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  1. Article ; Online: Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins.

    Zinder, John C / Lima, Christopher D

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

    2019  Volume 2062, Page(s) 427–448

    Abstract: 3' to 5' RNA degradation is primarily catalyzed by the RNA exosome subunits Dis3 and Rrp6 in the nucleus of Saccharomyces cerevisiae. These enzymes form a complex with the nine-subunit noncatalytic core (Exo9) to carry out their functions in vivo. ... ...

    Abstract 3' to 5' RNA degradation is primarily catalyzed by the RNA exosome subunits Dis3 and Rrp6 in the nucleus of Saccharomyces cerevisiae. These enzymes form a complex with the nine-subunit noncatalytic core (Exo9) to carry out their functions in vivo. Protein cofactors Rrp47, Mpp6, and the Mtr4 RNA helicase also assist the complex by modulating its activities and/or recruiting it to specific RNAs for processing or degradation. Here we present our preferred strategy for reconstituting RNA exosomes from S. cerevisiae using purified, recombinantly expressed components.
    MeSH term(s) DEAD-box RNA Helicases/metabolism ; DNA-Binding Proteins/metabolism ; Exoribonucleases/metabolism ; Exosome Multienzyme Ribonuclease Complex/metabolism ; Exosomes/metabolism ; Nuclear Proteins/metabolism ; RNA Stability/physiology ; RNA, Fungal/metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances DNA-Binding Proteins ; LRP1 protein, S cerevisiae ; Mpp6 protein, S cerevisiae ; Nuclear Proteins ; RNA, Fungal ; RNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Exoribonucleases (EC 3.1.-) ; Exosome Multienzyme Ribonuclease Complex (EC 3.1.-) ; MTR4 protein, S cerevisiae (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2019-11-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9822-7_21
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  2. Article ; Online: Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts.

    Weick, Eva-Maria / Zinder, John C / Lima, Christopher D

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

    2020  Volume 2062, Page(s) 417–425

    Abstract: The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome ... ...

    Abstract The eukaryotic RNA exosome is a conserved and ubiquitous multiprotein complex that possesses multiple RNase activities and is involved in a diverse array of RNA degradation and processing events. While much of our current understanding of RNA exosome function has been elucidated using genetics and cell biology based studies of protein functions, in particular in S. cerevisiae, many important contributions in the field have been enabled through use of in vitro reconstituted complexes. Here, we present an overview of our approach to purify exosome components from recombinant sources and reconstitute them into functional complexes. Three chapters following this overview provide detailed protocols for reconstituting exosome complexes from S. cerevisiae, S. pombe, and H. sapiens. We additionally provide insight on some of the drawbacks of these methods and highlight several important discoveries that have been achieved using reconstituted complexes.
    MeSH term(s) Animals ; Exoribonucleases/metabolism ; Exosome Multienzyme Ribonuclease Complex/metabolism ; Exosomes/metabolism ; Humans ; RNA Stability/physiology ; RNA, Fungal/metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances RNA, Fungal ; Recombinant Proteins ; Saccharomyces cerevisiae Proteins ; Exoribonucleases (EC 3.1.-) ; Exosome Multienzyme Ribonuclease Complex (EC 3.1.-)
    Language English
    Publishing date 2020-05-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9822-7_20
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  3. Article: The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage. I. Studies on the mechanism of B restriction in vivo.

    Hartman, N / Zinder, N D

    Journal of molecular biology

    2011  Volume 85, Issue 3, Page(s) 345–356

    MeSH term(s) Bacteriophages/genetics ; Chromosome Mapping ; Codon, Nonsense/genetics ; DNA Restriction Enzymes/genetics ; DNA Restriction Enzymes/metabolism ; DNA, Viral/genetics ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/virology ; Recombination, Genetic ; Viral Proteins/genetics
    Chemical Substances Codon, Nonsense ; DNA, Viral ; Viral Proteins ; DNA Restriction Enzymes (EC 3.1.21.-)
    Language English
    Publishing date 2011-06-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/0022-2836(74)90437-9
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  4. Article: The effect of B specific restriction and modification of DNA on linkage relationships in f1 bacteriophage. II. Evidence for a heteroduplex intermediate in f1 recombination.

    Hartman, N / Zinder, N D

    Journal of molecular biology

    2011  Volume 85, Issue 3, Page(s) 357–369

    MeSH term(s) Codon, Terminator/genetics ; Coliphages/genetics ; Crosses, Genetic ; DNA Methylation ; DNA Restriction Enzymes/metabolism ; DNA, Viral/genetics ; DNA, Viral/metabolism ; Escherichia coli/enzymology ; Escherichia coli/virology ; Genetic Linkage ; Mutation ; Recombination, Genetic
    Chemical Substances Codon, Terminator ; DNA, Viral ; DNA Restriction Enzymes (EC 3.1.21.-)
    Language English
    Publishing date 2011-06-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/0022-2836(74)90438-0
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  5. Article ; Online: Thermoregulation and Hydration in Female American Football Players During Practices.

    Lopez, Rebecca M / Ashley, Candi D / Zinder, Steven M / Tritsch, Amanda J

    Journal of strength and conditioning research

    2019  Volume 35, Issue 9, Page(s) 2552–2557

    Abstract: ... 3° C (n = 14). Average practice HR was 118 ± 11 b·min-1, while HRmax was 148 ± 13 b·min-1. Subjects ... Abstract: Lopez, RM, Ashley, CD, Zinder, SM, and Tritsch, AJ. Thermoregulation and hydration ...

