PreprintCited by 23Marine Invertebrate Physiology and EcologyMarine Sponges and Natural ProductsCellular Mechanics and Interactions

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

Open access

Preprint — published as 10.1016/j.cub.2023.12.021 · Paper page

Abstract

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling “contractions” that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. Highlights: Sponge deflation is driven by tension release in actomyosin stress fibers of epithelial pinacocytes Akt kinase/Nitric oxide/Protein kinase G/A regulate actomyosin relaxation Agitation-induced deflation coincides with an inflammatory state The sponge relaxant-inflammatory response is evolutionary related to similar responses in the vertebrate vascular system

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.08.02.551666

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 190

  1. 10.1074/jbc.RA117.001068 · DOI
  2. T L Simpson . The Cell Biology of Sponges. Springer Science & Business Media, December 2012.
  3. 2019, Hydrodynamics of the leucon sponge pump, J. R. Soc. Interface, 16, 20180630, 10.1098/rsif.2018.0630 · DOI
  4. Josephine Goldstein , Nicklas Bisbo , Peter Funch , and Hans Ulrik Riisgård . Contraction-Expansion and the effects on the aquiferous system in the demosponge halichondria panicea. Front. Mar. Sci., 7, February 2020. · DOI
  5. 10.1007/BF00348816 · DOI
  6. 2022, Sponges sneeze mucus to shed particulate waste from their seawater inlet pores, Curr. Biol, 32, 3855, 10.1016/j.cub.2022.07.017 · DOI
  7. Lars Kumala and Donald Eugene Canfield . Contraction dynamics and respiration of small Single-Osculum explants of the demosponge halichondria panicea. Front. Mar. Sci., 5, November 2018. · DOI
  8. 10.1242/jeb.003392 · DOI
  9. 10.1242/jeb.039859 · DOI
  10. 10.1186/1742-9994-3-7 · DOI
  11. 10.1007/s00359-006-0165-y · DOI
  12. 2022, MRTF specifies a muscle-like contractile module in porifera, Nat. Commun, 13, 4134, 10.1038/s41467-022-31756-9 · DOI
  13. 10.1126/science.abj2949 · DOI · Paper page
  14. 10.1186/1471-2148-14-3 · DOI
  15. 10.1242/jeb.01289 · DOI
  16. Michael Nickel . Like a ‘rolling stone’: quantitative analysis of the body movement and skeletal dynamics of the sponge Tethya wilhelma, 2006. · DOI
  17. 10.1242/jeb.049148 · DOI
  18. 2018, Early metazoan cell type diversity and the evolution of multicellular gene regulation, Nat Ecol Evol, 2, 1176, 10.1038/s41559-018-0575-6 · DOI
  19. 2019, Diverse cell junctions with unique molecular composition in tissues of a sponge (porifera), Evodevo, 10, 26, 10.1186/s13227-019-0139-0 · DOI
  20. 2019, Exhalant jet speed of single-osculum explants of the demosponge halichondria panicea and basic properties of the sponge-pump, J. Exp. Mar. Bio. Ecol, 511, 82, 10.1016/j.jembe.2018.11.009 · DOI
  21. 2022, Systematic discovery of biomolecular condensate-specific protein phosphorylation, Nat. Chem. Biol, 18, 1104, 10.1038/s41589-022-01062-y · DOI
  22. 10.1126/science.1255784 · DOI · Paper page
  23. 10.1038/s41586-020-3002-5 · DOI
  24. 2022, Muscular hydraulics drive larva-polyp morphogenesis, Curr. Biol, 32, 4707, 10.1016/j.cub.2022.08.065 · DOI
  25. 1990, Condensation rhythm of fresh-water sponges (spongillidae, porifera), Eur. J. Cell Biol, 53, 373
