LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 906

Search options

  1. Article ; Online: Breaking the deadlock in genetic code expansion.

    Hou, Ya-Ming / Nakano, Yuko

    Nature chemical biology

    2024  Volume 20, Issue 4, Page(s) 406–407

    MeSH term(s) Genetic Code
    Language English
    Publishing date 2024-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-024-01579-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6251: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 90: 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.

  2. Article ; Online: Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen

    Isao Masuda / Ya-Ming Hou

    STAR Protocols, Vol 4, Iss 2, Pp 102196- (2023)

    2023  

    Abstract: Summary: We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, ... ...

    Abstract Summary: We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3′-side of the tRNA anticodon.For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Genetics ; Genomics ; Sequencing ; Microbiology ; Molecular Biology ; Gene Expression ; Science (General) ; Q1-390
    Subject code 004
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Elsevier
    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: Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen.

    Masuda, Isao / Hou, Ya-Ming

    STAR protocols

    2023  Volume 4, Issue 2, Page(s) 102196

    Abstract: We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout ... ...

    Abstract We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m
    Language English
    Publishing date 2023-03-28
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2023.102196
    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: Synthesis of Stably Charged Arg-tRNA

    Yamaki, Yuka / Gamper, Howard / Hou, Ya-Ming

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

    2023  Volume 2620, Page(s) 263–271

    Abstract: Posttranslational protein arginylation catalyzed by arginyl transferases is a mechanism to regulate multiple physiological processes. This protein arginylation reaction uses a charged Arg- ... ...

    Abstract Posttranslational protein arginylation catalyzed by arginyl transferases is a mechanism to regulate multiple physiological processes. This protein arginylation reaction uses a charged Arg-tRNA
    MeSH term(s) Arginine/metabolism ; Arginine-tRNA Ligase/chemistry ; Arginine-tRNA Ligase/genetics ; Arginine-tRNA Ligase/metabolism ; RNA, Transfer, Arg/chemistry ; RNA, Transfer, Arg/genetics ; RNA, Transfer, Arg/metabolism ; Protein Binding ; RNA, Transfer/metabolism
    Chemical Substances Arginine (94ZLA3W45F) ; Arginine-tRNA Ligase (EC 6.1.1.19) ; RNA, Transfer, Arg ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2023-04-03
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2942-0_28
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text 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.

  5. Article ; Online: Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons.

    Gamper, Howard / Masuda, Isao / Hou, Ya-Ming

    Journal of molecular biology

    2022  Volume 434, Issue 8, Page(s) 167440

    Abstract: Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, ...

    Abstract Inducing tRNA +1 frameshifting to read a quadruplet codon has the potential to incorporate a non-canonical amino acid (ncAA) into the polypeptide chain. While this strategy is attractive for genome expansion in biotechnology and bioengineering endeavors, improving the yield is hampered by a lack of understanding of where the shift can occur in an elongation cycle of protein synthesis. Lacking a clear answer to this question, current efforts have focused on designing +1-frameshifting tRNAs with an extra nucleotide inserted to the anticodon loop for pairing with a quadruplet codon in the aminoacyl-tRNA binding (A) site of the ribosome. However, the designed and evolved +1-frameshifting tRNAs vary broadly in achieving successful genome expansion. Here we summarize recent work on +1-frameshifting tRNAs. We suggest that, rather than engineering the quadruplet anticodon-codon pairing scheme at the ribosome A site, efforts should be made to engineer the pairing scheme at steps after the A site, including the step of the subsequent translocation and the step that stabilizes the pairing scheme in the +1-frame in the peptidyl-tRNA binding (P) site.
    MeSH term(s) Anticodon/genetics ; Anticodon/metabolism ; Base Pairing ; Codon/genetics ; Escherichia coli/metabolism ; Frameshifting, Ribosomal/genetics ; Genetic Code ; Protein Engineering/methods ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/metabolism
    Chemical Substances Anticodon ; Codon ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2022-01-04
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167440
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: 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.

  6. Article ; Online: A Label-Free Assay for Aminoacylation of tRNA.

    Gamper, Howard / Hou, Ya-Ming

    Genes

    2020  Volume 11, Issue 10

    Abstract: Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the ... ...

    Abstract Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the rate of cell growth. Traditional assays for the quantification of tRNA aminoacylation involve radioactivity, either with a radioactive amino acid or with a [3'-
    MeSH term(s) Amino Acids/chemistry ; Amino Acyl-tRNA Synthetases/metabolism ; Biological Assay/methods ; Humans ; RNA, Transfer/analysis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Transfer RNA Aminoacylation
    Chemical Substances Amino Acids ; RNA, Transfer (9014-25-9) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
    Language English
    Publishing date 2020-10-07
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes11101173
    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.

  7. Article ; Online: Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases.

    Hou, Ya-Ming

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

    2016  Volume 1421, Page(s) 79–96

    Abstract: Methyl transfer from S-adenosyl methionine (abbreviated as AdoMet) to biologically active molecules such as mRNAs and tRNAs is one of the most fundamental and widespread reactions in nature, occurring in all three domains of life. The measurement of ... ...

