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  1. Article ; Online: Microbial community structures of novel Icelandic hot spring systems revealed by PhyloChip G3 analysis.

    Krebs, Jordan E / Vaishampayan, Parag / Probst, Alexander J / Tom, Lauren M / Marteinsson, Viggó Thór / Andersen, Gary L / Venkateswaran, Kasthuri

    Astrobiology

    2014  Volume 14, Issue 3, Page(s) 229–240

    Abstract: Microbial community profiles of recently formed hot spring systems ranging in temperatures from 57°C to 100°C and pH values from 2 to 4 in Hveragerði (Iceland) were analyzed with PhyloChip G3 technology. In total, 1173 bacterial operational taxonomic ... ...

    Abstract Microbial community profiles of recently formed hot spring systems ranging in temperatures from 57°C to 100°C and pH values from 2 to 4 in Hveragerði (Iceland) were analyzed with PhyloChip G3 technology. In total, 1173 bacterial operational taxonomic units (OTUs) spanning 576 subfamilies and 38 archaeal OTUs covering 32 subfamilies were observed. As expected, the hyperthermophilic (∼100°C) spring system exhibited both low microbial biomass and diversity when compared to thermophilic (∼ 60°C) springs. Ordination analysis revealed distinct bacterial and archaeal diversity in geographically distinct hot springs. Slight variations in temperature (from 57°C to 64°C) within the interconnected pools led to a marked fluctuation in microbial abundance and diversity. Correlation and PERMANOVA tests provided evidence that temperature was the key environmental factor responsible for microbial community dynamics, while pH, H2S, and SO2 influenced the abundance of specific microbial groups. When archaeal community composition was analyzed, the majority of detected OTUs correlated negatively with temperature, and few correlated positively with pH.
    MeSH term(s) Acidobacteria/genetics ; Actinobacteria/genetics ; Alphaproteobacteria/genetics ; Archaea/genetics ; Bacteria/genetics ; Betaproteobacteria/genetics ; Biodiversity ; Crenarchaeota/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Deltaproteobacteria/genetics ; Euryarchaeota/genetics ; Gammaproteobacteria/genetics ; Hot Springs/microbiology ; Iceland ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA
    Chemical Substances DNA, Archaeal ; DNA, Bacterial ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2014-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2047736-3
    ISSN 1557-8070 ; 1531-1074
    ISSN (online) 1557-8070
    ISSN 1531-1074
    DOI 10.1089/ast.2013.1008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

    El Khattabi, Laila / Aiden, Erez Lieberman / Asturias, Francisco J / Casellas, Rafael / Chauss, Daniel / Huang, Su-Chen / Jung, Seolkyoung / Kalchschmidt, Jens / Kieffer-Kwon, Kyong-Rim / Kieffer-Kwon, Philippe / Krebs, Jordan / Lopez, Andrea / Nóbrega, Marcelo A / Park, Solji / Pruett, Nathanael / Rao, Suhas S.P / Sadler, Erica / Sakabe, Noboru / Sobreira, Débora R /
    Tripathi, Subhash / Van Blerkom, Peter / Wang, Xiang / Young, Natalie / Zhao, Haiyan

    Cell. 2019 Aug. 22, v. 178, no. 5

    2019  

    Abstract: While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure ... ...

    Abstract While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator’s structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
    Keywords CRISPR-Cas systems ; cryo-electron microscopy ; DNA ; embryonic stem cells ; enzymes ; mammals ; mechanism of action ; models ; topology ; transcription factors
    Language English
    Dates of publication 2019-0822
    Size p. 1145-1158.e20.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.07.011
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

    El Khattabi, Laila / Zhao, Haiyan / Kalchschmidt, Jens / Young, Natalie / Jung, Seolkyoung / Van Blerkom, Peter / Kieffer-Kwon, Philippe / Kieffer-Kwon, Kyong-Rim / Park, Solji / Wang, Xiang / Krebs, Jordan / Tripathi, Subhash / Sakabe, Noboru / Sobreira, Débora R / Huang, Su-Chen / Rao, Suhas S P / Pruett, Nathanael / Chauss, Daniel / Sadler, Erica /
    Lopez, Andrea / Nóbrega, Marcelo A / Aiden, Erez Lieberman / Asturias, Francisco J / Casellas, Rafael

    Cell

    2019  Volume 178, Issue 5, Page(s) 1145–1158.e20

    Abstract: While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure ... ...