  26. Thibaut Brunet , Antje Hl Fischer , Patrick Rh Steinmetz , Antonella Lauri , Paola Bertucci , and Detlev Arendt . The evolutionary origin of bilaterian smooth and striated myocytes. Elife, 5, December 2016. · DOI
  27. 10.1038/nature11180 · DOI · Paper page
  28. 10.1038/sj.ijir.3901256 · DOI
  29. 10.1098/rsif.2010.0419 · DOI
  30. 10.1016/j.ajpath.2018.01.013 · DOI
  31. 10.1038/21224 · DOI · Paper page
  32. 10.1152/ajpheart.00501.2008 · DOI
  33. 10.1016/j.cellsig.2013.08.001 · DOI
  34. 10.1073/pnas.97.19.10661 · DOI
  35. 10.1124/mol.56.1.124 · DOI
  36. 10.1038/sj.bjp.0705791 · DOI
  37. 10.1016/j.semcancer.2017.05.011 · DOI
  38. 2021, Small chemical compounds Y16 and rhosin can inhibit calcium sensitization pathway in vascular smooth muscle cells of spontaneously hypertensive rats, J. Formos. Med. Assoc, 120, 1863, 10.1016/j.jfma.2021.03.031 · DOI
  39. 10.1016/j.exer.2004.12.013 · DOI
  40. 1999, Nitric oxide modulation of focal adhesions in endothelial cells, Am. J. Physiol, 276, C1271, 10.1152/ajpcell.1999.276.6.C1271 · DOI
  41. 2018, Reversal of stress fibre formation by nitric oxide mediated RhoA inhibition leads to reduction in the height of preformed thrombi, Sci. Rep, 8, 3032, 10.1038/s41598-018-21167-6 · DOI
  42. 2008, Non-neural reflexes: sponges and the origins of behaviour, Curr. Biol, 18, R70, 10.1016/j.cub.2007.11.022 · DOI
  43. 10.1091/mbc.E17-06-0401 · DOI
  44. 10.1242/jcs.180927 · DOI
  45. 10.1021/bi00668a038 · DOI
  46. 2022, Alterations to the broad-spectrum formin inhibitor SMIFH2 modulate potency but not specificity, Sci. Rep, 12, 13520, 10.1038/s41598-022-17685-z · DOI
  47. 10.1007/s12551-018-0468-6 · DOI
  48. 2021, Force-dependent activation of actin elongation factor mdia1 protects the cytoskeleton from mechanical damage and promotes stress fiber repair, Dev. Cell, 56, 3288, 10.1016/j.devcel.2021.11.004 · DOI
  49. 10.1139/z05-171 · DOI · Paper page
  50. 2014, A new flow-regulating cell type in the demosponge tethya wilhelma - functional cellular anatomy of a leuconoid canal system, PLoS One, 9, e113153, 10.1371/journal.pone.0113153 · DOI
  51. 10.1101/gad.900401 · DOI
  52. 2019, Arabidopsis ADF5 promotes stomatal closure by regulating actin cytoskeleton remodeling in response to ABA and drought stress, J. Exp. Bot, 70, 435, 10.1093/jxb/ery385 · DOI
  53. 2022, Controlling the gate: The functions of the cytoskeleton in stomatal movement, Front. Plant Sci, 13, 849729, 10.3389/fpls.2022.849729 · DOI
  54. 10.1111/ivb.12016 · DOI
  55. 1994, The sponge pump, J. Theor. Biol, 168, 53, 10.1006/jtbi.1994.1087 · DOI
  56. 10.1074/mcp.TIR117.000518 · DOI
  57. 2021, Impact of phosphorylation on thermal stability of proteins, Nat. Meth-ods, 18, 757, 10.1038/s41592-021-01177-5 · DOI · Paper page
  58. 10.1038/s41587-021-01051-x · DOI
  59. 10.1038/nprot.2015.101 · DOI
  60. 10.1186/s12953-017-0122-4 · DOI
  61. 10.15252/msb.20199232 · DOI · Paper page
  62. 2018, Pervasive protein thermal stability variation during the cell cycle, Cell, 173, 1495, 10.1016/j.cell.2018.03.053 · DOI
  63. 2020, GPS 5.0: An update on the prediction of kinase-specific phos-phorylation sites in proteins, Genomics Proteomics Bioinformatics, 18, 72, 10.1016/j.gpb.2020.01.001 · DOI
  64. 10.1529/biophysj.107.117960 · DOI
