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González-Penagos CE, Zamora-Briseño JA, Améndola-Pimenta M, Cruz-Quintana Y, Santana-Piñeros AM, Torres-García JR, Cañizares-Martínez MA, Pérez-Vega JA, Peñuela-Mendoza AC, Rodríguez-Canul R. Sargassum spp. Ethanolic Extract Elicits Toxic Responses and Malformations in Zebrafish (Danio rerio) Embryos. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38477677 DOI: 10.1002/etc.5840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/14/2024]
Abstract
The amount of Sargassum spp. arriving in the Caribbean Sea has increased steadily in the last few years, producing a profound environmental impact on the ecological dynamics of the coasts of the Yucatan Peninsula. We characterized the toxicological effects of an ethanolic extract of Sargassum spp. on zebrafish (Danio rerio) embryos (ZFEs) in a 96-h static bioassay using T1 (0.01 mg/L), T2 (0.1 mg/L), T3 (1 mg/L), T4 (10 mg/L), T5 (25 mg/L), T6 (50 mg/L), T7 (75 mg/L), T8 (100 mg/L), T9 (200 mg/L), and T10 (400 mg/L). In this extract, we detected 74 compounds by gas chromatography-mass spectrometry (GC-MS), of which hexadecanoic acid methyl ester, and 2-pentanone 4-hydroxy-4-methyl, were the most abundant. In ZFEs, a median lethal concentration of 251 mg/L was estimated. Exposed embryos exhibited extensive morphological changes, including edema in the yolk sac, scoliosis, and loss of pigmentation, as well as malformations of the head, tail, and eyes. By integrating these abnormalities using the Integrated Biological Response (IBRv2) and General Morphological Score (GMS) indices, we were able to determine that ZFEs exposed to 200 mg/L (T9) exhibited the most pronounced biological response in comparison with the other groups. In the comparative transcriptomic analysis, 66 genes were upregulated, and 246 genes were downregulated in the group exposed to 200 mg/L compared with the control group. In the upregulated genes, we identified several gene ontology-enriched terms, such as response to xenobiotic stimuli, cellular response to chemical stimulus, transcriptional regulation, pigment metabolic process, erythrocyte differentiation and embryonic hemopoiesis, extracellular matrix organization, and chondrocyte differentiation involved in endochondral bone morphogenesis, among others. In the down-regulated genes, we found many genes associated with nervous system processes, sensory and visual perception, response to abiotic stimulus, and the nucleoside phosphate biosynthetic process. The probable connections among the morphological changes observed in the transcriptome are thoroughly discussed. Our findings suggest that Sargassum spp. exposure can induce a wide negative impact on zebrafish embryos. Environ Toxicol Chem 2024;00:1-15. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Carlos E González-Penagos
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | | | - Mónica Améndola-Pimenta
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | - Yanis Cruz-Quintana
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental. Departamento de Acuicultura, Pesca y Recursos Naturales Renovables. Facultad de Acuicultura y Ciencias del Mar, Universidad Técnica de Manabí, Bahía de Caráquez, Manabí, Ecuador
| | - Ana M Santana-Piñeros
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental. Departamento de Acuicultura, Pesca y Recursos Naturales Renovables. Facultad de Acuicultura y Ciencias del Mar, Universidad Técnica de Manabí, Bahía de Caráquez, Manabí, Ecuador
| | - Jesús R Torres-García
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Michoacán, México
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Ciudad de México, México
| | - Mayra A Cañizares-Martínez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | - Juan A Pérez-Vega
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | - Ana C Peñuela-Mendoza
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | - Rossanna Rodríguez-Canul
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
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Kawasaki S, Kaneko T, Asano T, Maoka T, Takaichi S, Shomura Y. An ependymin-related blue carotenoprotein decorates marine blue sponge. J Biol Chem 2023; 299:105110. [PMID: 37517696 PMCID: PMC10470211 DOI: 10.1016/j.jbc.2023.105110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
Marine animals display diverse vibrant colors, but the mechanisms underlying their specific coloration remain to be clarified. Blue coloration is known to be achieved through a bathochromic shift of the orange carotenoid astaxanthin (AXT) by the crustacean protein crustacyanin, but other examples have not yet been well investigated. Here, we identified an ependymin (EPD)-related water-soluble blue carotenoprotein responsible for the specific coloration of the marine blue sponge Haliclona sp. EPD was originally identified in the fish brain as a protein involved in memory consolidation and neuronal regeneration. The purified blue protein, designated as EPD-related blue carotenoprotein-1, was identified as a secreted glycoprotein. We show that it consists of a heterodimer that binds orange AXT and mytiloxanthin and exhibits a bathochromic shift. Our crystal structure analysis of the natively purified EPD-related blue carotenoprotein-1 revealed that these two carotenoids are specifically bound to the heterodimer interface, where the polyene chains are aligned in parallel to each other like in β-crustacyanin, although the two proteins are evolutionary and structurally unrelated. Furthermore, using reconstitution assays, we found that incomplete bathochromic shifts occurred when the protein bound to only AXT or mytiloxanthin. Taken together, we identified an EPD in a basal metazoan as a blue protein that decorates the sponge body by binding specific structurally unrelated carotenoids.
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Affiliation(s)
- Shinji Kawasaki
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan.
| | - Takayuki Kaneko
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Tomomi Asano
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Yasuhito Shomura
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki, Japan.
