usui / Matthias Harbers

    PLoS ONE, Vol 11, Iss 2, p e

    Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

    2016  Band 0146950

    Abstract: Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require ... ...

    Abstract Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Defining the next generation of Plasmodium vivax diagnostic tests for control and elimination

    Xavier C Ding / Maria Paz Ade / J Kevin Baird / Qin Cheng / Jane Cunningham / Mehul Dhorda / Chris Drakeley / Ingrid Felger / Dionicia Gamboa / Matthias Harbers / Socrates Herrera / Naomi Lucchi / Alfredo Mayor / Ivo Mueller / Jetsumon Sattabongkot / Arsène Ratsimbason / Jack Richards / Marcel Tanner / Iveth J González

    PLoS Neglected Tropical Diseases, Vol 11, Iss 4, p e

    Target product profiles.

    2017  Band 0005516

    Abstract: The global prevalence of malaria has decreased over the past fifteen years, but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional malaria control interventions aimed principally at P. ... ...

    Abstract The global prevalence of malaria has decreased over the past fifteen years, but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional malaria control interventions aimed principally at P. falciparum. Approximately half of all malaria cases outside of Africa are caused by P. vivax. This species places dormant forms in human liver that cause repeated clinical attacks without involving another mosquito bite. The diagnosis of acute patent P. vivax malaria relies primarily on light microscopy. Specific rapid diagnostic tests exist but typically perform relatively poorly compared to those for P. falciparum. Better diagnostic tests are needed for P. vivax. To guide their development, FIND, in collaboration with P. vivax experts, identified the specific diagnostic needs associated with this species and defined a series of three distinct target product profiles, each aimed at a particular diagnostic application: (i) point-of-care of acutely ill patients for clinical care purposes; (ii) point-of-care asymptomatic and otherwise sub-patent residents for public health purposes, e.g., mass screen and treat campaigns; and (iii) ultra-sensitive not point-of-care diagnosis for epidemiological research/surveillance purposes. This report presents and discusses the rationale for these P. vivax-specific diagnostic target product profiles. These contribute to the rational development of fit-for-purpose diagnostic tests suitable for the clinical management, control and elimination of P. vivax malaria.
    Schlagwörter Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2017-04-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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