  65. 10.1103/PhysRevE.74.051912 · DOI
  66. 10.1016/J.CELREP.2019.09.043 · DOI
  67. 10.1242/jcs.02874 · DOI
  68. 10.1021/bi0500776 · DOI
  69. 10.1128/MCB.00661-07 · DOI
  70. Timothy R Baffi , Gema Lordén , Jacob M Wozniak , Andreas Feichtner , Wayland Yeung , Alexandr P Kornev , Charles C King , Jason C Del Rio , Ameya J Limaye , Julius Bogomolovas , Christine M Gould , Ju Chen , Eileen J Kennedy , Natarajan Kannan , David J Gonzalez , Eduard Stefan , Susan S Taylor , and Alexandra C Newton . mTORC2 controls the activity of PKC and akt by phosphorylating a conserved TOR interaction motif. Sci. Signal., 14(678), April 2021. · DOI
  71. 10.4331/wjbc.v5.i3.346 · DOI
  72. 2019, Phosphorylation of forkhead protein FoxO1 at S253 regulates glucose homeostasis in mice, Endocrinology, 160, 1333, 10.1210/en.2018-00853 · DOI
  73. 10.1016/S0092-8674(00)80595-4 · DOI · Paper page
  74. 10.1046/j.1432-1327.1999.00146.x · DOI
  75. John C Salerno , Dipak K Ghosh , Raj Razdan , Katy A Helms , Christopher C Brown , Jonathan L McMurry , Emily A Rye , and Carol A Chrestensen . Endothelial nitric oxide synthase is regulated by ERK phosphorylation at ser602. Biosci. Rep., 34(5), September 2014. · DOI
  76. 10.1074/jbc.274.36.25273 · DOI
  77. 2022, SignalP 6.0 predicts all five types of signal peptides using protein language models, Nat. Biotechnol, 40, 1023, 10.1038/s41587-021-01156-3 · DOI
  78. 2022, ColabFold: making protein folding accessible to all, Nat. Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  79. 2023, Cross-phyla protein annotation by structural prediction and alignment, Genome Biol, 24, 113, 10.1186/s13059-023-02942-9 · DOI · Paper page
  80. 2011, Purification and characterization of a novel extracellular tripeptidyl peptidase from rhizopus oligosporus, J. Agric. Food Chem, 59, 11330, 10.1021/jf201879e · DOI
  81. Eva Vidak , Urban Javoršek , Matej Vizovišek , and Boris Turk . Cysteine cathepsins and their extracellular roles: Shaping the microenvironment. Cells, 8(3), March 2019. · DOI
  82. 10.1074/jbc.M707680200 · DOI
  83. 10.1074/jbc.M115.638395 · DOI
  84. 10.2174/138920309788922207 · DOI
  85. 10.1093/nar/gkr931 · DOI
  86. Luis Alfonso Yañez-Guerra , Daniel Thiel , and Gáspár Jékely . Premetazoan origin of neu-ropeptide signaling. Mol. Biol. Evol., 39(4), April 2022. · DOI
  87. 2021, Processing of progranulin into granulins involves multiple lysosomal proteases and is affected in frontotemporal lobar degeneration, Mol. Neurodegener, 16, 51, 10.1186/s13024-021-00472-1 · DOI · Paper page
  88. 10.1371/journal.pone.0026454 · DOI
  89. 10.1091/mbc.E02-05-0311 · DOI
  90. 10.1371/journal.pone.0076679 · DOI
  91. 2018, Analysis of Progranulin-Mediated akt and MAPK activation, Methods Mol. Biol, 1806, 121, 10.1007/978-1-4939-8559-3_9 · DOI
  92. 10.1038/sj.onc.1210318 · DOI · Paper page
  93. 10.1016/j.cellsig.2005.06.013 · DOI
  94. 10.1016/j.bbrc.2009.09.112 · DOI
  95. 10.1089/ars.2012.5149 · DOI · Paper page
  96. 10.3390/biom5020472 · DOI
  97. 2017, Extra-Cellular but Extra-Ordinarily im-portant for cells: Apoplastic reactive oxygen species metabolism, Front. Plant Sci, 8, 1353, 10.3389/fpls.2017.01353 · DOI
  98. 2011, zn-superoxide dismutase 1 (SOD1) is a novel target of puromycin-sensitive aminopep-tidase (PSA/NPEPPS): PSA/NPEPPS is a possible modifier of amyotrophic lateral sclero-sis, Mol. Neurodegener, 6, 29, 10.1186/1750-1326-6-29 · DOI