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3
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Kung TA, Chen PJ. Exploring specific biomarkers regarding neurobehavioral toxicity of lead dioxide nanoparticles in medaka fish in different water matrices. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159268. [PMID: 36208768 DOI: 10.1016/j.scitotenv.2022.159268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Nano-scale lead dioxide (nPbO2) is an industrial metal oxide nanoparticle that can be also formed as a corrosion by-product from chlorination of Pb-containing plumbing materials. nPbO2 governs release of toxic lead ion in drinking water and receiving organisms; however, its modes of toxic action regarding neurobehavioral toxicity remain unclear. This study evaluated the toxicity mechanism of nPbO2 (10 and 20 mg/L) versus its released Pb(II)aq (100 μg/L) in terms of aqueous chemistry, bioavailability and neurobehavioral toxicity to medaka fish in different water matrices. In very hard water (VHW), dissolved salts enhanced the aggregation and sedimentation of nPbO2, resulting in higher bioavailability and altered locomotion of treated fish than those fish exposed to nPbO2 in soft water with humic acid (SW + HA). Transcriptomic results identified six differentially expressed genes with greater altered expression with nPbO2 than the control or Pb(II)aq exposure. With VHW exposure, nPbO2 caused greater altered expression of genes involved in cell adhesion (nlgn1 and epd), cell cytoskeleton (α1-tubulin), and relevant apoptosis (c-fos, birc5.1-a and casp3), as compared with SW + HA or Pb(II)aq exposure. This study provides novel molecular mechanistic insights into the neurobehavioral nanotoxicity using nPbO2 and medaka fish as surrogates, suggesting nPbO2 promotes neurobehavioral dysfunction, leading to adverse outcomes from gene alteration to the organismal level. The identified biomarkers responded specifically to the nPbO2-induced neurotoxicity in different water matrices can be used for evaluating toxicity risks of small metal oxide particulates on human or aquatic life under environmentally relevant exposures.
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Affiliation(s)
- Te-An Kung
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan; Institute of Food Safety Management, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Pei-Jen Chen
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.
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Su F, Yang H, Sun L. A Review of Histocytological Events and Molecular Mechanisms Involved in Intestine Regeneration in Holothurians. BIOLOGY 2022; 11:1095. [PMID: 35892951 PMCID: PMC9332576 DOI: 10.3390/biology11081095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
Most species of the class Holothuroidea are able to regenerate most of their internal organs following a typical evisceration process, which is a unique mechanism that allows sea cucumbers to survive in adverse environments. In this review, we compare autotomy among different type of sea cucumber and summarize the histocytological events that occur during the five stages of intestinal regeneration. Multiple cytological activities, such as apoptosis and dedifferentiation, take place during wound healing and anlage formation. Many studies have focused on the molecular regulation mechanisms that underlie regeneration, and herein we describe the techniques that have been used as well as the development-related signaling pathways and key genes that are significantly expressed during intestinal regeneration. Future analyses of the underlying mechanisms responsible for intestinal regeneration should include mapping at the single-cell level. Studies of visceral regeneration in echinoderms provide a unique perspective for understanding whole-body regeneration or appendage regeneration.
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Affiliation(s)
- Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
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Medina-Feliciano JG, García-Arrarás JE. Regeneration in Echinoderms: Molecular Advancements. Front Cell Dev Biol 2021; 9:768641. [PMID: 34977019 PMCID: PMC8718600 DOI: 10.3389/fcell.2021.768641] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Which genes and gene signaling pathways mediate regenerative processes? In recent years, multiple studies, using a variety of animal models, have aimed to answer this question. Some answers have been obtained from transcriptomic and genomic studies where possible gene and gene pathway candidates thought to be involved in tissue and organ regeneration have been identified. Several of these studies have been done in echinoderms, an animal group that forms part of the deuterostomes along with vertebrates. Echinoderms, with their outstanding regenerative abilities, can provide important insights into the molecular basis of regeneration. Here we review the available data to determine the genes and signaling pathways that have been proposed to be involved in regenerative processes. Our analyses provide a curated list of genes and gene signaling pathways and match them with the different cellular processes of the regenerative response. In this way, the molecular basis of echinoderm regenerative potential is revealed, and is available for comparisons with other animal taxa.
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Identification and localization of growth factor genes in the sea cucumber , Holothuria scabra. Heliyon 2021; 7:e08370. [PMID: 34825084 PMCID: PMC8605306 DOI: 10.1016/j.heliyon.2021.e08370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
The sea cucumber Holothuria scabra is both an economically important species in Asian countries and an emerging experimental model for research studies in regeneration and medicinal bioactives. Growth factors and their receptors are known to be key components that guide tissue repair and renewal, yet validation of their presence in H. scabra has not been established. We performed a targeted in silico search of H. scabra transcriptome data to elucidate conserved growth factor family and receptor genes. In total, 42 transcripts were identified, of which 9 were validated by gene cloning and sequencing. The H. scabra growth factor genes, such as bone morphogenetic protein 2A (BMP 2A), bone morphogenetic protein 5-like (BMP5-like), neurotrophin (NT) and fibroblast growth factor 18 (FGF18), were selected for further analyses, including phylogenetic comparison and spatial gene expression using RT-PCR and in situ hybridization. Expression of all genes investigated were widespread in multiple tissues. However, BMP 2A, BMP5-like and NT were found extensively in the radial nerve cord cells, while FGF18 was highly expressed in connective tissue layer of the body wall. Our identification and expression analysis of the H. scabra growth factor genes provided the molecular information of growth factors in this species which may ultimately complement the research in regenerative medicine.
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Eisapour M, Salamat N, Salari MA, Bahabadi MN, Salati AP. Digestive tract regeneration in the posteriorly eviscerating sea cucumber Holothuria parva (Holothuroidea, Echinodermata). ZOOMORPHOLOGY 2021. [DOI: 10.1007/s00435-020-00511-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Sci Rep 2021; 11:346. [PMID: 33431961 PMCID: PMC7801731 DOI: 10.1038/s41598-020-79436-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 h and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
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Park JK, Kim KY, Sim YW, Kim YI, Kim JK, Lee C, Han J, Kim CU, Lee JE, Park S. Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder. IUCRJ 2019; 6:729-739. [PMID: 31316816 PMCID: PMC6608618 DOI: 10.1107/s2052252519007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation.
