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  1. Book: PCR protocols

    Park, Daniel J.

    (Methods in molecular biology ; 687 ; Springer protocols)

    2011  

    Author's details ed. by Daniel J. Park
    Series title Methods in molecular biology ; 687
    Springer protocols
    Collection
    Language English
    Size XI, 348 S. : Ill., graph. Darst.
    Edition 3. ed.
    Publisher Humana Press
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT016528666
    ISBN 978-1-60761-943-7 ; 1-60761-943-1 ; 9781607619444 ; 160761944X
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2010 A 5975 order for loan Magazin

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  2. Article ; Online: Impact of Data and Study Characteristics on Microbiome Volatility Estimates.

    Park, Daniel J / Plantinga, Anna M

    Genes

    2023  Volume 14, Issue 1

    Abstract: The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the microbiome (the ... ...

    Abstract The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the microbiome (the magnitude of changes in their composition across time, called volatility) has been associated with human health. However, the effect of unbalanced sampling intervals and differential read depth on the estimates of microbiome volatility has not been thoroughly assessed. Using four publicly available gut and vaginal microbiome time series, we subsampled the datasets to several sampling intervals and read depths and then compared additive, multiplicative, centered log ratio (CLR)-based, qualitative, and distance-based measures of microbiome volatility between the conditions. We find that longer sampling intervals are associated with larger quantitative measures of change (particularly for common taxa), but not with qualitative measures of change or distance-based volatility quantification. A lower sequencing read depth is associated with smaller multiplicative, CLR-based, and qualitative measures of change (particularly for less common taxa). Strategic subsampling may serve as a useful sensitivity analysis in unbalanced longitudinal studies investigating clinical associations with microbiome volatility.
    MeSH term(s) Female ; Humans ; Microbiota ; Bacteria/genetics ; Longitudinal Studies ; Time Factors ; Specimen Handling
    Language English
    Publishing date 2023-01-14
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010218
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Impact of Data and Study Characteristics on Microbiome Volatility Estimates

    Park, Daniel J. / Plantinga, Anna M.

    Genes (Basel). 2023 Jan. 14, v. 14, no. 1

    2023  

    Abstract: The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the microbiome (the ... ...

    Abstract The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the microbiome (the magnitude of changes in their composition across time, called volatility) has been associated with human health. However, the effect of unbalanced sampling intervals and differential read depth on the estimates of microbiome volatility has not been thoroughly assessed. Using four publicly available gut and vaginal microbiome time series, we subsampled the datasets to several sampling intervals and read depths and then compared additive, multiplicative, centered log ratio (CLR)-based, qualitative, and distance-based measures of microbiome volatility between the conditions. We find that longer sampling intervals are associated with larger quantitative measures of change (particularly for common taxa), but not with qualitative measures of change or distance-based volatility quantification. A lower sequencing read depth is associated with smaller multiplicative, CLR-based, and qualitative measures of change (particularly for less common taxa). Strategic subsampling may serve as a useful sensitivity analysis in unbalanced longitudinal studies investigating clinical associations with microbiome volatility.
    Keywords data collection ; digestive system ; human health ; humans ; microbiome ; temporal variation ; time series analysis
    Language English
    Dates of publication 2023-0114
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010218
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana.

    Park, HaJeung / Youn, BuHyun / Park, Daniel J / Puthanveettil, Sathyanarayanan V / Kang, ChulHee

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 9622

    Abstract: The vacuolar sorting receptors (VSRs) are specific to plants and are responsible for sorting and transporting particular proteins from the trans-Golgi network to the vacuole. This process is critically important for various cellular functions, including ... ...