  99. 10.1042/bj2560251 · DOI
  100. 2021, B6 vitamers as generators and scavengers of reactive oxygen species, Journal of Photochemistry and Photobiology, 7, 100041, 10.1016/j.jpap.2021.100041 · DOI
  101. 10.1038/ncomms4773 · DOI
  102. 2022, FOXO3a-ROS pathway is involved in androgen-induced proliferation of prostate cancer cell, BMC Urol, 22, 1
  103. 10.1038/emboj.2010.292 · DOI
  104. 2022, Rheology of marine sponges reveals anisotropic mechanics and tuned dynamics, J. R. Soc. Interface, 19, 20220476, 10.1098/rsif.2022.0476 · DOI
  105. 10.1098/rstb.2004.1566 · DOI
  106. 10.1038/ncomms13969 · DOI
  107. 10.1242/jeb.02501 · DOI
  108. 10.1016/S0002-9440(10)63209-9 · DOI
  109. 10.1186/1741-7007-8-11 · DOI
  110. 10.1113/jphysiol.2005.096537 · DOI
  111. 10.2307/1536773 · DOI
  112. 10.1242/jeb.110817 · DOI · Paper page
  113. 1966, The reactions of the sponge cliona celata to applied stimuli, Comp. Biochem. Physiol, 18, 805, 10.1016/0010-406X(66)90215-5 · DOI
  114. 1991, Mechanisms of calcium relaxation of vascular smooth muscle, Am. J. Physiol, 261, H1411
  115. 2021, Editorial: The role of reactive oxygen species in protective immunity, Front. Immunol, 12, 832946
  116. 10.1038/nri1200 · DOI
  117. 10.1034/j.1600-065X.2000.917307.x · DOI
  118. 2022, Molecular machineries of ciliogenesis, cell survival, and vasculogenesis are differentially expressed during regeneration in explants of the demo-sponge halichondria panicea, BMC Genomics, 23, 858, 10.1186/s12864-022-09035-0 · DOI
  119. 10.1038/s41598-018-34330-w · DOI
  120. 2022, Wounding response in porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer, Sci. Rep, 12, 1307, 10.1038/s41598-022-05230-x · DOI
  121. Alpha S Yap , Kinga Duszyc , and Virgile Viasnoff . Mechanosensing and mechanotransduction at Cell-Cell junctions. Cold Spring Harb. Perspect. Biol., 10(8), August 2018. · DOI
  122. 10.3389/fphys.2020.00861 · DOI
  123. 2016, PI16 is a shear stress and inflammation-regulated inhibitor of MMP2, Sci. Rep, 6, 39553, 10.1038/srep39553 · DOI · Paper page
  124. 10.1038/labinvest.3700299 · DOI
  125. 10.2147/VHRM.S3933 · DOI
  126. 2018, Differential regulations of fibronectin and laminin in smad2 activation in vascular endothelial cells in response to disturbed flow, J. Biomed. Sci, 25, 1, 10.1186/s12929-017-0402-4 · DOI
  127. 2022, Mechanical regulation of talin through binding and history-dependent unfolding, Sci Adv, 8, eabl7719, 10.1126/sciadv.abl7719 · DOI
  128. 2018, Laminar flow attenuates macrophage migration inhibitory factor expression in endothelial cells, Sci. Rep, 8, 2360, 10.1038/s41598-018-20885-1 · DOI
  129. 2001, Cyclic strain induces reactive oxygen species production via an endothelial NAD(P)H oxidase, J. Cell. Biochem. Suppl, 36, 99
  130. 10.1016/j.yjmcc.2004.04.012 · DOI
  131. 10.1242/jeb.146076 · DOI
  132. 2023, Nudibranch predation boosts sponge silicon cycling, Sci. Rep, 13, 1178, 10.1038/s41598-023-27411-y · DOI
  133. 2001, Life cycles and ecological interactions of freshwater sponges (porifera, spongillidae) in the river rhine in germany, Limnologica, 31, 185, 10.1016/S0075-9511(01)80020-7 · DOI