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Affiliation(s)
- Jeong Kuk Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Keon Young Kim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yeo Won Sim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
| | - Yong-In Kim
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Jin Kyun Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Cheol Lee
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jeongran Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - J. Eugene Lee
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - SangYoun Park
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
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10
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Shabelnikov SV, Bobkov DE, Sharlaimova NS, Petukhova OA. Injury affects coelomic fluid proteome of the common starfish, Asterias rubens. ACTA ACUST UNITED AC 2019; 222:jeb.198556. [PMID: 30877231 DOI: 10.1242/jeb.198556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 01/04/2023]
Abstract
Echinoderms, possessing outstanding regenerative capabilities, provide a unique model system for the study of response to injury. However, little is known about the proteomic composition of coelomic fluid, an important biofluid circulating throughout the animal's body and reflecting the overall biological status of the organism. In this study, we used LC-MALDI tandem mass spectrometry to characterize the proteome of the cell-free coelomic fluid of the starfish Asterias rubens and to follow the changes occurring in response to puncture wound and blood loss. In total, 91 proteins were identified, of which 61 were extracellular soluble and 16 were bound to the plasma membrane. The most represented functional terms were 'pattern recognition receptor activity' and 'peptidase inhibitor activity'. A series of candidate proteins involved in early response to injury was revealed. Ependymin, β-microseminoprotein, serum amyloid A and avidin-like proteins, which are known to be involved in intestinal regeneration in the sea cucumber, were also identified as injury-responsive proteins. Our results expand the list of proteins potentially involved in defense and regeneration in echinoderms and demonstrate dramatic effects of injury on the coelomic fluid proteome.
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Affiliation(s)
- Sergey V Shabelnikov
- Laboratory of Regulation of Gene Expression, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Danila E Bobkov
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Natalia S Sharlaimova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Olga A Petukhova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
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11
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McDougall C, Hammond MJ, Dailey SC, Somorjai IML, Cummins SF, Degnan BM. The evolution of ependymin-related proteins. BMC Evol Biol 2018; 18:182. [PMID: 30514200 PMCID: PMC6280359 DOI: 10.1186/s12862-018-1306-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/23/2018] [Indexed: 12/19/2022] Open
Abstract
Background Ependymins were originally defined as fish-specific secreted glycoproteins involved in central nervous system plasticity and memory formation. Subsequent research revealed that these proteins represent a fish-specific lineage of a larger ependymin-related protein family (EPDRs). EPDRs have now been identified in a number of bilaterian animals and have been implicated in diverse non-neural functions. The recent discoveries of putative EPDRs in unicellular holozoans and an expanded EPDR family with potential roles in conspecific communication in crown-of-thorns starfish suggest that the distribution and diversity of EPDRs is significantly broader than currently understood. Results We undertook a systematic survey to determine the distribution and evolution of EPDRs in eukaryotes. In addition to Bilateria, EPDR genes were identified in Cnidaria, Placozoa, Porifera, Choanoflagellatea, Filasterea, Apusozoa, Amoebozoa, Charophyta and Percolozoa, and tentatively in Cercozoa and the orphan group Malawimonadidae. EPDRs appear to be absent from prokaryotes and many eukaryote groups including ecdysozoans, fungi, stramenopiles, alveolates, haptistans and cryptistans. The EPDR family can be divided into two major clades and has undergone lineage-specific expansions in a number of metazoan lineages, including in poriferans, molluscs and cephalochordates. Variation in a core set of conserved residues in EPDRs reveals the presence of three distinct protein types; however, 3D modelling predicts overall protein structures to be similar. Conclusions Our results reveal an early eukaryotic origin of the EPDR gene family and a dynamic pattern of gene duplication and gene loss in animals. This research provides a phylogenetic framework for the analysis of the functional evolution of this gene family. Electronic supplementary material The online version of this article (10.1186/s12862-018-1306-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carmel McDougall
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.,Australian Rivers Institute, Griffith University, Nathan, Queensland, 4111, Australia
| | - Michael J Hammond
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Simon C Dailey
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Ildiko M L Somorjai
- Gatty Marine Laboratory, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Scott F Cummins
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Bernard M Degnan
- Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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12
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Sun L, Lin C, Li X, Xing L, Huo D, Sun J, Zhang L, Yang H. Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers. Front Physiol 2018; 9:836. [PMID: 30018572 PMCID: PMC6037860 DOI: 10.3389/fphys.2018.00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/14/2018] [Indexed: 12/29/2022] Open
Abstract
Sea cucumbers exposed to stressful circumstances eviscerate most internal organs, and then regenerate them rapidly under favorable environments. Reversible protein phosphorylation and acetylation are major modifications regulating protein function. Herein, for the first time, we perform quantitative phospho- and acetyl proteomics analyses of intestine regeneration in a sea cucumber species Apostichopus japonicus. We identified 1,862 phosphorylation sites in 1,169 proteins, and 712 acetylation sites in 470 proteins. Of the 147 and 251 proteins differentially modified by phosphorylation and acetylation, respectively, most were related to cytoskeleton biogenesis, protein synthesis and modification, signal recognition and transduction, energy production and conversion, or substance transport and metabolism. Phosphorylation appears to play a more important role in signal recognition and transduction than acetylation, while acetylation is of greater importance in posttranslational modification, protein turnover, chaperones; energy production and conversion; amino acid and lipid transport and metabolism. These results expanded our understanding of the regulatory mechanisms of posttranslational modifications in intestine regeneration of sea cucumbers after evisceration.
