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  1. AU=Dutta Arnob
  2. AU="Ma, Shengbin" AU="Ma, Shengbin"
  3. AU="Shailendra Gurav"
  4. AU="Hikmet Budak"
  5. AU=Kurd Ramzi
  6. AU=Szefel Jaros?aw
  7. AU="Vaisse, Christian"
  8. AU="Jean-Baptiste Poline"
  9. AU="Halekoh, Ulrich"
  10. AU="H. Fayaz"
  11. AU="Saddam Hussain"
  12. AU="Leary, Steven"
  13. AU="Schuit, Ewoud"
  14. AU=Sun Bingbing
  15. AU=d'Arminio Monforte Antonella
  16. AU="Sylvain Latour"
  17. AU="Velhal, S"
  18. AU="Lutz, Richard A"
  19. AU="Raveesh Kumar"
  20. AU="Andreas von Deimling"
  21. AU="Erik MeersauthorLaboratory of Analytical and Applied Ecochemistry, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, 9000 Ghent, Belgium"
  22. AU="Thakkar, Nitya"
  23. AU="Hongtao Tie"
  24. AU="Bhati, Saurabh Kumar"
  25. AU="Choi, Hyunho"
  26. AU="Jayaprakash, Balamuralikrishna"
  27. AU="Lee, Brian H"
  28. AU="May, Susann"
  29. AU="Remondes-Costa, Sónia"
  30. AU="Lauren Sauer"
  31. AU="G Saiz, Paula"
  32. AU="Stoica, George"
  33. AU=Odorizzi Pamela M.
  34. AU=Pollaers Katherine
  35. AU="Stefanova, Veselina"
  36. AU="Geraldine M. O’Connor"
  37. AU="Jim E. Banta"
  38. AU="Marti-Bonmati, Luis"
  39. AU="Doris Kampner"
  40. AU="Luca Soraci"

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  1. Artikel ; Online: SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence.

    Gutierrez, J Ignacio / Brittingham, Gregory P / Karadeniz, Yonca / Tran, Kathleen D / Dutta, Arnob / Holehouse, Alex S / Peterson, Craig L / Holt, Liam J

    eLife

    2022  Band 11

    Abstract: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the ... ...

    Abstract It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in
    Mesh-Begriff(e) Carbon ; Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/metabolism ; Hydrogen-Ion Concentration ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/metabolism
    Chemische Substanzen Chromosomal Proteins, Non-Histone ; Saccharomyces cerevisiae Proteins ; Transcription Factors ; Carbon (7440-44-0)
    Sprache Englisch
    Erscheinungsdatum 2022-02-07
    Erscheinungsland England
    Dokumenttyp 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 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.70344
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Fabrication of PNIPAm-based thermoresponsive hydrogel microwell arrays for tumor spheroid formation.

    Dhamecha, Dinesh / Le, Duong / Chakravarty, Tomali / Perera, Kalindu / Dutta, Arnob / Menon, Jyothi U

    Materials science & engineering. C, Materials for biological applications

    2021  Band 125, Seite(n) 112100

    Abstract: Complex three-dimensional (3D) cell cultures are being increasingly implemented in biomedical research as they provide important insights into complex cancer biology, and cell-cell and cell-matrix interactions in the tumor microenvironment. However, most ...