  134. 2013, Rapid respiratory responses of the deep-water sponge geodia barretti exposed to suspended sediments, Aquat. Biol, 19, 65, 10.3354/ab00522 · DOI
  135. 1999, Ecological biomechanics of benthic organisms: life history, mechanical design and temporal patterns of mechanical stress, J. Exp. Biol, 202, 3469
  136. 2021, Individuality in the immune repertoire and induced response of the sponge halichondria panicea, Front. Immunol, 12, 689051, 10.3389/fimmu.2021.689051 · DOI
  137. 10.1113/jphysiol.2006.115212 · DOI · Paper page
  138. 10.1172/JCI80454 · DOI
  139. Joshua P Scallan , Luz A Knauer , Huayan Hou , Jorge A Castorena-Gonzalez , Michael J Davis , and Ying Yang . Foxo1 deletion promotes the growth of new lymphatic valves. J. Clin. Invest., 131(14), July 2021. · DOI
  140. 10.1007/s00441-005-1151-3 · DOI
  141. 2003, A review of the l-arginine - nitric oxide - guanylate cyclase pathway as a mediator of lower urinary tract physiology and symptoms, Can. J. Urol, 10, 1971
  142. 10.1016/S0014-2999(98)00981-9 · DOI
  143. 10.1074/jbc.M500528200 · DOI
  144. 2016, Fluid shear stress suppresses TNF-α-induced apoptosis in MC3T3-E1 cells: Involvement of ERK5-AKT-FoxO3a-Bim/FasL sig-naling pathways, Exp. Cell Res, 343, 208, 10.1016/j.yexcr.2016.03.014 · DOI
  145. 10.4049/jimmunol.1200596 · DOI
  146. Qian Zhong , Yixin Liu , Michele Ramos Correa , Crystal Nicole Marconett , Parviz Minoo , Changgong Li , David K Ann , Beiyun Zhou , and Zea Borok . FOXO1 couples KGF and PI-3K/AKT signaling to NKX2.1-Regulated differentiation of alveolar epithelial cells. Cells, 11(7), March 2022. · DOI
  147. 10.1084/jem.193.4.545 · DOI
  148. 10.1186/s12931-021-01865-y · DOI
  149. 10.1371/journal.pone.0011686 · DOI
  150. 10.1016/j.tree.2015.03.003 · DOI · Paper page
  151. 10.1038/ncomms10623 · DOI
  152. 10.1038/s41586-023-05828-9 · DOI
  153. 10.1093/NAR/GKAB1038 · DOI · Paper page
  154. 10.1093/nar/gkz1019 · DOI
  155. 10.1038/nbt.2377 · DOI
  156. 2017, MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics, Nat. Methods, 14, 513, 10.1038/nmeth.4256 · DOI
  157. 10.1093/molbev/msu300 · DOI · Paper page
  158. 10.1038/nbt.3988 · DOI · Paper page
  159. Michel van Kempen , Stephanie S Kim , Charlotte Tumescheit , Milot Mirdita , Jeongjae Lee , Cameron L M Gilchrist , Johannes Söding , and Martin Steinegger . Fast and accurate protein structure search with foldseek. Nat. Biotechnol., May 2023. · DOI · Paper page
  160. 10.1093/molbev/mst010 · DOI · Paper page
  161. 10.1093/bioinformatics/btp033 · DOI
  162. 10.1093/NAR/GKAB301 · DOI
  163. 10.1038/s41598-018-28948-z · DOI
  164. 10.1101/2021.06.03.446934 · DOI
  165. 10.1038/nmeth.3393 · DOI
  166. 10.1038/s41592-019-0582-9 · DOI
  167. 10.1038/nmeth.2019 · DOI · Paper page
  168. 10.1038/75556 · DOI · Paper page
  169. Gene Ontology Consortium , Suzi A Aleksander , James Balhoff , Seth Carbon , J Michael Cherry , Harold J Drabkin , Dustin Ebert , Marc Feuermann , Pascale Gaudet , Nomi L Harris , David P Hill , Raymond Lee , Huaiyu Mi , Sierra Moxon , Christopher J Mungall , Anushya Muruganugan , Tremayne Mushayahama , Paul W Sternberg , Paul D Thomas , Kimberly Van Auken , Jolene Ramsey , Deborah A Siegele , Rex L Chisholm , Petra Fey , Maria Cristina Aspromonte , Maria Victoria Nugnes , Federica Quaglia , Silvio Tosatto , Michelle