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Affiliation(s)
- Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chenggang Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoni Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingchun Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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García-Arrarás JE, Lázaro-Peña MI, Díaz-Balzac CA. Holothurians as a Model System to Study Regeneration. Results Probl Cell Differ 2018; 65:255-283. [PMID: 30083924 DOI: 10.1007/978-3-319-92486-1_13] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Echinoderms possess an incredible regenerative capacity. Within this phylum, holothurians, better known as sea cucumbers, can regenerate most of their internal and external organs. While regeneration has been studied in several species, the most recent and extensive studies have been done in the species Holothuria glaberrima, the focus of most of our discussion. This chapter presents the model system and integrates the work that has been done to determine the major steps that take place, during regeneration of the intestinal and nervous system, from wound healing to the reestablishment of original function. We describe the cellular and molecular events associated with the regeneration processes and also describe the techniques that have been used, discuss the results, and explain the gaps in our knowledge that remain. We expect that the information provided here paves the road for new and young investigators to continue the study of the amazing potential of regeneration in members of the Echinodermata and how these studies will shed some light into the mechanisms that are common to many regenerative processes.
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Affiliation(s)
- José E García-Arrarás
- Department of Biology, University of Puerto Rico - Río Piedras Campus, San Juan, Puerto Rico.
| | - María I Lázaro-Peña
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Carlos A Díaz-Balzac
- Department of Medicine, University of Rochester Medical Center, Strong Memorial Hospital, Rochester, NY, USA
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14
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Sun L, Sun J, Xu Q, Li X, Zhang L, Yang H. Metabolic responses to intestine regeneration in sea cucumbers Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:32-38. [PMID: 28189056 DOI: 10.1016/j.cbd.2017.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/27/2017] [Accepted: 02/02/2017] [Indexed: 02/08/2023]
Abstract
Sea cucumbers are excellent models for studying organ regeneration due to their striking capacity to regenerate most of their viscera after evisceration. In this study, we applied NMR-based metabolomics to determine the metabolite changes that occur during the process of intestine regeneration in sea cucumbers. Partial least-squares discriminant analysis showed that there was significant differences in metabolism between regenerative intestines at 3, 7, and 14days post evisceration (dpe) and normal intestines. Changes in the concentration of 13 metabolites related to regeneration were observed and analyzed. These metabolites included leucine, isoleucine, valine, arginine, glutamate, hypotaurine, dimethylamine, N,N-dimethylglycine, betaine, taurine, inosine, homarine, and histidine. Three important genes (betaine-aldehyde dehydrogenase, betaine-homocysteine S-methyltransferase 1, and dimethylglycine dehydrogenase) were differentially expressed to regulate the levels of betaine and N,N-dimethylglycine during intestine regeneration. These results provide an important basis for studying regenerative mechanisms and developing regenerative matrixes.
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Affiliation(s)
- Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jingchun Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Ecology and Environmental Science and Engineering, First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Xiaoni Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Libin Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Hongsheng Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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15
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Sun L, Sun J, Li X, Zhang L, Yang H, Wang Q. Understanding regulation of microRNAs on intestine regeneration in the sea cucumber Apostichopus japonicus using high-throughput sequencing. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:1-9. [PMID: 28160609 DOI: 10.1016/j.cbd.2017.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/20/2016] [Accepted: 01/21/2017] [Indexed: 12/13/2022]
Abstract
The sea cucumber, as a member of the Echinodermata, has the capacity to restore damaged organs and body parts, which has always been a key scientific issue. MicroRNAs (miRNAs), a class of short noncoding RNAs, play important roles in regulating gene expression. In the present study, we applied high-throughput sequencing to investigate alterations of miRNA expression in regenerative intestine compared to normal intestine. A total of 73 differentially expressed miRNAs were obtained, including 59 up-regulated miRNAs and 14 down-regulated miRNAs. Among these molecules, Aja-miR-1715-5p, Aja-miR-153, Aja-miR-252a, Aja-miR-153-5p, Aja-miR-252b, Aja-miR-2001, Aja-miR-64d-3p, and Aja-miR-252-5p were differentially expressed over 10-fold at 3days post-evisceration (dpe). Notably, real-time PCR revealed that Aja-miR-1715-5p was up-regulated 1390-fold at 3dpe. Moreover, putative target gene co-expression analyses, gene ontology, and pathway analyses suggest that these miRNAs play important roles in specific cellular events (cell proliferation, migration, and apoptosis), metabolic regulation, and energy redistribution. These results will provide a basis for future studies of miRNA regulation in sea cucumber regeneration.
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Affiliation(s)
- Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jingchun Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoni Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libin Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Hongsheng Yang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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16
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Brown TD, Hori TS, Xue X, Ye CL, Anderson DM, Rise ML. Functional Genomic Analysis of the Impact of Camelina (Camelina sativa) Meal on Atlantic Salmon (Salmo salar) Distal Intestine Gene Expression and Physiology. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:418-35. [PMID: 27255337 PMCID: PMC4911373 DOI: 10.1007/s10126-016-9704-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 05/05/2016] [Indexed: 05/24/2023]
Abstract
The inclusion of plant meals in diets of farmed Atlantic salmon can elicit inflammatory responses in the distal intestine (DI). For the present work, fish were fed a standard fish meal (FM) diet or a diet with partial replacement of FM with solvent-extracted camelina meal (CM) (8, 16, or 24 % CM inclusion) during a 16-week feeding trial. A significant decrease in growth performance was seen in fish fed all CM inclusion diets (Hixson et al. in Aquacult Nutr 22:615-630, 2016). A 4x44K oligonucleotide microarray experiment was carried out and significance analysis of microarrays (SAM) and rank products (RP) methods were used to identify differentially expressed genes between the DIs of fish fed the 24 % CM diet and those fed the FM diet. Twelve features representing six known transcripts and two unknowns were identified as CM responsive by both SAM and RP. The six known transcripts (including thioredoxin and ependymin), in addition to tgfb, mmp13, and GILT, were studied using qPCR with RNA templates from all four experimental diet groups. All six microarray-identified genes were confirmed to be CM responsive, as was tgfb and mmp13. Histopathological analyses identified signs of inflammation in the DI of salmon fed CM-containing diets, including lamina propria and sub-epithelial mucosa thickening, infiltration of eosinophilic granule cells, increased goblet cells and decreased enterocyte vacuolization. All of these were significantly altered in 24 % CM compared to all other diets, with the latter two also altered in 16 % CM compared with 8 % CM and control diet groups. Significant correlation was seen between histological parameters as well as between five of the qPCR analyzed genes and histological parameters. These molecular biomarkers of inflammation arising from long-term dietary CM exposure will be useful in the development of CM-containing diets that do not have deleterious effects on salmon growth or physiology.