    Abstract The vacuolar sorting receptors (VSRs) are specific to plants and are responsible for sorting and transporting particular proteins from the trans-Golgi network to the vacuole. This process is critically important for various cellular functions, including storing nutrients during seed development. Despite many years of intense studies on VSRs, a complete relation between function and structure has not yet been revealed. Here, we present the crystal structure of the entire luminal region of glycosylated VSR1 from Arabidopsis thaliana (AtVSR1) for the first time. The structure provides insights into the tertiary and quaternary structures of VSR1, which are composed of an N-terminal protease-associated (PA) domain, a unique central region, and one epidermal growth factor (EGF)-like domain followed by two disordered EGF-like domains. The structure of VSR1 exhibits unique characteristics, the significance of which is yet to be fully understood.
    MeSH term(s) Arabidopsis Proteins/metabolism ; Arabidopsis Proteins/chemistry ; Arabidopsis Proteins/genetics ; Arabidopsis/metabolism ; Vacuoles/metabolism ; Protein Domains ; Models, Molecular ; Crystallography, X-Ray ; Protein Transport
    Chemical Substances Arabidopsis Proteins
    Language English
    Publishing date 2024-04-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-57975-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Lariat-dependent nested PCR for flanking sequence determination.

    Park, Daniel J

    Methods in molecular biology (Clifton, N.J.)

    2011  Volume 687, Page(s) 43–55

    Abstract: Methods detailed in this chapter relate to the use of Lariat-dependent Nested (LaNe) PCR to characterize unknown RNA or DNA sequence flanking known regions. A multitude of approaches designed to determine flanking sequences have been described in the ... ...

    Abstract Methods detailed in this chapter relate to the use of Lariat-dependent Nested (LaNe) PCR to characterize unknown RNA or DNA sequence flanking known regions. A multitude of approaches designed to determine flanking sequences have been described in the literature. Variously, problems related to these approaches include lack of resolution or failure, depending on experimental context, and complex handling. LaNe-based methods are designed to harness "two-sided" gene-specific PCR with the option of nesting but without the requirement for inefficient and involved enzyme preprocessing steps.
    MeSH term(s) Base Sequence ; DNA/genetics ; DNA Primers ; Polymerase Chain Reaction/methods ; RNA/genetics
    Chemical Substances DNA Primers ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2011
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-60761-944-4_4
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  6. Article ; Online: Enhanced solid phase PCR for increased loading of amplicon onto solid support.

    Park, Daniel J

    Methods in molecular biology (Clifton, N.J.)

    2011  Volume 687, Page(s) 257–264

    Abstract: The loading of amplicons onto solid supports such as beads during multiplex PCR or emulsion PCR conventionally has been performed by use of Solid Phase PCR or asymmetric Solid Phase PCR. These approaches are restrictive with respect to amplification ... ...

    Abstract The loading of amplicons onto solid supports such as beads during multiplex PCR or emulsion PCR conventionally has been performed by use of Solid Phase PCR or asymmetric Solid Phase PCR. These approaches are restrictive with respect to amplification efficiency and degree of amplicon loading. This chapter details Enhanced Solid Phase PCR principles and methodologies to enable higher amplicon -loading in the context of uncompromised amplification efficiency.
    MeSH term(s) DNA Primers ; Flow Cytometry ; Polymerase Chain Reaction/methods
    Chemical Substances DNA Primers
    Language English
    Publishing date 2011
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-60761-944-4_18
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Perish and publish: Dynamics of biomedical publications by deceased authors.

    Jung, Chol-Hee / Boutros, Paul C / Park, Daniel J / Corcoran, Niall M / Pope, Bernard J / Hovens, Christopher M

    PloS one

    2022  Volume 17, Issue 9, Page(s) e0273783

    Abstract: The question of whether it is appropriate to attribute authorship to deceased individuals of original studies in the biomedical literature is contentious. Authorship guidelines utilized by journals do not provide a clear consensus framework that is ... ...

