Analysis and modeling of the inverted bioconvection in Chlamydomonas reinhardtii: emergence of plumes from the layer of accumulated cells
Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic...
Saved in:
| Published in | Heliyon Vol. 4; no. 3; p. e00586 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Elsevier Ltd
01.03.2018
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2405-8440 2405-8440 |
| DOI | 10.1016/j.heliyon.2018.e00586 |
Cover
| Abstract | Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of Chlamydomonas reinhardtii in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions. |
|---|---|
| AbstractList | Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of
in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions. Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of Chlamydomonas reinhardtii in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions. Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of Chlamydomonas reinhardtii in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions.Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of Chlamydomonas reinhardtii in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions. Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which has been studied both experimentally and theoretically. We formulate here an inverted bioconvection occurring in a suspension of phototactic cells in a high-density medium, which is illuminated from the bottom. We used a highly phototactic strain 137c of Chlamydomonas reinhardtii in the experiments. Using a custom-made lateral microscope, we observed a close view of cellular dynamics in the initiation of inverted bioconvection. In conventional bioconvection, convective flows of cells are formed spontaneously with or without formation of the surface cell layer. In inverted convection, a crowded cell layer was initially formed at the bottom, which was a prerequisite for the subsequent emergence of plumes, namely, floating populations of cells. The plume formation was a result of neither uneven initial cell density nor unequal light intensity. Based on detailed analysis of individual cells, we constructed a model of inverted bioconvection, in which each cell experiences a transition between two modes of movement: phototactically swimming cell and non-motile cell aggregate. A simulation using the CompuCell3D software reproduced basic behaviors of the plume formation. The modal transition has not been a subject of basic studies, but provides an interesting target of study of cell-to-cell interactions. |
| ArticleNumber | e00586 |
| Author | Sato, Kaoru Sato, Naoki Toyoshima, Masakazu |
| AuthorAffiliation | b Department of Social Engineering, Graduate School of Decision Science and Technology, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan a Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan |
| AuthorAffiliation_xml | – name: a Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan – name: b Department of Social Engineering, Graduate School of Decision Science and Technology, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan |
| Author_xml | – sequence: 1 givenname: Naoki surname: Sato fullname: Sato, Naoki email: naokisat@bio.c.u-tokyo.ac.jp organization: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan – sequence: 2 givenname: Kaoru surname: Sato fullname: Sato, Kaoru organization: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan – sequence: 3 givenname: Masakazu surname: Toyoshima fullname: Toyoshima, Masakazu organization: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29862349$$D View this record in MEDLINE/PubMed |