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Affiliation(s)
- Tyler D Brown
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL, A1C 5S7, Canada
| | - Tiago S Hori
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL, A1C 5S7, Canada
| | - Chang Lin Ye
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada, B2N 5E3
| | - Derek M Anderson
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada, B2N 5E3
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL, A1C 5S7, Canada.
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17
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Ba H, Yao F, Yang L, Qin T, Luan H, Li Z, Zou X, Hou L. Identification and expression patterns of extracellular matrix-associated genes fibropellin-ia and tenascin involved in regeneration of sea cucumber Apostichopus japonicus. Gene 2015; 565:96-105. [PMID: 25841990 DOI: 10.1016/j.gene.2015.03.071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
Abstract
Sea cucumbers have a strong regenerative capacity. Many important genes involved in the molecular mechanism of regeneration and associated with intercellular signaling pathways of regeneration have been identified. The product of the fibropellin-ia gene forms a layer known as the apical lamina that surrounds the sea cucumber embryo throughout development. Meanwhile, the tenascin gene displays highly restricted and dynamic patterns of expression in the embryo and is expressed in the adult during normal processes such as wound healing, nerve regeneration and tissue involution. In this study, we cloned for the first time full-length cDNAs of fibropellin-ia (1390 bp, encoding a 199 amino acid protein) and tenascin (1366 bp, encoding a 179 amino acid protein) from Apostichopus japonicus (designated Aj-fnia and Aj-tenascin, respectively) using rapid amplification of cDNA ends. The structures and characteristics of these two genes were analyzed bioinformatically, and their expression patterns associated with extracellular matrix remodeling in regeneration of A. japonicus were investigated by real-time PCR and in situ hybridization (ISH). Expression levels of Aj-fnia and Aj-tenascin in the regeneration tissues were higher than those in normal tissues. The highest expression levels of Aj-fnia and Aj-tenascin were shown in the intestine and respiratory tree on the 15th and 20th days after sea cucumbers were eviscerated. In the body wall, the highest expression levels of Aj-fnia and Aj-tenascin occurred at 35 and 45 min during early regeneration and then emerged between 5 and 7 days again during late regeneration after the body wall was injured. ISH analysis revealed expression of these genes in the body wall, longitudinal muscle, intestine and respiratory tree. These findings suggest that Aj-fnia and Aj-tenascin are crucial genes that play important roles in the regeneration of the sea cucumber.
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Affiliation(s)
- Huazhong Ba
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Feng Yao
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Lei Yang
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Tong Qin
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Hong Luan
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Zhengmin Li
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China
| | - Xiangyang Zou
- Department of Biology, Dalian Medical University, Dalian 116044, People's Republic of China.
| | - Lin Hou
- College of Life Sciences, Liaoning Normal University, 1, Liushu South Street, Ganjingzi District, Dalian 116081, People's Republic of China.
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18
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Ferraz Franco C, Santos R, Varela Coelho A. Proteolytic events are relevant cellular responses during nervous system regeneration of the starfish Marthasterias glacialis. J Proteomics 2014; 99:1-25. [DOI: 10.1016/j.jprot.2013.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 01/12/2023]
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19
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Andreeva AM. Identification of some proteins of blood and tissue fluid in the fish with enciphered genome. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093013060029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Ben Khadra Y, Said K, Thorndyke M, Martinez P. Homeobox genes expressed during echinoderm arm regeneration. Biochem Genet 2013; 52:166-80. [PMID: 24309817 DOI: 10.1007/s10528-013-9637-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/25/2013] [Indexed: 10/25/2022]
Abstract
Regeneration in echinoderms has proved to be more amenable to study in the laboratory than the more classical vertebrate models, since the smaller genome size and the absence of multiple orthologs for different genes in echinoderms simplify the analysis of gene function during regeneration. In order to understand the role of homeobox-containing genes during arm regeneration in echinoderms, we isolated the complement of genes belonging to the Hox class that are expressed during this process in two major echinoderm groups: asteroids (Echinaster sepositus and Asterias rubens) and ophiuroids (Amphiura filiformis), both of which show an extraordinary capacity for regeneration. By exploiting the sequence conservation of the homeobox, putative orthologs of several Hox genes belonging to the anterior, medial, and posterior groups were isolated. We also report the isolation of a few Hox-like genes expressed in the same systems.
