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Benninger RKP, Hutchens T, Head WS, McCaughey MJ, Zhang M, Le Marchand SJ, Satin LS, Piston DW. Intrinsic islet heterogeneity and gap junction coupling determine spatiotemporal Ca²⁺ wave dynamics. Biophys J 2014; 107:2723-33. [PMID: 25468351 DOI: 10.1016/j.bpj.2014.10.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/09/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022] Open
Abstract
Insulin is released from the islets of Langerhans in discrete pulses that are linked to synchronized oscillations of intracellular free calcium ([Ca(2+)]i). Associated with each synchronized oscillation is a propagating calcium wave mediated by Connexin36 (Cx36) gap junctions. A computational islet model predicted that waves emerge due to heterogeneity in β-cell function throughout the islet. To test this, we applied defined patterns of glucose stimulation across the islet using a microfluidic device and measured how these perturbations affect calcium wave propagation. We further investigated how gap junction coupling regulates spatiotemporal [Ca(2+)]i dynamics in the face of heterogeneous glucose stimulation. Calcium waves were found to originate in regions of the islet having elevated excitability, and this heterogeneity is an intrinsic property of islet β-cells. The extent of [Ca(2+)]i elevation across the islet in the presence of heterogeneity is gap-junction dependent, which reveals a glucose dependence of gap junction coupling. To better describe these observations, we had to modify the computational islet model to consider the electrochemical gradient between neighboring β-cells. These results reveal how the spatiotemporal [Ca(2+)]i dynamics of the islet depend on β-cell heterogeneity and cell-cell coupling, and are important for understanding the regulation of coordinated insulin release across the islet.
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Affiliation(s)
- Richard K P Benninger
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee; Department of Bioengineering, University of Colorado, Aurora, Colorado; Barbara Davis Center, University of Colorado, Aurora, Colorado.
| | - Troy Hutchens
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
| | - W Steven Head
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Michael J McCaughey
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Min Zhang
- Department of Pharmacology, Virginia Commonwealth University, Richmond, Virginia
| | - Sylvain J Le Marchand
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Leslie S Satin
- Department of Pharmacology, Virginia Commonwealth University, Richmond, Virginia; Department of Pharmacology, University of Michigan, Ann Arbor, Michigan; Brehm Diabetes Center, University of Michigan, Ann Arbor, Michigan
| | - David W Piston
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee.
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Maidak BL, Cole JR, Parker CT, Garrity GM, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, Pramanik S, Schmidt TM, Tiedje JM, Woese CR. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 1999; 27:171-3. [PMID: 9847171 PMCID: PMC148126 DOI: 10.1093/nar/27.1.171] [Citation(s) in RCA: 676] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.
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Affiliation(s)
- B L Maidak
- Department of Microbiology, Michigan State University, 294 Giltner Hall, East Lansing, MI 48824-1101, USA
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Abstract
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree.
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Affiliation(s)
- B L Maidak
- Department of Microbiology, University of Illinois, B103 C&LSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA.
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Abstract
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.
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Affiliation(s)
- B L Maidak
- Department of Microbiology, University of Illinois, Urbana 61801-3704, USA
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Abstract
The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment.
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Affiliation(s)
- B L Maidak
- Department of Microbiology, University of Illinois, Urbana 61801
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Abstract
The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server.
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Affiliation(s)
- N Larsen
- Department of Microbiology, University of Illinois, Urbana 61801
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Olsen GJ, Overbeek R, Larsen N, Marsh TL, McCaughey MJ, Maciukenas MA, Kuan WM, Macke TJ, Xing Y, Woese CR. The Ribosomal Database Project. Nucleic Acids Res 1992; 20 Suppl:2199-200. [PMID: 1598241 PMCID: PMC333993 DOI: 10.1093/nar/20.suppl.2199] [Citation(s) in RCA: 176] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.
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Affiliation(s)
- G J Olsen
- Department of Microbiology, University of Illinois, Urbana 61801
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