    Abstract While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
    MeSH term(s) Animals ; CD4-Positive T-Lymphocytes/cytology ; CD4-Positive T-Lymphocytes/metabolism ; CRISPR-Cas Systems/genetics ; Cell Cycle Proteins/metabolism ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/metabolism ; Cryoelectron Microscopy ; Enhancer Elements, Genetic ; Gene Editing ; Humans ; Male ; Mediator Complex/chemistry ; Mediator Complex/genetics ; Mediator Complex/metabolism ; Mice ; Mice, Inbred C57BL ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Promoter Regions, Genetic ; Protein Structure, Quaternary ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Cohesins
    Chemical Substances Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Mediator Complex ; Saccharomyces cerevisiae Proteins ; RNA Polymerase II (EC 2.7.7.-)
    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.
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.07.011
    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:
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    Zs.MG 58: Show issues

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  4. Article: Dipyrrolidinomethylaminophosphoric acid triamide (DPMPA) as an activator for the samarium diiodide-mediated reduction of alkyl and aryl halides

    McDonald, Chriss E / Ramsey, Jeremy R / Sampsell, David G / Anderson, Laura A / Krebs, Jordan E / Smith, Samantha N

    Tetrahedron. 2013 Apr. 8, v. 69, no. 14

    2013  

    Abstract: The use of the conjugate base of dipyrrolidinomethylaminophosphoric triamide (DPMPA⁻) as an activator of samarium diiodide is reported. This phosphoramidate has been shown to be a very potent ligand, allowing for the efficient, low-temperature reduction ... ...

    Abstract The use of the conjugate base of dipyrrolidinomethylaminophosphoric triamide (DPMPA⁻) as an activator of samarium diiodide is reported. This phosphoramidate has been shown to be a very potent ligand, allowing for the efficient, low-temperature reduction of alkyl and aryl chlorides. Reductive cyclizations of haloalkenylnaphthalenes are also reported.
    Keywords chemical reactions ; chemical structure ; chlorides ; organic compounds ; samarium
    Language English
    Dates of publication 2013-0408
    Size p. 2947-2953.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 204285-x
    ISSN 1464-5416 ; 0040-4020 ; 0563-2064
    ISSN (online) 1464-5416
    ISSN 0040-4020 ; 0563-2064
    DOI 10.1016/j.tet.2013.02.025
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1076: Show issues Location:
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  5. Article ; Online: Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

    Juan, Aster H / Wang, Stan / Ko, Kyung Dae / Zare, Hossein / Tsai, Pei-Fang / Feng, Xuesong / Vivanco, Karinna O / Ascoli, Anthony M / Gutierrez-Cruz, Gustavo / Krebs, Jordan / Sidoli, Simone / Knight, Adam L / Pedersen, Roger A / Garcia, Benjamin A / Casellas, Rafael / Zou, Jizhong / Sartorelli, Vittorio

    Cell reports

    2017  Volume 18, Issue 1, Page(s) 297

    Language English
    Publishing date 2017-01-03
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2016.12.036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

    Juan, Aster H / Wang, Stan / Ko, Kyung Dae / Zare, Hossein / Tsai, Pei-Fang / Feng, Xuesong / Vivanco, Karinna O / Ascoli, Anthony M / Gutierrez-Cruz, Gustavo / Krebs, Jordan / Sidoli, Simone / Knight, Adam L / Pedersen, Roger A / Garcia, Benjamin A / Casellas, Rafael / Zou, Jizhong / Sartorelli, Vittorio

    Cell reports

    2016  Volume 17, Issue 5, Page(s) 1369–1382

    Abstract: The polycomb repressive complex 2 (PRC2) methylates lysine 27 of histone H3 (H3K27) through its catalytic subunit Ezh2. PRC2-mediated di- and tri-methylation (H3K27me2/H3K27me3) have been interchangeably associated with gene repression. However, it ... ...