Giglio , Suvarna Nadendla , Giulia Antonazzo , Helen Attrill , Gil Dos Santos , Steven Marygold , Victor Strelets , Christopher J Tabone , Jim Thurmond , Pinglei Zhou , Saadullah H Ahmed , Praoparn Asanitthong , Diana Luna Buitrago , Meltem N Erdol , Matthew C Gage , Mohamed Ali Kadhum , Kan Yan Chloe Li , Miao Long , Aleksandra Michalak , Angeline Pesala , Armalya Pritazahra , Shirin C C Saverimuttu , Renzhi Su , Kate E Thurlow , Ruth C Lovering , Colin Logie , Snezhana Oliferenko , Judith Blake , Karen Christie , Lori Corbani , Mary E Dolan , Harold J Drabkin , David P Hill , Li Ni , Dmitry Sitnikov , Cynthia Smith , Alayne Cuzick , James Seager , Laurel Cooper , Justin Elser , Pankaj Jaiswal , Parul Gupta , Pankaj Jaiswal , Sushma Naithani , Manuel Lera-Ramirez , Kim Rutherford , Valerie Wood , Jeffrey L De Pons , Melinda R Dwinell , G Thomas Hayman , Mary L Kaldunski , Anne E Kwitek , Stanley J F Laulederkind , Marek A Tutaj , Mahima Vedi , Shur-Jen Wang , Peter D’Eustachio , Lucila Aimo , Kristian Axelsen , Alan Bridge , Nevila Hyka-Nouspikel , Anne Morgat , Suzi A Aleksander , J Michael Cherry , Stacia R Engel , Kalpana Karra , Stuart R Miyasato , Robert S Nash , Marek S Skrzypek , Shuai Weng , Edith D Wong , Erika Bakker , Tanya Z Berardini , Leonore Reiser , Andrea Auchincloss , Kristian Axelsen , Ghislaine Argoud-Puy , Marie-Claude Blatter , Emmanuel Boutet , Lionel Breuza , Alan Bridge , Cristina Casals-Casas , Elisabeth Coudert , Anne Estreicher , Maria Livia Famiglietti , Marc Feuermann , Arnaud Gos , Nadine Gruaz-Gumowski , Chantal Hulo , Nevila Hyka-Nouspikel , Florence Jungo , Philippe Le Mercier , Damien Lieberherr , Patrick Masson , Anne Morgat , Ivo Pedruzzi , Lucille Pourcel , Sylvain Poux , Catherine Rivoire , Shyamala Sundaram , Alex Bateman , Emily Bowler-Barnett , Hema Bye-A-Jee , Paul Denny , Alexandr Ignatchenko , Rizwan Ishtiaq , Antonia Lock , Yvonne Lussi , Michele Magrane , Maria J Martin , Sandra Orchard , Pedro Raposo , Elena Speretta , Nidhi Tyagi , Kate Warner , Rossana Zaru , Alexander D Diehl , Raymond Lee , Juancarlos Chan , Stavros Diamantakis , Daniela Raciti , Magdalena Zarowiecki , Malcolm Fisher , Christina James-Zorn , Virgilio Ponferrada , Aaron Zorn , Sridhar Ramachandran , Leyla Ruzicka , and Monte Westerfield . The gene ontology knowl-edgebase in 2023. Genetics, 224(1), May 2023. · DOI
  170. Optical coherence tomography, 2015. · DOI
  171. Olaf Ronneberger , Philipp Fischer , and Thomas Brox . U-Net: Convolutional networks for biomedical image segmentation. In Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015, pages 234–241. Springer International Publishing, 2015. · DOI · Paper page
  172. 2021, Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising, Nat. Methods, 18, 1395, 10.1038/s41592-021-01225-0 · DOI
  173. 10.1016/j.bone.2010.08.023 · DOI
  174. 10.1093/bioinformatics/btw413 · DOI
  175. 10.1093/molbev/msy033 · DOI
  176. 10.1038/nmeth.3652 · DOI
  177. 10.1038/nchembio.2185 · DOI · Paper page
  178. 10.15252/msb.20145625 · DOI
  179. G K Smyth . limma: Linear models for microarray data. In Robert Gentleman , Vincent J Carey , Wolfgang Huber , Rafael A Irizarry , and Sandrine Dudoit , editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer New York, New York, NY, 2005.