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Affiliation(s)
- Yousra Ben Khadra
- Genetics Department, University of Barcelona, Av. Diagonal 645, 08028, Barcelona, Spain,
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21
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Sun L, Yang H, Chen M, Ma D, Lin C. RNA-Seq reveals dynamic changes of gene expression in key stages of intestine regeneration in the sea cucumber Apostichopus japonicus. [corrected]. PLoS One 2013; 8:e69441. [PMID: 23936330 PMCID: PMC3735544 DOI: 10.1371/journal.pone.0069441] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 06/14/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to ~30000 ESTs. RESULTS We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe). This was compared to profiles obtained from a normally-functioning intestine. Approximately 5 million (M) reads were sequenced in every library. Over 2400 up-regulated genes (>10%) and over 1000 down-regulated genes (~5%) were observed at 3 and 7dpe (log2Ratio ≥ 1, FDR ≤ 0.001). Specific "Go terms" revealed that the DEGs (Differentially Expressed Genes) performed an important function at every regeneration stage. Besides some expected pathways (for example, Ribosome and Spliceosome pathway term), the "Notch signaling pathway," the "ECM-receptor interaction" and the "Cytokine-cytokine receptor interaction" were significantly enriched. We also investigated the expression profiles of developmental genes, ECM-associated genes and Cytoskeletal genes. Twenty of the most important differentially expressed genes (DEGs) were verified by Real-time PCR, which resulted in a trend concordance of almost 100% between the two techniques. CONCLUSION Our studies demonstrated dynamic changes in global gene expression during intestine regeneration and presented a series of candidate genes and enriched pathways that contribute to intestine regeneration in sea cucumbers. This provides a foundation for future studies on the genetics/molecular mechanisms associated with intestine regeneration.
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Affiliation(s)
- Lina Sun
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Hongsheng Yang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Muyan Chen
- Ocean University of China, Qingdao, PR China
| | - Deyou Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Chenggang Lin
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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22
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Franco C, Soares R, Pires E, Koci K, Almeida AM, Santos R, Coelho AV. Understanding regeneration through proteomics. Proteomics 2013; 13:686-709. [DOI: 10.1002/pmic.201200397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Catarina Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Kamila Koci
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - André M. Almeida
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
- Instituto de Investigação Científica Tropical; Lisboa Portugal
| | - Romana Santos
- Unidade de Investigação em Ciências Orais e Biomédicas, Faculdade de Medicina Dentária; Universidade de Lisboa; Portugal
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
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23
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Franco CF, Soares R, Pires E, Santos R, Coelho AV. Radial nerve cord protein phosphorylation dynamics during starfish arm tip wound healing events. Electrophoresis 2012; 33:3764-78. [DOI: 10.1002/elps.201200274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/05/2012] [Accepted: 07/14/2012] [Indexed: 01/14/2023]
Affiliation(s)
- Catarina F. Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
| | | | - Ana V. Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras; Portugal
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24
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Clark MS, Denekamp NY, Thorne MAS, Reinhardt R, Drungowski M, Albrecht MW, Klages S, Beck A, Kube M, Lubzens E. Long-term survival of hydrated resting eggs from Brachionus plicatilis. PLoS One 2012; 7:e29365. [PMID: 22253713 PMCID: PMC3253786 DOI: 10.1371/journal.pone.0029365] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 11/27/2011] [Indexed: 11/18/2022] Open
Abstract
Background Several organisms display dormancy and developmental arrest at embryonic stages. Long-term survival in the dormant form is usually associated with desiccation, orthodox plant seeds and Artemia cysts being well documented examples. Several aquatic invertebrates display dormancy during embryonic development and survive for tens or even hundreds of years in a hydrated form, raising the question of whether survival in the non-desiccated form of embryonic development depends on pathways similar to those occurring in desiccation tolerant forms. Methodology/Principal Findings To address this question, Illumina short read sequencing was used to generate transcription profiles from the resting and amictic eggs of an aquatic invertebrate, the rotifer, Brachionus plicatilis. These two types of egg have very different life histories, with the dormant or diapausing resting eggs, the result of the sexual cycle and amictic eggs, the non-dormant products of the asexual cycle. Significant transcriptional differences were found between the two types of egg, with amictic eggs rich in genes involved in the morphological development into a juvenile rotifer. In contrast, representatives of classical “stress” proteins: a small heat shock protein, ferritin and Late Embryogenesis Abundant (LEA) proteins were identified in resting eggs. More importantly however, was the identification of transcripts for messenger ribonucleoprotein particles which stabilise RNA. These inhibit translation and provide a valuable source of useful RNAs which can be rapidly activated on the exit from dormancy. Apoptotic genes were also present. Although apoptosis is inconsistent with maintenance of prolonged dormancy, an altered apoptotic pathway has been proposed for Artemia, and this may be the case with the rotifer. Conclusions These data represent the first transcriptional profiling of molecular processes associated with dormancy in a non-desiccated form and indicate important similarities in the molecular pathways activated in resting eggs compared with desiccated dormant forms, specifically plant seeds and Artemia.