    Abstract The polycomb repressive complex 2 (PRC2) methylates lysine 27 of histone H3 (H3K27) through its catalytic subunit Ezh2. PRC2-mediated di- and tri-methylation (H3K27me2/H3K27me3) have been interchangeably associated with gene repression. However, it remains unclear whether these two degrees of H3K27 methylation have different functions. In this study, we have generated isogenic mouse embryonic stem cells (ESCs) with a modified H3K27me2/H3K27me3 ratio. Our findings document dynamic developmental control in the genomic distribution of H3K27me2 and H3K27me3 at regulatory regions in ESCs. They also reveal that modifying the ratio of H3K27me2 and H3K27me3 is sufficient for the acquisition and repression of defined cell lineage transcriptional programs and phenotypes and influences induction of the ESC ground state.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Cell Lineage ; Embryoid Bodies/cytology ; Embryoid Bodies/metabolism ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Gene Expression Regulation ; Genome ; Histones/metabolism ; Lysine/metabolism ; Methylation ; Mice ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Neurons/cytology ; RNA Editing ; Regulatory Sequences, Nucleic Acid/genetics ; Transcription Activator-Like Effector Nucleases/metabolism ; Transcription, Genetic
    Chemical Substances Histones ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; Ezh2 protein, mouse (EC 2.1.1.43) ; Transcription Activator-Like Effector Nucleases (EC 3.1.-) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2016-12-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2016.09.087
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Chryseobacterium angstadtii sp. nov., isolated from a newt tank.

    Kirk, Karen E / Hoffman, Jessica A / Smith, Katherine A / Strahan, Brittane L / Failor, Kevin C / Krebs, Jordan E / Gale, Andrew N / Do, Tri D / Sontag, Thomas C / Batties, Allison M / Mistiszyn, Kimberly / Newman, Jeffrey D

    International journal of systematic and evolutionary microbiology

    2013  Volume 63, Issue Pt 12, Page(s) 4777–4783

    Abstract: As part of an undergraduate microbiology course, a yellow-orange-pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain was isolated from a glass tank housing several red-spotted newts (Notophthalmus viridescens). The sequence of the ... ...

    Abstract As part of an undergraduate microbiology course, a yellow-orange-pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain was isolated from a glass tank housing several red-spotted newts (Notophthalmus viridescens). The sequence of the 16S rRNA gene of this strain, designated KM(T), was 97.4-98.0 % similar to those of the type strains of Chryseobacterium luteum, C. shigense and C. vrystaatense, while the similarity levels for protein-coding genes were less than 94.7 % for rpoB, less than 92.1 % for groEL and less than 87.1 % for gyrB. These values are lower than for many other established distinct species. Polyphasic characterization and comparison to these relatives revealed that strain KM(T) was similar to other Chryseobacterium strains in that it contained MK-6 as its major respiratory quinone and phosphatidylethanolamine as the most abundant polar lipid, produced flexirubin-type pigments, oxidase and catalase and primarily contained the fatty acids iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). Based on the results of this study, strain KM(T) represents a novel species, for which the name Chryseobacterium angstadtii sp. nov. is proposed. The type strain is KM(T) ( = ATCC BAA-2160(T) = NRRL B-59516(T) = KCTC 23297(T)).
    MeSH term(s) Animals ; Bacterial Typing Techniques ; Base Composition ; Chaperonin 60/genetics ; Chryseobacterium/classification ; Chryseobacterium/genetics ; Chryseobacterium/isolation & purification ; DNA Gyrase/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Phosphatidylethanolamines/chemistry ; Phylogeny ; Polyenes/chemistry ; RNA, Ribosomal, 16S/genetics ; Salamandridae ; Sequence Analysis, DNA ; Vitamin K 2/analogs & derivatives ; Vitamin K 2/chemistry
    Chemical Substances Chaperonin 60 ; DNA, Bacterial ; Fatty Acids ; Phosphatidylethanolamines ; Polyenes ; RNA, Ribosomal, 16S ; Vitamin K 2 (11032-49-8) ; phosphatidylethanolamine (39382-08-6) ; flexirubins (54363-90-5) ; menaquinone 6 (71ANL51TLA) ; DNA Gyrase (EC 5.99.1.3)
    Language English
    Publishing date 2013-08-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijs.0.054478-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 409: Show issues Location:
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