| BookMark | eNqFks9u1DAQxiNUREvpI4By5LKLYzuJAxJVteJPpUpc4GxN7PGuV4692MlK-wi8NU53i1ouPdme-ebn0cz3ujjzwWNRvK3IsiJV82G73KCzh-CXlFRiiYTUonlRXFBO6oXgnJw9up8XVyltCSFVFnUte1Wc0040lPHuovhz48Edkk0leF0OQWeuX5fBlOMGS-v3GEfUZW-DCvmhRht8DperjYPhoMMQPKQyovUbiHq09mOJA8Y1eoUzZeemAVNpYhjuiQ4OGOcEKDUNk4OZrtC59KZ4acAlvDqdl8Wvr19-rr4v7n58u13d3C1Uw-i4EEq1uheG9YIxoJyzrlGip0I0BFrTsp7WihpRa43a9Lwl1AAA0dB0rEbBLovbI1cH2MpdtAPEgwxg5X0gxLWEOFrlUNbQCC6QKN4K3leqR94DYaQ1wpi-4Zn1-cjaTf2AWqEfI7gn0KcZbzdyHfay7hpRcZoB70-AGH5PmEY52DSPAzyGKUlaU54XSUT7vJTwrstiPrf17nFb__p5WHsWfDoKVAwpRTRS2RHm3eYurZMVkbPP5FaefCZnn8mjz3J1_V_1wwfP1V0f6zCvd28xyqTsbBRtY3ZWnr99hvAXsTn0AA |
| CitedBy_id | crossref_primary_10_1146_annurev_fluid_010518_040558 crossref_primary_10_1140_epje_i2020_11949_8 crossref_primary_10_1007_s10652_024_09981_1 crossref_primary_10_1007_s00709_024_01990_7 |
| Cites_doi | 10.1016/j.jsb.2005.06.002 10.1038/nphys3926 10.1016/B978-0-12-388403-9.00013-8 10.2187/bss.24.145 10.1016/S0932-4739(11)80005-2 10.1017/S0022112090001914 10.1017/S0022112088002393 10.1146/annurev.fl.24.010192.001525 10.1128/JB.180.13.3285-3294.1998 10.1038/313218a0 10.1017/S0022112096008579 10.1016/0962-8924(93)90091-E 10.1098/rstb.2007.2079 10.1073/pnas.122243399 10.1038/248441a0 10.1073/pnas.54.6.1665 10.1109/TIP.2005.852787 10.1103/PhysRevE.76.046301 10.1017/S0022112098001979 10.1016/S0006-3495(04)74291-5 10.1016/0022-5193(76)90174-0 10.1046/j.1462-2920.2002.00328.x 10.1242/jeb.01167 10.1073/pnas.032568799 10.1083/jcb.92.3.722 10.1126/science.133.3466.1766 10.1002/cm.970050307 10.1016/j.jmb.2015.08.008 10.2323/jgam.6.283 10.1016/j.fluiddyn.2005.03.002 10.1046/j.1462-2920.1999.00066.x |
| ContentType | Journal Article |
| Copyright | 2018 The Authors 2018 The Authors 2018 |
| Copyright_xml | – notice: 2018 The Authors – notice: 2018 The Authors 2018 |
| DBID | 6I. AAFTH AAYXX CITATION NPM 7X8 7S9 L.6 5PM DOA |
| DOI | 10.1016/j.heliyon.2018.e00586 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
| DatabaseTitle | CrossRef PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | PubMed MEDLINE - Academic AGRICOLA |
| Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Medicine |
| EISSN | 2405-8440 |
| ExternalDocumentID | oai_doaj_org_article_5a6848e0c4784b1cbe4ba0307f8ffb64 PMC5968142 29862349 10_1016_j_heliyon_2018_e00586 S2405844017337957 |
| Genre | Journal Article |
| GroupedDBID | 0R~ 0SF 457 53G 5VS 6I. AACTN AAEDW AAFTH AAFWJ ABMAC ACGFS ACLIJ ADBBV ADEZE AEXQZ AFPKN AFTJW AGHFR AITUG ALMA_UNASSIGNED_HOLDINGS AMRAJ AOIJS BAWUL BCNDV DIK EBS EJD FDB GROUPED_DOAJ HYE IPNFZ KQ8 M~E NCXOZ O9- OK1 RIG ROL RPM SSZ AALRI AAYWO AAYXX ACVFH ADCNI ADVLN AEUPX AFJKZ AFPUW AIGII AKBMS AKRWK AKYEP APXCP CITATION NPM 7X8 7S9 L.6 5PM |
| ID | FETCH-LOGICAL-c632t-8cc7db8f3b833a244396c8b28860a7f73b25c2f85ddedfb4702faaa0da6935e83 |
| IEDL.DBID | DOA |
| ISSN | 2405-8440 |
| IngestDate | Wed Aug 27 01:31:11 EDT 2025 Thu Aug 21 13:29:40 EDT 2025 Fri Jul 11 02:25:14 EDT 2025 Fri Jul 11 10:47:21 EDT 2025 Wed Feb 19 02:42:14 EST 2025 Tue Jul 01 00:37:27 EDT 2025 Thu Apr 24 22:58:38 EDT 2025 Tue Jul 25 21:06:21 EDT 2023 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 3 |