    Abstract Complex three-dimensional (3D) cell cultures are being increasingly implemented in biomedical research as they provide important insights into complex cancer biology, and cell-cell and cell-matrix interactions in the tumor microenvironment. However, most methods used today for 3D cell culture are limited by high cost, the need for specialized skills, low throughput and the use of unnatural culture environments. We report the development of a unique biomimetic hydrogel microwell array platform for the generation and stress-free isolation of cancer spheroids. The poly N-isopropylacrylamide-based hydrogel microwell array (PHMA) has thermoresponsive properties allowing for the attachment and growth of cell aggregates/ spheroids at 37 °C, and their easy isolation at room temperature (RT). The reversible phase transition of the microwell arrays at 35 °C was confirmed visually and by differential scanning calorimetry. Swelling/ shrinking studies and EVOS imaging established that the microwell arrays are hydrophilic and swollen at temperatures <35 °C, while they shrink and are hydrophobic at temperatures >35 °C. Spheroid development within the PHMA was optimized for seeding density, incubation time and cell viability. Spheroids of A549, HeLa and MG-63 cancer cell lines, and human lung fibroblast (HLF) cell line generated within the PHMAs had relatively spherical morphology with hypoxic cores. Finally, using MG-63 cell spheroids as representative models, a proof-of-concept drug response study using doxorubicin hydrochloride was conducted. Overall, we demonstrate that the PHMAs are an innovative alternative to currently used 3D cell culture techniques, for the high-throughput generation of cell spheroids for disease modeling and drug screening applications.
    Mesh-Begriff(e) Cell Culture Techniques ; Cell Line, Tumor ; Cell Survival ; Humans ; Hydrogels ; Neoplasms ; Spheroids, Cellular ; Tumor Microenvironment
    Chemische Substanzen Hydrogels
    Sprache Englisch
    Erscheinungsdatum 2021-04-14
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 2012160-X
    ISSN 1873-0191 ; 0928-4931
    ISSN (online) 1873-0191
    ISSN 0928-4931
    DOI 10.1016/j.msec.2021.112100
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence

    J Ignacio Gutierrez / Gregory P Brittingham / Yonca Karadeniz / Kathleen D Tran / Arnob Dutta / Alex S Holehouse / Craig L Peterson / Liam J Holt

    eLife, Vol

    2022  Band 11

    Abstract: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the ... ...

    Abstract It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.
    Schlagwörter transcription ; chromatin ; pH ; low-complexity sequences ; polyglutamine ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 570
    Sprache Englisch
    Erscheinungsdatum 2022-02-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Remodelling without a power stroke.

    Dutta, Arnob / Workman, Jerry L

    EMBO reports

    2013  Band 14, Heft 12, Seite(n) 1030–1031

    Mesh-Begriff(e) Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/metabolism ; Animals ; Chromatin Assembly and Disassembly ; Humans ; Nucleosomes/metabolism ; Protein Structure, Tertiary ; Transcription Factors/chemistry ; Transcription Factors/metabolism
    Chemische Substanzen ISWI protein ; Nucleosomes ; Transcription Factors ; Adenosine Triphosphatases (EC 3.6.1.-)
    Sprache Englisch
    Erscheinungsdatum 2013-10-25
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.1038/embor.2013.166
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Diverse Activities of Histone Acylations Connect Metabolism to Chromatin Function.

    Dutta, Arnob / Abmayr, Susan M / Workman, Jerry L

    Molecular cell

    2016  Band 63, Heft 4, Seite(n) 547–552

    Abstract: Modifications of histones play important roles in balancing transcriptional output. The discovery of acyl marks, besides histone acetylation, has added to the functional diversity of histone modifications. Since all modifications use metabolic ... ...

    Abstract Modifications of histones play important roles in balancing transcriptional output. The discovery of acyl marks, besides histone acetylation, has added to the functional diversity of histone modifications. Since all modifications use metabolic intermediates as substrates for chromatin-modifying enzymes, the prevalent landscape of histone modifications in any cell type is a snapshot of its metabolic status. Here, we review some of the current findings of how differential use of histone acylations regulates gene expression as response to metabolic changes and differentiation programs.
    Mesh-Begriff(e) Acylation ; Animals ; Chromatin Assembly and Disassembly ; Energy Metabolism ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; Signal Transduction ; Transcription, Genetic
    Chemische Substanzen Histones
    Sprache Englisch
    Erscheinungsdatum 2016-08-18
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.06.038
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Diverse Activities of Histone Acylations Connect Metabolism to Chromatin Function

    Dutta, Arnob / Jerry L. Workman / Susan M. Abmayr

    Molecular cell. 2016 Aug. 18, v. 63, no. 4

    2016  

    Abstract: Modifications of histones play important roles in balancing transcriptional output. The discovery of acyl marks, besides histone acetylation, has added to the functional diversity of histone modifications. Since all modifications use metabolic ... ...

