LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 4 of total 4

Search options

  1. Article ; Online: Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue.

    Whitworth, Isabella T / Henke, Katherine B / Yang, Bing / Scalf, Mark / Frey, Brian L / Jarrard, David F / Smith, Lloyd M

    Analytical chemistry

    2023  Volume 95, Issue 18, Page(s) 7087–7092

    Abstract: RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein complexes. ... ...

    Abstract RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein complexes. However, these studies have all been done in immortalized cell lines that do not capture the complexity of heterogeneous tissue samples. Here, we develop hybridization purification of RNA-protein complexes followed by mass spectrometry (HyPR-MS) for use in tissue samples. We isolated both polyadenylated RNA and the specific long noncoding RNA MALAT1 and characterized their protein interactomes. These results demonstrate the feasibility of HyPR-MS in tissue for the multiplexed characterization of specific RNA-protein complexes.
    MeSH term(s) RNA, Long Noncoding/genetics ; Cell Line ; RNA, Messenger
    Chemical Substances RNA, Long Noncoding ; RNA, Messenger
    Language English
    Publishing date 2023-04-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c05635
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue

    Whitworth, Isabella T. / Henke, Katherine B. / Yang, Bing / Scalf, Mark / Frey, Brian L. / Jarrard, David F. / Smith, Lloyd M.

    Analytical Chemistry. 2023 Apr. 24, v. 95, no. 18 p.7087-7092

    2023  

    Abstract: RNA–protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA–protein complexes. ... ...

    Abstract RNA–protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA–protein complexes. However, these studies have all been done in immortalized cell lines that do not capture the complexity of heterogeneous tissue samples. Here, we develop hybridization purification of RNA–protein complexes followed by mass spectrometry (HyPR-MS) for use in tissue samples. We isolated both polyadenylated RNA and the specific long noncoding RNA MALAT1 and characterized their protein interactomes. These results demonstrate the feasibility of HyPR-MS in tissue for the multiplexed characterization of specific RNA–protein complexes.
    Keywords analytical chemistry ; homeostasis ; hybridization ; mass spectrometry ; messenger RNA ; non-coding RNA ; protein-protein interactions
    Language English
    Dates of publication 2023-0424
    Size p. 7087-7092.
    Publishing place American Chemical Society
    Document type Article ; Online
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c05635
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 4' 52/94: Show issues
    Z 2.9: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    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: Identifying Protein Interactomes of Target RNAs Using HyPR-MS.

    Henke, Katherine B / Miller, Rachel M / Knoener, Rachel A / Scalf, Mark / Spiniello, Michele / Smith, Lloyd M

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

    2021  Volume 2404, Page(s) 219–244

    Abstract: RNA-protein interactions are integral to maintaining proper cellular function and homeostasis, and the disruption of key RNA-protein interactions is central to many disease states. HyPR-MS (hybridization purification of RNA-protein complexes followed by ... ...

    Abstract RNA-protein interactions are integral to maintaining proper cellular function and homeostasis, and the disruption of key RNA-protein interactions is central to many disease states. HyPR-MS (hybridization purification of RNA-protein complexes followed by mass spectrometry) is a highly versatile and efficient technology which enables multiplexed discovery of specific RNA-protein interactomes. This chapter provides extensive guidance for successful application of HyPR-MS to the system and target RNA(s) of interest, as well as a detailed description of the fundamental HyPR-MS procedure, including: (1) experimental design of controls, capture oligonucleotides, and qPCR assays; (2) formaldehyde cross-linking of cell culture; (3) cell lysis and RNA solubilization; (4) isolation of target RNA(s); (5) RNA purification and RT-qPCR analysis; (6) protein preparation and mass spectrometric analysis; and (7) mass spectrometric data analysis.
    MeSH term(s) Mass Spectrometry ; Nucleic Acid Hybridization ; Oligonucleotides ; Proteomics ; RNA/genetics
    Chemical Substances Oligonucleotides ; RNA (63231-63-0)
    Language English
    Publishing date 2021-10-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1851-6_12
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    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: Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens.

    Bowes, Devin A / Henke, Katherine B / Driver, Erin M / Newell, Melanie Engstrom / Block, Izabella / Shaffer, Gray / Varsani, Arvind / Scotch, Matthew / Halden, Rolf U

    The Science of the total environment

    2023  Volume 903, Page(s) 166230

    Abstract: A recent outbreak of the mpox virus (MPXV) occurred in non-endemic regions of the world beginning in May 2022. Pathogen surveillance systems faced pressure to quickly establish response protocols, offering an opportunity to employ wastewater-based ... ...

    Abstract A recent outbreak of the mpox virus (MPXV) occurred in non-endemic regions of the world beginning in May 2022. Pathogen surveillance systems faced pressure to quickly establish response protocols, offering an opportunity to employ wastewater-based epidemiology (WBE) for population-level monitoring. The pilot study reported herein aimed to: (i) develop a reliable protocol for MPXV DNA detection in wastewater which would reduce false negative reporting, (ii) test this protocol on wastewater from various regions across the United States, and (iii) conduct a state of the science review of the current literature reporting on experimental methods for MPXV detection using WBE. Twenty-four-hour composite samples of untreated municipal wastewater were collected from the states of New Jersey, Georgia, Illinois, Texas, Arizona, and Washington beginning July 3rd, 2022 through October 16th, 2022 (n = 60). Samples underwent vacuum filtration, DNA extraction from captured solids, MPXV DNA pre-amplification, and qPCR analysis. Of the 60 samples analyzed, a total of eight (13%) tested positive for MPXV in the states of Washington, Texas, New Jersey, and Illinois. The presence of clade IIb MPXV DNA in these samples was confirmed via Sanger sequencing and integration of pre-amplification prior to qPCR decreased the rate of false negative detections by 87% as compared to qPCR analysis alone. Wastewater-derived detections of MPXV were compared to clinical datasets, with 50% of detections occurring as clinical cases were increasing/peaking and 50% occurring as clinical cases waned. Results from the literature review (n = 9 studies) revealed successful strategies for the detection of MPXV DNA in wastewater, however also emphasized a need for further method optimization and standardization. Overall, this work highlights the use of pre-amplification prior to qPCR detection as a means to capture the presence of MPXV DNA in community wastewater and offers guidance for monitoring low-titer pathogens via WBE.
    Language English
    Publishing date 2023-08-11
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.166230
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 949: 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)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top