| Keywords | Cell biology Mathematical biosciences Biophysics Systems biology |
| Language | English |
| License | This is an open access article under the CC BY-NC-ND license. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c632t-8cc7db8f3b833a244396c8b28860a7f73b25c2f85ddedfb4702faaa0da6935e83 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan. |
| OpenAccessLink | https://doaj.org/article/5a6848e0c4784b1cbe4ba0307f8ffb64 |
| PMID | 29862349 |
| PQID | 2049942444 |
| PQPubID | 23479 |
| ParticipantIDs | doaj_primary_oai_doaj_org_article_5a6848e0c4784b1cbe4ba0307f8ffb64 pubmedcentral_primary_oai_pubmedcentral_nih_gov_5968142 proquest_miscellaneous_2524240087 proquest_miscellaneous_2049942444 pubmed_primary_29862349 crossref_citationtrail_10_1016_j_heliyon_2018_e00586 crossref_primary_10_1016_j_heliyon_2018_e00586 elsevier_sciencedirect_doi_10_1016_j_heliyon_2018_e00586 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2018-03-01 |
| PublicationDateYYYYMMDD | 2018-03-01 |
| PublicationDate_xml | – month: 03 year: 2018 text: 2018-03-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Heliyon |
| PublicationTitleAlternate | Heliyon |
| PublicationYear | 2018 |
| Publisher | Elsevier Ltd Elsevier |
| Publisher_xml | – name: Elsevier Ltd – name: Elsevier |
| References | Fuhrmann (bib4) 2001 Pedley, Kessler (bib19) 1992; 24 Pedley, Hill, Kessler (bib20) 1988; 195 Brokaw, Luck, Huang (bib1) 1982; 92 Swat, Thomas, Belmonte, Shirinifard, Hmeljak, Glazier (bib28) 2012; 110 Platt (bib21) 1961; 133 Plesset, Whipple, Winet (bib23) 1976; 59 Witman (bib32) 1993; 3 Rüffer, Nultsch (bib24) 1985; 5 Watanabe (bib31) 1960; 6 Kessler (bib12) 1985; 313 Kitsunezaki, Komori, Harumoto (bib13) 2007; 76 Mendelson, Lega (bib15) 1998; 180 Metcalfe, Pedley (bib16) 1998; 370 Gentien, Lunven, Lazure, Youenou, Crassous (bib5) 2007; 362 Dervaux, Resta, Brunet (bib2) 2017; 13 Govorunova, Jung, Sineshchekov, Spudich (bib8) 2004; 86 Sbalzarini, Koumoutsakos (bib26) 2005; 151 Yamamoto, Okayama, Sato, Takaoki (bib33) 1992; 28 Sineshchekov, Jung, Spudich (bib27) 2002; 99 Pedley, Kessler (bib18) 1990; 212 Vincent, Hill (bib29) 1996; 327 Du, Kawabe, Schilde, Chen, Schaap (bib3) 2015; 427 Hill, Pedley (bib9) 2005; 37 Mogami, Yamane, Gino, Baba (bib17) 2004; 207 Wager (bib30) 1910–1911; 201 Hosoya, Akiyama, Kage, Baba, Mogami (bib10) 2010; 24 Jánosi, Czirók, Silhavy, Holczinger (bib11) 2002; 4 Sage, Neumann, Hediger, Gasser, Unser (bib25) 2005; 14 George, Glimm, Li, Marchese, Xu (bib6) 2002; 99 Mendelson (bib14) 1999; 1 Plesset, Winet (bib22) 1974; 248 Gorman, Levine (bib7) 1965; 54 Kitsunezaki (10.1016/j.heliyon.2018.e00586_bib13) 2007; 76 Pedley (10.1016/j.heliyon.2018.e00586_bib18) 1990; 212 Pedley (10.1016/j.heliyon.2018.e00586_bib19) 1992; 24 Govorunova (10.1016/j.heliyon.2018.e00586_bib8) 2004; 86 Du (10.1016/j.heliyon.2018.e00586_bib3) 2015; 427 Rüffer (10.1016/j.heliyon.2018.e00586_bib24) 1985; 5 Mendelson (10.1016/j.heliyon.2018.e00586_bib14) 1999; 1 Sage (10.1016/j.heliyon.2018.e00586_bib25) 2005; 14 Kessler (10.1016/j.heliyon.2018.e00586_bib12) 1985; 313 Gorman (10.1016/j.heliyon.2018.e00586_bib7) 1965; 54 Metcalfe (10.1016/j.heliyon.2018.e00586_bib16) 1998; 370 Swat (10.1016/j.heliyon.2018.e00586_bib28) 2012; 110 Fuhrmann (10.1016/j.heliyon.2018.e00586_bib4) 2001 Watanabe (10.1016/j.heliyon.2018.e00586_bib31) 1960; 6 Jánosi (10.1016/j.heliyon.2018.e00586_bib11) 2002; 4 Yamamoto (10.1016/j.heliyon.2018.e00586_bib33) 1992; 28 George (10.1016/j.heliyon.2018.e00586_bib6) 2002; 99 Witman (10.1016/j.heliyon.2018.e00586_bib32) 1993; 3 Plesset (10.1016/j.heliyon.2018.e00586_bib22) 1974; 248 Brokaw (10.1016/j.heliyon.2018.e00586_bib1) 1982; 92 Gentien (10.1016/j.heliyon.2018.e00586_bib5) 2007; 362 Sbalzarini (10.1016/j.heliyon.2018.e00586_bib26) 2005; 151 Platt (10.1016/j.heliyon.2018.e00586_bib21) 1961; 133 Hosoya (10.1016/j.heliyon.2018.e00586_bib10) 2010; 24 Sineshchekov (10.1016/j.heliyon.2018.e00586_bib27) 2002; 99 Vincent (10.1016/j.heliyon.2018.e00586_bib29) 1996; 327 Dervaux (10.1016/j.heliyon.2018.e00586_bib2) 2017; 13 Hill (10.1016/j.heliyon.2018.e00586_bib9) 2005; 37 Mogami (10.1016/j.heliyon.2018.e00586_bib17) 2004; 207 Wager (10.1016/j.heliyon.2018.e00586_bib30) 1910; 201 Mendelson (10.1016/j.heliyon.2018.e00586_bib15) 1998; 180 Pedley (10.1016/j.heliyon.2018.e00586_bib20) 1988; 195 Plesset (10.1016/j.heliyon.2018.e00586_bib23) 1976; 59 |
| References_xml | – volume: 133 start-page: 1766 year: 1961 end-page: 1777 ident: bib21 article-title: “Bioconvection patterns” in cultures of free-swimming organisms publication-title: Science – volume: 99 start-page: 2587 year: 2002 end-page: 2592 ident: bib6 article-title: A comparison of experimental, theoretical, and numerical simulation Rayleigh-Taylor mixing rates publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 212 start-page: 155 year: 1990 end-page: 182 ident: bib18 article-title: A new continuum model for suspensions of gyrotactic micro-organisms publication-title: J. Fluid Mech. – volume: 99 start-page: 8689 year: 2002 end-page: 8694 ident: bib27 article-title: Two rhodopsins mediate phototaxis to low- and high-intensity light in publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 362 start-page: 1937 year: 2007 end-page: 1946 ident: bib5 article-title: Motility and autotoxicity in publication-title: Phil. Trans. Roy. Soc. Lond. B – volume: 24 start-page: 145 year: 2010 end-page: 152 ident: bib10 article-title: Reverse bioconvection of publication-title: Biol. Sci. Space – volume: 427 start-page: 3722 year: 2015 end-page: 3733 ident: bib3 article-title: The evolution of aggregative multicellularity and cell-cell communication in the Dictyostelia publication-title: J. Mol. Biol. – year: 2001 ident: bib4 article-title: Grün fluoreszierendes Protein und gezielte Genstilllegung in – volume: 5 start-page: 251 year: 1985 end-page: 263 ident: bib24 article-title: High-speed cinematographic analysis of the movement of Chlamydomonas publication-title: Cell Motil. – volume: 28 start-page: 415 year: 1992 end-page: 420 ident: bib33 article-title: Relation of pattern formation to external conditions in the flagellate, publication-title: Eur. J. Pristol. – volume: 6 start-page: 283 year: 1960 end-page: 292 ident: bib31 article-title: List of algal strains in collection at the Institute of applied microbiology, University of Tokyo publication-title: J. Gen. Appl. Microbiol. – volume: 86 start-page: 2342 year: 2004 end-page: 2349 ident: bib8 article-title: sensory rhodopsins A and B: cellular content and role in photophobic responses publication-title: Biophys. J. – volume: 54 start-page: 1665 year: 1965 end-page: 1669 ident: bib7 article-title: Cytochrome publication-title: Proc. Natl. Acad. Sci. U. S. A. – volume: 37 start-page: 1 year: 2005 end-page: 20 ident: bib9 article-title: Bioconvection publication-title: Fluid Dynam. Res. – volume: 201 start-page: 339 year: 1910–1911 end-page: 390 ident: bib30 article-title: On the effect of gravity upon the movements and aggregation of publication-title: Phil. Trans. Roy. Soc. Lond. B – volume: 313 start-page: 218 year: 1985 end-page: 220 ident: bib12 article-title: Hydrodynamic focusing of motile algal cells publication-title: Nature – volume: 76 year: 2007 ident: bib13 article-title: Bioconvection and front formation of publication-title: Phys. Rev. E – volume: 370 start-page: 249 year: 1998 end-page: 270 ident: bib16 article-title: Bacterial bioconvection: weakly nonlinear theory for pattern selection publication-title: J. Fluid Mech. – volume: 14 start-page: 1372 year: 2005 end-page: 1383 ident: bib25 article-title: Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics publication-title: IEEE Trans. Image Process. – volume: 24 start-page: 313 year: 1992 end-page: 358 ident: bib19 article-title: Hydrodynamic phenomena in suspensions of swimming microorganisms publication-title: Annu. Rev. Fluid Mech. – volume: 1 start-page: 471 year: 1999 end-page: 477 ident: bib14 article-title: macrofibres, colonies and bioconvection patterns use different strategies to achieve multicellular organization publication-title: Environ. Microbiol. – volume: 248 start-page: 441 year: 1974 end-page: 443 ident: bib22 article-title: Bioconvection patterns in swimming microorganism cultures as an example of Rayleigh-Taylor instability publication-title: Nature – volume: 59 start-page: 331 year: 1976 end-page: 351 ident: bib23 article-title: Rayleigh-Taylor instability of surface layers as the mechanism for bioconvection in cell cultures publication-title: J. Theor. Biol. – volume: 151 start-page: 182 year: 2005 end-page: 195 ident: bib26 article-title: Feature point tracking and trajectory analysis for video imaging in cell biology publication-title: J. Struct. Biol. – volume: 3 start-page: 403 year: 1993 end-page: 408 ident: bib32 article-title: phototaxis publication-title: Trends Cell Biol. – volume: 327 start-page: 343 year: 1996 end-page: 371 ident: bib29 article-title: Bioconvection in a suspension of phototactic algae publication-title: J. Fluid Mech. – volume: 110 start-page: 325 year: 2012 end-page: 366 ident: bib28 article-title: Multi-scale modeling of tissues using CompuCell3D publication-title: Meth. Cell Biol. – volume: 13 start-page: 306 year: 2017 end-page: 312 ident: bib2 article-title: Light-controlled flows in active fluids publication-title: Nat. Phys. – volume: 180 start-page: 3285 year: 1998 end-page: 3294 ident: bib15 article-title: A complex pattern of traveling stripes is produced by swimming cells of publication-title: J. Bacteriol. – volume: 4 start-page: 525 year: 2002 end-page: 531 ident: bib11 article-title: Is bioconvection enhancing bacterial growth in quiescent environments? publication-title: Environ. Microbiol. – volume: 92 start-page: 722 year: 1982 end-page: 732 ident: bib1 article-title: Analysis of the movement of publication-title: J. Cell Biol. – volume: 207 start-page: 3349 year: 2004 end-page: 3359 ident: bib17 article-title: Bioconvective pattern formation of publication-title: J. Exp. Biol. – volume: 195 start-page: 223 year: 1988 end-page: 237 ident: bib20 article-title: The growth of bioconvection patterns in a uniform suspension of gyrotactic micro-organisms