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Affiliation(s)
- Melody S. Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | | | - Michael A. S. Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | | | - Mario Drungowski
- Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany
| | | | - Sven Klages
- Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany
| | - Alfred Beck
- Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany
| | - Michael Kube
- Max Planck Institute for Molecular Genetics, Berlin-Dahlem, Germany
| | - Esther Lubzens
- Israel Oceanographic and Limnological Research, Haifa, Israel
- * E-mail:
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25
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Popesku JT, Martyniuk CJ, Trudeau VL. Meta-type analysis of dopaminergic effects on gene expression in the neuroendocrine brain of female goldfish. Front Endocrinol (Lausanne) 2012; 3:130. [PMID: 23130016 PMCID: PMC3487223 DOI: 10.3389/fendo.2012.00130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/12/2012] [Indexed: 12/14/2022] Open
Abstract
Dopamine (DA) is a major neurotransmitter important for neuroendocrine control and recent studies have described genomic signaling pathways activated and inhibited by DA agonists and antagonists in the goldfish brain. Here we perform a meta-type analysis using microarray datasets from experiments conducted with female goldfish to characterize the gene expression responses that underlie dopaminergic signaling. Sexually mature, pre-spawning [gonadosomatic index (GSI) = 4.5 ± 1.3%] or sexually regressing (GSI = 3 ± 0.4%) female goldfish (15-40 g) injected intraperitoneally with either SKF 38393, LY 171555, SCH 23390, sulpiride, or a combination of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and α-methyl-p-tyrosine. Microarray meta-type analysis identified 268 genes in the telencephalon and hypothalamus as having reciprocal (i.e., opposite between agonism and antagonism/depletion) fold change responses, suggesting that these transcripts are likely targets for DA-mediated regulation. Noteworthy genes included ependymin, vimentin, and aromatase, genes that support the significance of DA in neuronal plasticity and tissue remodeling. Sub-network enrichment analysis (SNEA) was used to identify common gene regulators and binding proteins associated with the differentially expressed genes mediated by DA. SNEA analysis identified gene expression targets that were related to three major categories that included cell signaling (STAT3, SP1, SMAD, Jun/Fos), immune response (IL-6, IL-1β, TNFs, cytokine, NF-κB), and cell proliferation and growth (IGF1, TGFβ1). These gene networks are also known to be associated with neurodegenerative disorders such as Parkinsons' disease, well-known to be associated with loss of dopaminergic neurons. This study identifies genes and networks that underlie DA signaling in the vertebrate CNS and provides targets that may be key neuroendocrine regulators. The results provide a foundation for future work on dopaminergic regulation of gene expression in fish model systems.
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Affiliation(s)
- Jason T. Popesku
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of OttawaOttawa, ON, Canada
- *Correspondence: Jason T. Popesku, Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5. e-mail: ; Vance L. Trudeau, Department of Biology, University of Ottawa, Room 160, Gendron Hall, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5. e-mail:
| | - Christopher J. Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New BrunswickSaint John, NB, Canada
| | - Vance L. Trudeau
- Centre for Advanced Research in Environmental Genomics, Department of Biology, University of OttawaOttawa, ON, Canada
- *Correspondence: Jason T. Popesku, Centre for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5. e-mail: ; Vance L. Trudeau, Department of Biology, University of Ottawa, Room 160, Gendron Hall, 30 Marie Curie, Ottawa, ON, Canada K1N 6N5. e-mail:
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García-Arrarás JE, Valentín-Tirado G, Flores JE, Rosa RJ, Rivera-Cruz A, San Miguel-Ruiz JE, Tossas K. Cell dedifferentiation and epithelial to mesenchymal transitions during intestinal regeneration in H. glaberrima. BMC DEVELOPMENTAL BIOLOGY 2011; 11:61. [PMID: 22004330 PMCID: PMC3207902 DOI: 10.1186/1471-213x-11-61] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Determining the type and source of cells involved in regenerative processes has been one of the most important goals of researchers in the field of regeneration biology. We have previously used several cellular markers to characterize the cells involved in the regeneration of the intestine in the sea cucumber Holothuria glaberrima. RESULTS We have now obtained a monoclonal antibody that labels the mesothelium; the outer layer of the gut wall composed of peritoneocytes and myocytes. Using this antibody we studied the role of this tissue layer in the early stages of intestinal regeneration. We have now shown that the mesothelial cells of the mesentery, specifically the muscle component, undergo dedifferentiation from very early on in the regeneration process. Cell proliferation, on the other hand, increases much later, and mainly takes place in the mesothelium or coelomic epithelium of the regenerating intestinal rudiment. Moreover, we have found that the formation of the intestinal rudiment involves a novel regenerative mechanism where epithelial cells ingress into the connective tissue and acquire mesenchymal phenotypes. CONCLUSIONS Our results strongly suggest that the dedifferentiating mesothelium provides the initial source of cells for the formation of the intestinal rudiment. At later stages, cell proliferation supplies additional cells necessary for the increase in size of the regenerate. Our data also shows that the mechanism of epithelial to mesenchymal transition provides many of the connective tissue cells found in the regenerating intestine. These results present some new and important information as to the cellular basis of organ regeneration and in particular to the process of regeneration of visceral organs.
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Mashanov VS, García-Arrarás JE. Gut regeneration in holothurians: a snapshot of recent developments. THE BIOLOGICAL BULLETIN 2011; 221:93-109. [PMID: 21876113 DOI: 10.1086/bblv221n1p93] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Visceral regeneration in sea cucumbers has been studied since early last century; however, it is only within the last 15 years that real progress has been made in understanding the cellular and molecular events involved. In the present review, we bring together these recent studies, providing readers with basic information on the anatomy and histology of the normal gut and detailing the changes in tissue organization and gene expression that occur during the regenerative process. We discuss the nature and possible sources of cells involved in the formation of the intestinal regenerate as well as the role of cell death and proliferation in this process. In addition, we compare gut formation during regeneration and during embryogenesis. Finally, we describe the molecular studies that have helped advance regenerative studies in holothurians and integrate the gene expression information with data on cellular events. Studies on visceral regeneration in these echinoderms provide a unique view that complements regeneration studies in other animal phyla, which are mainly focused on whole-animal regeneration or appendage regeneration.