    Abstract Methyl transfer from S-adenosyl methionine (abbreviated as AdoMet) to biologically active molecules such as mRNAs and tRNAs is one of the most fundamental and widespread reactions in nature, occurring in all three domains of life. The measurement of kinetic constants of AdoMet-dependent methyl transfer is therefore important for understanding the reaction mechanism in the context of biology. When kinetic constants of methyl transfer are measured in steady state over multiple rounds of turnover, the meaning of these constants is difficult to define and is often limited by non-chemical steps of the reaction, such as product release after each turnover. Here, the measurement of kinetic constants of methyl transfer by tRNA methyltransferases in rapid equilibrium binding condition for one methyl transfer is described. The advantage of such a measurement is that the meaning of kinetic constants can be directly assigned to the steps associated with the chemistry of methyl transfer, including the substrate binding affinity to the methyltransferase, the pre-chemistry re-arrangement of the active site, and the chemical step of methyl transfer. An additional advantage is that kinetic constants measured for one methyl transfer can be correlated with structural information of the methyltransferase to gain direct insight into its reaction mechanism.
    MeSH term(s) Denaturing Gradient Gel Electrophoresis/methods ; Enzyme Assays/methods ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Kinetics ; Methylation ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; S-Adenosylmethionine/metabolism ; Substrate Specificity ; Transcription, Genetic ; tRNA Methyltransferases/genetics ; tRNA Methyltransferases/metabolism
    Chemical Substances Escherichia coli Proteins ; S-Adenosylmethionine (7LP2MPO46S) ; RNA, Transfer (9014-25-9) ; TrmD protein, E coli (EC 2.1.1.-) ; tRNA Methyltransferases (EC 2.1.1.-)
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-3591-8_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text 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.

  8. Article ; Online: Preparation of an Enriched tRNA

    Avcilar-Kucukgoze, Irem / Gamper, Howard / Hou, Ya-Ming / Kashina, Anna S

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

    2022  Volume 2620, Page(s) 101–106

    Abstract: The method described here provides a fast and efficient way to obtain an enriched preparation of tRNA of interest, which is also posttranscriptionally modified by the intracellular machinery of the host cells, E. coli. While this preparation also ... ...

    Abstract The method described here provides a fast and efficient way to obtain an enriched preparation of tRNA of interest, which is also posttranscriptionally modified by the intracellular machinery of the host cells, E. coli. While this preparation also contains a mixture of total E. coli tRNA, the enriched tRNA of interest is obtained in high yields (milligram) and is highly efficient for biochemical assays in vitro. It is routinely used in our lab for arginylation.
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; RNA, Transfer, Arg/metabolism ; RNA, Transfer/genetics
    Chemical Substances RNA, Transfer, Arg ; RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2022-11-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2942-0_13
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text 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.

  9. Article ; Online: Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis.

    Gamper, Howard / McCormick, Caroline / Makhamreh, Amr / Wanunu, Meni / Rouhanifard, Sara H / Hou, Ya-Ming

    Methods in enzymology

    2023  Volume 692, Page(s) 127–153

    Abstract: Synthesis of RNA standards that contain an internal site-specific modification is important for mapping and quantification of the modified nucleotide in sequencing analysis. While RNA containing a site-specific modification can be readily synthesized by ... ...

    Abstract Synthesis of RNA standards that contain an internal site-specific modification is important for mapping and quantification of the modified nucleotide in sequencing analysis. While RNA containing a site-specific modification can be readily synthesized by solid-state coupling for less than 100-mer nucleotides, longer RNA must be synthesized by enzymatic ligation in the presence of a DNA splint. However, long RNAs have structural heterogeneity, and those generated by in vitro transcription have 3'-end sequence heterogeneity, which together substantially reduce the yield of ligation. Here we describe a method of 3-part splint ligation that joins an in vitro transcribed left-arm RNA, an in vitro transcribed right-arm RNA, and a chemically synthesized modification-containing middle RNA, with an efficiency higher than previously reported. We report that the improved efficiency is largely attributed to the inclusion of a pair of DNA disruptors proximal to the ligation sites, and to a lesser extent to the homogeneous processing of the 3'-end of the left-arm RNA. The yields of the ligated long RNA are sufficiently high to afford purification to homogeneity for practical RNA research. We also verify the sequence accuracy at each ligation junction by nanopore sequencing.
    MeSH term(s) RNA/genetics ; RNA/chemistry ; DNA ; Pseudouridine
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2) ; Pseudouridine (1445-07-4)
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.04.024
    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.

  10. Article: A Label-Free Assay for Aminoacylation of tRNA

    Gamper, Howard / Hou, Ya-Ming

    Genes. 2020 Oct. 07, v. 11, no. 10

    2020  

    Abstract: Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the ... ...

    Abstract Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the rate of cell growth. Traditional assays for the quantification of tRNA aminoacylation involve radioactivity, either with a radioactive amino acid or with a [3′-³²P]-labeled tRNA. We describe here a label-free assay that monitors aminoacylation by biotinylation-streptavidin (SA) conjugation to the α-amine or the α-imine of the aminoacyl group on the aa-tRNA. The conjugated aa-tRNA product is readily separated from the unreacted tRNA by a denaturing polyacrylamide gel, allowing for quantitative measurement of aminoacylation. This label-free assay is applicable to a wide range of amino acids and tRNA sequences and to both classes of aminoacylation. It is more sensitive and robust than the assay with a radioactive amino acid and has the potential to explore a wider range of tRNA than the assay with a [3′-³²P]-labeled tRNA. This label-free assay reports kinetic parameters of aminoacylation quantitatively similar to those reported by using a radioactive amino acid, suggesting its broad applicability to research relevant to human health and disease.
    Keywords aminoacylation ; cell growth ; gels ; human health ; polyacrylamide ; quantitative analysis ; radioactivity ; ribosomes
    Language English
    Dates of publication 2020-1007
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes11101173
    Database NAL-Catalogue (AGRICOLA)

    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.

To top