publication-title: J. Fluid Mech. – volume: 151 start-page: 182 year: 2005 ident: 10.1016/j.heliyon.2018.e00586_bib26 article-title: Feature point tracking and trajectory analysis for video imaging in cell biology publication-title: J. Struct. Biol. doi: 10.1016/j.jsb.2005.06.002 – volume: 13 start-page: 306 year: 2017 ident: 10.1016/j.heliyon.2018.e00586_bib2 article-title: Light-controlled flows in active fluids publication-title: Nat. Phys. doi: 10.1038/nphys3926 – volume: 110 start-page: 325 year: 2012 ident: 10.1016/j.heliyon.2018.e00586_bib28 article-title: Multi-scale modeling of tissues using CompuCell3D publication-title: Meth. Cell Biol. doi: 10.1016/B978-0-12-388403-9.00013-8 – volume: 24 start-page: 145 year: 2010 ident: 10.1016/j.heliyon.2018.e00586_bib10 article-title: Reverse bioconvection of Chlamydomonas in the hyper-density medium publication-title: Biol. Sci. Space doi: 10.2187/bss.24.145 – volume: 28 start-page: 415 year: 1992 ident: 10.1016/j.heliyon.2018.e00586_bib33 article-title: Relation of pattern formation to external conditions in the flagellate, Chlamydomonas reinhardtii publication-title: Eur. J. Pristol. doi: 10.1016/S0932-4739(11)80005-2 – volume: 212 start-page: 155 year: 1990 ident: 10.1016/j.heliyon.2018.e00586_bib18 article-title: A new continuum model for suspensions of gyrotactic micro-organisms publication-title: J. Fluid Mech. doi: 10.1017/S0022112090001914 – volume: 195 start-page: 223 year: 1988 ident: 10.1016/j.heliyon.2018.e00586_bib20 article-title: The growth of bioconvection patterns in a uniform suspension of gyrotactic micro-organisms publication-title: J. Fluid Mech. doi: 10.1017/S0022112088002393 – volume: 24 start-page: 313 year: 1992 ident: 10.1016/j.heliyon.2018.e00586_bib19 article-title: Hydrodynamic phenomena in suspensions of swimming microorganisms publication-title: Annu. Rev. Fluid Mech. doi: 10.1146/annurev.fl.24.010192.001525 – volume: 180 start-page: 3285 year: 1998 ident: 10.1016/j.heliyon.2018.e00586_bib15 article-title: A complex pattern of traveling stripes is produced by swimming cells of Bacillus subtilis publication-title: J. Bacteriol. doi: 10.1128/JB.180.13.3285-3294.1998 – volume: 313 start-page: 218 year: 1985 ident: 10.1016/j.heliyon.2018.e00586_bib12 article-title: Hydrodynamic focusing of motile algal cells publication-title: Nature doi: 10.1038/313218a0 – volume: 327 start-page: 343 year: 1996 ident: 10.1016/j.heliyon.2018.e00586_bib29 article-title: Bioconvection in a suspension of phototactic algae publication-title: J. Fluid Mech. doi: 10.1017/S0022112096008579 – volume: 3 start-page: 403 year: 1993 ident: 10.1016/j.heliyon.2018.e00586_bib32 article-title: Chlamydomonas phototaxis publication-title: Trends Cell Biol. doi: 10.1016/0962-8924(93)90091-E – volume: 362 start-page: 1937 year: 2007 ident: 10.1016/j.heliyon.2018.e00586_bib5 article-title: Motility and autotoxicity in Karenia mikimotoi (Dinophyceae) publication-title: Phil. Trans. Roy. Soc. Lond. B doi: 10.1098/rstb.2007.2079 – volume: 99 start-page: 8689 year: 2002 ident: 10.1016/j.heliyon.2018.e00586_bib27 article-title: Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.122243399 – volume: 248 start-page: 441 year: 1974 ident: 10.1016/j.heliyon.2018.e00586_bib22 article-title: Bioconvection patterns in swimming microorganism cultures as an example of Rayleigh-Taylor instability publication-title: Nature doi: 10.1038/248441a0 – volume: 54 start-page: 1665 year: 1965 ident: 10.1016/j.heliyon.2018.e00586_bib7 article-title: Cytochrome f and plastocyanin: their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardi publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.54.6.1665 – volume: 14 start-page: 1372 year: 2005 ident: 10.1016/j.heliyon.2018.e00586_bib25 article-title: Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics publication-title: IEEE Trans. Image Process. doi: 10.1109/TIP.2005.852787 – volume: 76 year: 2007 ident: 10.1016/j.heliyon.2018.e00586_bib13 article-title: Bioconvection and front formation of Paramecium tetraurelia publication-title: Phys. Rev. E doi: 10.1103/PhysRevE.76.046301 – volume: 370 start-page: 249 year: 1998 ident: 10.1016/j.heliyon.2018.e00586_bib16 article-title: Bacterial bioconvection: weakly nonlinear theory for pattern selection publication-title: J. Fluid Mech. doi: 10.1017/S0022112098001979 – volume: 86 start-page: 2342 year: 2004 ident: 10.1016/j.heliyon.2018.e00586_bib8 article-title: Chlamydomonas sensory rhodopsins A and B: cellular content and role in photophobic responses publication-title: Biophys. J. doi: 10.1016/S0006-3495(04)74291-5 – volume: 59 start-page: 331 year: 1976 ident: 10.1016/j.heliyon.2018.e00586_bib23 article-title: Rayleigh-Taylor instability of surface layers as the mechanism for bioconvection in cell cultures publication-title: J. Theor. Biol. doi: 10.1016/0022-5193(76)90174-0 – volume: 4 start-page: 525 year: 2002 ident: 10.1016/j.heliyon.2018.e00586_bib11 article-title: Is bioconvection enhancing bacterial growth in quiescent environments? publication-title: Environ. Microbiol. doi: 10.1046/j.1462-2920.2002.00328.x – volume: 207 start-page: 3349 year: 2004 ident: 10.1016/j.heliyon.2018.e00586_bib17 article-title: Bioconvective pattern formation of Tetrahymena under altered gravity publication-title: J. Exp. Biol. doi: 10.1242/jeb.01167 – volume: 99 start-page: 2587 year: 2002 ident: 10.1016/j.heliyon.2018.e00586_bib6 article-title: A comparison of experimental, theoretical, and numerical simulation Rayleigh-Taylor mixing rates publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.032568799 – volume: 92 start-page: 722 year: 1982 ident: 10.1016/j.heliyon.2018.e00586_bib1 article-title: Analysis of the movement of Chlamydomonas flagella: the function of the radial-spoke system is revealed by comparison of wild-type and mutant flagella publication-title: J. Cell Biol. doi: 10.1083/jcb.92.3.722 – volume: 133 start-page: 1766 year: 1961 ident: 10.1016/j.heliyon.2018.e00586_bib21 article-title: “Bioconvection patterns” in cultures of free-swimming organisms publication-title: Science doi: 10.1126/science.133.3466.1766 – volume: 5 start-page: 251 year: 1985 ident: 10.1016/j.heliyon.2018.e00586_bib24 article-title: High-speed cinematographic analysis of the movement of Chlamydomonas publication-title: Cell Motil. doi: 10.1002/cm.970050307 – volume: 427 start-page: 3722 year: 2015 ident: 10.1016/j.heliyon.2018.e00586_bib3 article-title: The evolution of aggregative multicellularity and cell-cell communication in the Dictyostelia publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2015.08.008 – volume: 6 start-page: 283 year: 1960 ident: 10.1016/j.heliyon.2018.e00586_bib31 article-title: List of algal strains in collection at the Institute of applied microbiology, University