    Abstract Modifications of histones play important roles in balancing transcriptional output. The discovery of acyl marks, besides histone acetylation, has added to the functional diversity of histone modifications. Since all modifications use metabolic intermediates as substrates for chromatin-modifying enzymes, the prevalent landscape of histone modifications in any cell type is a snapshot of its metabolic status. Here, we review some of the current findings of how differential use of histone acylations regulates gene expression as response to metabolic changes and differentiation programs.
    Schlagwörter acetylation ; chromatin ; enzymes ; functional diversity ; gene expression ; histones ; landscapes ; metabolism ; transcription (genetics)
    Sprache Englisch
    Erscheinungsverlauf 2016-0818
    Umfang p. 547-552.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.06.038
    Datenquelle NAL Katalog (AGRICOLA)

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    Verfügbar in ZB MED Bonn

    Z 2005/501: Hefte anzeigen

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  7. Artikel ; Online: Topological scoring of protein interaction networks

    Mihaela E. Sardiu / Joshua M. Gilmore / Brad D. Groppe / Arnob Dutta / Laurence Florens / Michael P. Washburn

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Band 14

    Abstract: Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of ... ...

    Abstract Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of each bait relative to the other baits.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2019-03-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Topological scoring of protein interaction networks

    Mihaela E. Sardiu / Joshua M. Gilmore / Brad D. Groppe / Arnob Dutta / Laurence Florens / Michael P. Washburn

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Band 14

    Abstract: Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of ... ...

    Abstract Inferring direct protein−protein interactions (PPIs) and modules in PPI networks remains a challenge. Here, the authors introduce an algorithm to infer potential direct PPIs from quantitative proteomic AP-MS data by identifying enriched interactions of each bait relative to the other baits.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2019-03-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Nucleosome positioning: multiple mechanisms toward a unifying goal.

    Dutta, Arnob / Workman, Jerry L

    Molecular cell

    2012  Band 48, Heft 1, Seite(n) 1–2

    Abstract: In this issue, Hughes et al. (2012) show that nucleosome positioning is determined not by any single mechanism, but by the coordinated action of multiple factors, including the underlying DNA sequence, species-specific DNA binding proteins, chromatin ... ...

    Abstract In this issue, Hughes et al. (2012) show that nucleosome positioning is determined not by any single mechanism, but by the coordinated action of multiple factors, including the underlying DNA sequence, species-specific DNA binding proteins, chromatin remodelers, and the transcription machinery.
    Sprache Englisch
    Erscheinungsdatum 2012-10-10
    Erscheinungsland United States
    Dokumenttyp Comment ; Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2012.09.015
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Topological scoring of protein interaction networks.

    Sardiu, Mihaela E / Gilmore, Joshua M / Groppe, Brad D / Dutta, Arnob / Florens, Laurence / Washburn, Michael P

    Nature communications

    2019  Band 10, Heft 1, Seite(n) 1118

    Abstract: It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate ... ...

    Abstract It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic datasets from affinity purifications. Data is analyzed in a parallel fashion where a prey protein is scored in an individual affinity purification by aggregating information from the entire dataset. Topological scores span a broad range of values indicating the enrichment of an individual protein in every bait protein purification. TopS is applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS highlights potential direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides important insights into protein interaction networks.
    Mesh-Begriff(e) Algorithms ; Chromatin Assembly and Disassembly ; DNA Repair ; Databases, Protein/statistics & numerical data ; Humans ; Likelihood Functions ; Protein Interaction Mapping/statistics & numerical data ; Protein Interaction Maps ; Proteomics/statistics & numerical data ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
    Chemische Substanzen Saccharomyces cerevisiae Proteins
    Sprache Englisch
    Erscheinungsdatum 2019-03-08
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-019-09123-y
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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