    Abstract The question of whether it is appropriate to attribute authorship to deceased individuals of original studies in the biomedical literature is contentious. Authorship guidelines utilized by journals do not provide a clear consensus framework that is binding on those in the field. To guide and inform the implementation of authorship frameworks it would be useful to understand the extent of the practice in the scientific literature, but studies that have systematically quantified the prevalence of this phenomenon in the biomedical literature have not been performed to date. To address this issue, we quantified the prevalence of publications by deceased authors in the biomedical literature from the period 1990-2020. We screened 2,601,457 peer-reviewed papers from the full text Europe PubMed Central database. We applied natural language processing, stringent filtering and manual curation to identify a final set of 1,439 deceased authors. We then determined these authors published a total of 38,907 papers over their careers with 5,477 published after death. The number of deceased publications has been growing rapidly, a 146-fold increase since the year 2000. This rate of increase was still significant when accounting for the growing total number of publications and pool of authors. We found that more than 50% of deceased author papers were first submitted after the death of the author and that over 60% of these papers failed to acknowledge the deceased authors status. Most deceased authors published less than 10 papers after death but a small pool of 30 authors published significantly more. A pool of 266 authors published more than 90% of their total publications after death. Our analysis indicates that the attribution of deceased authorship in the literature is not an occasional occurrence but a burgeoning trend. A consensus framework to address authorship by deceased scientists is warranted.
    MeSH term(s) Authorship ; Europe ; Humans ; Peer Review ; PubMed ; Publishing
    Language English
    Publishing date 2022-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0273783
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Total Synthesis of the Four Stereoisomers of Cyclo(l-Trp-l-Arg) Raises Uncertainty of the Structures of the Natural Products and Invalidates Their Promising Antimicrobial Activities.

    Chen, Dan / Park, Daniel J / Cadelis, Melissa M / Douafer, Hana / Bourguet-Kondracki, Marie Lise / Brunel, Jean Michel / Copp, Brent R

    Molecules (Basel, Switzerland)

    2022  Volume 27, Issue 18

    Abstract: New therapeutic options to combat the growing incidence of antimicrobial resistance are urgently needed. A 2015 publication reported the isolation and biological evaluation of two diketopiperazine natural products, cyclo(l-Trp-l-Arg) (CDP 2) and cyclo(d- ... ...

    Abstract New therapeutic options to combat the growing incidence of antimicrobial resistance are urgently needed. A 2015 publication reported the isolation and biological evaluation of two diketopiperazine natural products, cyclo(l-Trp-l-Arg) (CDP 2) and cyclo(d-Trp-d-Arg) (CDP 3), from an
    MeSH term(s) Ampicillin ; Anti-Bacterial Agents/chemistry ; Anti-Infective Agents/pharmacology ; Biological Products/pharmacology ; Cytidine Diphosphate ; Diketopiperazines/chemistry ; Dipeptides/chemistry ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; Microbial Sensitivity Tests ; Peptides, Cyclic/chemistry ; Stereoisomerism ; Uncertainty
    Chemical Substances Anti-Bacterial Agents ; Anti-Infective Agents ; Biological Products ; Diketopiperazines ; Dipeptides ; Peptides, Cyclic ; Cytidine Diphosphate (63-38-7) ; Ampicillin (7C782967RD)
    Language English
    Publishing date 2022-09-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules27185913
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.MO 81: Show issues

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  9. Article ; Online: Benchmarking Metagenomics Tools for Taxonomic Classification.

    Ye, Simon H / Siddle, Katherine J / Park, Daniel J / Sabeti, Pardis C

    Cell

    2019  Volume 178, Issue 4, Page(s) 779–794

    Abstract: Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the ... ...

    Abstract Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
    MeSH term(s) Bacteria/classification ; Bacteria/genetics ; Benchmarking/methods ; Databases, Genetic ; Fungi/classification ; Fungi/genetics ; Metagenome/genetics ; Metagenomics/methods ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Software ; Viruses/classification ; Viruses/genetics
    Language English
    Publishing date 2019-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.07.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1167: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 58: Show issues

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  10. Book: PCR protocols

    Park, Daniel J

    (Springer protocols ; Methods in molecular biology, ; 687)

    2011  

    Series title Springer protocols
    Methods in molecular biology, ; 687
    Keywords Polymerase chain reaction ; polymerase chain reaction ; methodology
    Language English
    Size xi, 348 p. :, ill. ;, 27 cm.
    Edition 3rd ed. /
    Publisher Humana Press
    Publishing place New York, N.Y
    Document type Book
    ISBN 9781607619437 ; 1607619431 ; 9781607619444 ; 160761944X
    Database NAL-Catalogue (AGRICOLA)

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