of Tokyo publication-title: J. Gen. Appl. Microbiol. doi: 10.2323/jgam.6.283 – year: 2001 ident: 10.1016/j.heliyon.2018.e00586_bib4 – volume: 37 start-page: 1 year: 2005 ident: 10.1016/j.heliyon.2018.e00586_bib9 article-title: Bioconvection publication-title: Fluid Dynam. Res. doi: 10.1016/j.fluiddyn.2005.03.002 – volume: 201 start-page: 339 year: 1910 ident: 10.1016/j.heliyon.2018.e00586_bib30 article-title: On the effect of gravity upon the movements and aggregation of Euglena viridis, Ehrb., and other micro-organisms publication-title: Phil. Trans. Roy. Soc. Lond. B – volume: 1 start-page: 471 year: 1999 ident: 10.1016/j.heliyon.2018.e00586_bib14 article-title: Bacillus subtilis macrofibres, colonies and bioconvection patterns use different strategies to achieve multicellular organization publication-title: Environ. Microbiol. doi: 10.1046/j.1462-2920.1999.00066.x |
| SSID | ssj0001586973 |
| Score | 2.065211 |
| Snippet | Bioconvection is a convective flow found in a suspension of motile cells that swim against gravity, and is a primitive form of order formation of cells, which... |
| SourceID | doaj pubmedcentral proquest pubmed crossref elsevier |
| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | e00586 |
| SubjectTerms | Biophysics cell aggregates Cell biology Chlamydomonas reinhardtii computer software convection gravity light intensity Mathematical biosciences phototaxis Systems biology |
| Title | Analysis and modeling of the inverted bioconvection in Chlamydomonas reinhardtii: emergence of plumes from the layer of accumulated cells |
| URI | https://dx.doi.org/10.1016/j.heliyon.2018.e00586 https://www.ncbi.nlm.nih.gov/pubmed/29862349 https://www.proquest.com/docview/2049942444 https://www.proquest.com/docview/2524240087 https://pubmed.ncbi.nlm.nih.gov/PMC5968142 https://doaj.org/article/5a6848e0c4784b1cbe4ba0307f8ffb64 |
| Volume | 4 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Lb9QwELZQD4gL4k1KQUbimm3iV5zeoKKqkOBEpd4i27G1qZak6u4e-hP418zYybIBib1wjZ2J7PnimZFnviHkQxts6RhzEKaWLhfGlrnhlcxd6SEaaUOlXMy2-KYur8SXa3m91-oLc8ISPXDauFNplBbaF05UWoBc64U1iMygQ7AqMoEWdbEXTKX6YK3qeL0MFkvmWojid_nO6c1i6Vfd_YD8p6VeeOytp2aGKfL3z-zT3_7nn2mUe3bp4gl5PDqU9GNayFPywPfPyMOv45X5c_Jzoh2hpm9pbHwD1ooOgYLrR7se-zH7ltpuiAnoscwBHtPzJWDlvh0ApmZN73zXY33WpuvOqB9LNj1KucXTbU2xTCVKXBlw4nHAOLf9gc3BQDpeD6xfkKuLz9_PL_Ox_0LuFGebXDtXtVYHbjXnBvwAXiunLdNaFaYKFbdMOha0hCMSdC6qggVjTNEaVXPpNX9Jjvqh968JbYNilpVGgFIE88YoyYSz4D1ChGpNmxExbX7jRnJy7JGxaqYstJtm1FmDOmuSzjKy2L12m9g5Dr3wCTW7m4zk2vEBQK4ZIdccglxG9ISLZvRTkv8BorpD338_4aiB_xh33_R-2K5hEsSeWHUo_jFHYjEPsghm5FXC3m4lrIbYlIs6I9UMlbOlzkf6bhn5xGWtdCnY8f_YmzfkES43ZemdkKPN3da_BbdtY9_FP_QX7tFEiA |
| linkProvider | Directory of Open Access Journals |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Analysis+and+modeling+of+the+inverted+bioconvection+in+Chlamydomonas+reinhardtii+%3A+emergence+of+plumes+from+the+layer+of+accumulated+cells&rft.jtitle=Heliyon&rft.au=Sato%2C+Naoki&rft.au=Sato%2C+Kaoru&rft.au=Toyoshima%2C+Masakazu&rft.date=2018-03-01&rft.issn=2405-8440&rft.eissn=2405-8440&rft.volume=4&rft.issue=3&rft.spage=e00586&rft_id=info:doi/10.1016%2Fj.heliyon.2018.e00586&rft_id=info%3Apmid%2F29862349&rft.externalDocID=29862349 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2405-8440&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2405-8440&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2405-8440&client=summon |