    Abstract Abstract: Lopez, RM, Ashley, CD, Zinder, SM, and Tritsch, AJ. Thermoregulation and hydration in female American football players during practices. J Strength Cond Res 35(9): 2552-2557, 2021-Little is known about hydration practices and thermoregulation in female tackle football players. The purpose of the study was to examine the thermoregulatory and hydration responses of female professional American football players. Fifteen females from the same tackle football team volunteered for this observational field study. Each subject was observed for 4 practices for the following measures: gastrointestinal temperature (TGI), maximum TGI, heart rate (HR), maximum HR (HRmax), fluid consumption, sweat rate, percent body mass loss (%BML), urine specific gravity (USG), urine color (Ucol), perceptual measures of thirst, thermal sensations, and rating of perceived exertion (RPE). Descriptive data (mean ± SD) were calculated for all measures. Main measures were analyzed using a repeated-measures analysis of variance. Trials took place during evening practices. Average TGI during practices was 38.0 ± 0.3° C while maximum TGI was 38.4 ± 0.3° C (n = 14). Average practice HR was 118 ± 11 b·min-1, while HRmax was 148 ± 13 b·min-1. Subjects arrived at practices with Ucol of 3 ± 1 and USG of 1.018 ± 0.007. Postpractice USG (1.022 ± 0.007) was significantly higher than prepractice across all days (p < 0.001). The average sweat rate across 4 practices was 0.6 ml·h-1. Average %BML was 0.3 ± 0.4%. Thirst and thermal sensations were moderate (4 ± 1 and 5 ± 1, respectively), while RPE was 11 ± 1. Female football players tended to have similar physiological responses to males. Although subjects seemed to adequately match their sweat losses with fluid consumed during practice, there was considerable variability in hydration indices and hydration habits, with some subjects experiencing hypohydration and others overestimating their fluid needs. Those working with this population should emphasize the need for hydration education and establish individualized hydration regimens.
    MeSH term(s) Body Temperature Regulation ; Dehydration/prevention & control ; Female ; Football ; Hot Temperature ; Humans ; Sweating ; United States
    Language English
    Publishing date 2019-05-02
    Publishing country United States
    Document type Journal Article ; Observational Study
    ZDB-ID 1156349-7
    ISSN 1533-4287 ; 1064-8011
    ISSN (online) 1533-4287
    ISSN 1064-8011
    DOI 10.1519/JSC.0000000000003180
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  6. Article: Bacterial transduction.

    ZINDER, N D

    Journal of cellular physiology. Supplement

    2003  Volume 45, Issue Suppl. 2, Page(s) 23–49

    MeSH term(s) Bacteria ; Genetics ; Salmonella
    Language English
    Publishing date 2003-10-03
    Publishing country United States
    Document type Journal Article
    ISSN 0737-1462
    ISSN 0737-1462
    DOI 10.1002/jcp.1030450504
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  7. Article: Hybrids of Escherichia and Salmonella.

    ZINDER, N D

    Science (New York, N.Y.)

    2003  Volume 131, Issue 3403, Page(s) 813–815

    MeSH term(s) Escherichia ; Escherichia coli/genetics ; Hybridization, Genetic ; Nucleic Acid Hybridization ; Salmonella/genetics
    Language English
    Publishing date 2003-05-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.131.3403.813
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  8. Article: Infective heredity in bacteria.

    ZINDER, N D

    Cold Spring Harbor symposia on quantitative biology

    2003  Volume 18, Page(s) 261–269

    MeSH term(s) Bacteria ; Heredity ; Humans
    Language English
    Publishing date 2003-08-28
    Publishing country United States
    Document type Journal Article
    ISSN 0091-7451
    ISSN 0091-7451
    DOI 10.1101/sqb.1953.018.01.037
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  9. Article: A bacteriophage specific for F- Salmonella strains.

    ZINDER, N D

    Science (New York, N.Y.)

    2003  Volume 133, Issue 3470, Page(s) 2069–2070

    Abstract: A bacteriophage is described which grows on recipient (F-) and not on donor ( Hfr, F+, or F') salmonella. The reason for this differential is unknown, since the phage attaches to all mating types, but progeny ensue only from female bacteria. Purification ...

    Abstract A bacteriophage is described which grows on recipient (F-) and not on donor ( Hfr, F+, or F') salmonella. The reason for this differential is unknown, since the phage attaches to all mating types, but progeny ensue only from female bacteria. Purification of this phage has been accomplished. A procedure is described for quantitatively determining either the acquisition or loss of the F agent by bacteria.
    MeSH term(s) Bacteriophages ; Salmonella
    Language English
    Publishing date 2003-05-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.133.3470.2069
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  10. Article: Sexuality and mating in salmonella.

    ZINDER, N D

    Science (New York, N.Y.)

    2003  Volume 131, Issue 3404, Page(s) 924–926

    Abstract: Another criterion for the presence of the agent (F) promoting genetic exchange in Escherichia coli was found. It involves a staining reaction of Hfr and F+ coli, but not F- coli, when mixed with strains of Salmonella typhimurium. This reaction was used ... ...

    Abstract Another criterion for the presence of the agent (F) promoting genetic exchange in Escherichia coli was found. It involves a staining reaction of Hfr and F+ coli, but not F- coli, when mixed with strains of Salmonella typhimurium. This reaction was used as a guide in following the transfer of the F agent to Salmonella and back to E. coli. The F agent in Salmonella seems to promote the same kinds of events that it promotes in E. coli.
    MeSH term(s) Escherichia coli ; Salmonella ; Salmonella typhimurium ; Sexuality
    Language English
    Publishing date 2003-05-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.131.3404.924
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