  180. 10.1093/bioinformatics/18.suppl_1.S96 · DOI · Paper page
  181. 10.1093/bioinformatics/btn209 · DOI
  182. 10.1093/nar/gky1085 · DOI
  183. 10.1093/bioinformatics/btq224 · DOI
  184. 10.1038/nmeth.4285 · DOI · Paper page
  185. 10.1093/molbev/msx281 · DOI · Paper page
  186. 10.1186/s13059-017-1382-0 · DOI · Paper page
  187. 1765, XXXI. on the nature and formation of sponges: In a letter from john ellis, esquire, f. r. s. to dr. solander, f. r. S, Philos. Trans. R. Soc. Lond, 55, 280
  188. 1962, Oscular contractions in sponges, Comp. Biochem. Physiol, 6, 69, 10.1016/0010-406X(62)90044-0 · DOI
  189. 1981, Etude de la contraction spontanée chez l’éponge d’eau douce ephydatia fluviatilis cultivée in vitro, Ann. Soc. R. Zool. Belg./Ann. K. Belg. Ver. Dierkd, 111, 21
  190. 10.1007/BF00312010 · DOI

Metadata

Authors
Ruperti, F., Becher, I., Stokkermans, A., Wang, L., Marschlich, N., Potel, C., Maus, E., Stein, F., Drotleff, B., Schippers, K., Nickel, M., Prevedel, R., Musser, J. M., Savitski, M. M., & Arendt, D.
Affiliations
  • Heidelberg University (DE)
  • European Molecular Biology Laboratory (DE)
  • Hubrecht Institute for Developmental Biology and Stem Cell Research (NL)
  • Yale University (US)
Corresponding author
  • Wang, Ling
  • Musser, Jacob M
  • Savitski, Mikhail M
  • Arendt, Detlev
Venue
Current Biology
Publisher
openRxiv
Published
2023-08-02
Volume
34
Issue
2
Pages
361-375.e9
ISSN
0960-9822 (ISSN-L)
OpenAlex
W4390579554
Cited by
23
References
1
Citations by year
2026: 6 · 2025: 7 · 2024: 7 · 2023: 3
FWCI
6.29
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Current Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Lirias (submittedVersion)
  • PubMed Central (submittedVersion, cc-by-nc)
Funders
  • European Molecular Biology Laboratory
  • Paul G. Allen Frontiers Group
  • European Commission (664726, HORIZON2020, 788921, 764840, 101094250, 864027)
  • Horizon 2020 Framework Programme
  • HORIZON EUROPE Framework Programme (101094250/IMAGINE)
  • European Research Council
  • Horizon 2020
  • H2020 European Research Council (788921, 864027 / Brillouin4Life)
  • H2020 Marie Skłodowska-Curie Actions (764840, HORIZON-INFRA-2022-TECH-01, HORIZON2020, 664726)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Marine Sponges and Natural Products
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular Mechanics and Interactions
Keywords
mechanotransduction, epithelial cell junctions, reactive oxygen species, antioxidant depletion, proteinase secretion, cytokines, granulin, paracrine signaling, whole-body coordination, mechanosensitive signaling, thermal proteome profiling, phosphoproteomics, metabolomics, sponges

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review