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Affiliation(s)
- V S Mashanov
- Department of Biology, University of Puerto Rico, San Juan
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Sun L, Chen M, Yang H, Wang T, Liu B, Shu C, Gardiner DM. Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:195-205. [DOI: 10.1016/j.cbd.2011.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/16/2011] [Accepted: 03/18/2011] [Indexed: 11/29/2022]
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Thomson JS, Watts PC, Pottinger TG, Sneddon LU. Physiological and genetic correlates of boldness: characterising the mechanisms of behavioural variation in rainbow trout, Oncorhynchus mykiss. Horm Behav 2011; 59:67-74. [PMID: 20965192 DOI: 10.1016/j.yhbeh.2010.10.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/17/2010] [Accepted: 10/13/2010] [Indexed: 01/19/2023]
Abstract
Bold, risk-taking animals have previously been putatively linked with a proactive stress coping style whereas it is suggested shyer, risk-averse animals exhibit a reactive coping style. The aim of this study was to investigate whether differences in the expression of bold-type behaviour were evident within and between two lines of rainbow trout, Oncorhynchus mykiss, selectively bred for a low (LR) or high (HR) endocrine response to stress, and to link boldness and stress responsiveness with the expression of related candidate genes. Boldness was determined in individual fish over two trials by measuring the latency to approach a novel object. Differences in plasma cortisol concentrations and the expression of eight novel candidate genes previously identified as being linked with divergent behaviours or stress were determined. Bold and shy individuals, approaching the object within 180 s or not approaching within 300 s respectively, were evident within each line, and this was linked with activity levels in the HR line. Post-stress plasma cortisol concentrations were significantly greater in the HR line compared with the LR line, and six of the eight tested genes were upregulated in the brains of LR fish compared with HR fish. However, no direct relationship between boldness and either stress responsiveness or gene expression was found, although clear differences in stress physiology and, for the first time, gene expression could be identified between the lines. This lack of correlation between physiological and molecular responses and behavioural variation within both lines highlights the complexity of the behavioural-physiological complex.
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Affiliation(s)
- Jack S Thomson
- School of Biological Sciences, University of Liverpool, Liverpool, UK, L69 7ZB.
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Shemesh H, Ovadia O, Novoplansky A. Anticipating future conditions via trajectory sensitivity. PLANT SIGNALING & BEHAVIOR 2010; 5:1501-1503. [PMID: 21057218 PMCID: PMC3115267 DOI: 10.4161/psb.5.11.13660] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/17/2010] [Indexed: 05/23/2023]
Abstract
Plants are known to be highly responsive to environmental heterogeneity and normally allocate more biomass to organs which grow in richer patches. However, recent evidence demonstrates that plants can discriminately allocate more resources to roots that develop in patches with increasing nutrient levels, even when their other roots develop in richer patches. Responsiveness to the direction and steepness of spatial and temporal trajectories of environmental variables might enable plants to increase their performance by improving their readiness to anticipated resource availabilities in their immediate proximity. Exploring the ecological implications and mechanisms of trajectory- sensitivity in plants is expected to shed new light on the ways plants learn their environment and anticipate its future challenges and opportunities.
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Affiliation(s)
- Hagai Shemesh
- Life Sciences Department; Ben-Gurion University of the Negev; Be'er Sheva, Israel
- Miterani Department of Desert Ecology; Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Beer Sheva, Israel
| | - Ofer Ovadia
- Life Sciences Department; Ben-Gurion University of the Negev; Be'er Sheva, Israel
| | - Ariel Novoplansky
- Miterani Department of Desert Ecology; Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Beer Sheva, Israel
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Ortiz-Pineda PA, Ramírez-Gómez F, Pérez-Ortiz J, González-Díaz S, Santiago-De Jesús F, Hernández-Pasos J, Del Valle-Avila C, Rojas-Cartagena C, Suárez-Castillo EC, Tossas K, Méndez-Merced AT, Roig-López JL, Ortiz-Zuazaga H, García-Arrarás JE. Gene expression profiling of intestinal regeneration in the sea cucumber. BMC Genomics 2009; 10:262. [PMID: 19505337 PMCID: PMC2711116 DOI: 10.1186/1471-2164-10-262] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/08/2009] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Among deuterostomes, the regenerative potential is maximally expressed in echinoderms, animals that can quickly replace most injured organs. In particular, sea cucumbers are excellent models for studying organ regeneration since they regenerate their digestive tract after evisceration. However, echinoderms have been sidelined in modern regeneration studies partially because of the lack of genome-wide profiling approaches afforded by modern genomic tools.For the last decade, our laboratory has been using the sea cucumber Holothuria glaberrima to dissect the cellular and molecular events that allow for such amazing regenerative processes. We have already established an EST database obtained from cDNA libraries of normal and regenerating intestine at two different regeneration stages. This database now has over 7000 sequences. RESULTS In the present work we used a custom-made microchip from Agilent with 60-mer probes for these ESTs, to determine the gene expression profile during intestinal regeneration. Here we compared the expression profile of animals at three different intestinal regeneration stages (3-, 7- and 14-days post evisceration) against the profile from normal (uneviscerated) intestines. The number of differentially expressed probes ranged from 70% at p < 0.05 to 39% at p < 0.001. Clustering analyses show specific profiles of expression for early (first week) and late (second week) regeneration stages. We used semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR) to validate the expression profile of fifteen microarray detected differentially expressed genes which resulted in over 86% concordance between both techniques. Most of the differentially expressed ESTs showed no clear similarity to sequences in the databases and might represent novel genes associated with regeneration. However, other ESTs were similar to genes known to be involved in regeneration-related processes, wound healing, cell proliferation, differentiation, morphological plasticity, cell survival, stress response, immune challenge, and neoplastic transformation. Among those that have been validated, cytoskeletal genes, such as actins, and developmental genes, such as Wnt and Hox genes, show interesting expression profiles during regeneration. CONCLUSION Our findings set the base for future studies into the molecular basis of intestinal regeneration. Moreover, it advances the use of echinoderms in regenerative biology, animals that because of their amazing properties and their key evolutionary position, might provide important clues to the genetic basis of regenerative processes.
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Affiliation(s)
- Pablo A Ortiz-Pineda
- University of Puerto Rico, Rio Piedras, Department of Biology, San Juan, PR, USA.
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Ganss B, Hoffmann W. Calcium-induced conformational transition of trout ependymins monitored by tryptophan fluorescence. Open Biochem J 2009; 3:14-7. [PMID: 19401757 PMCID: PMC2669641 DOI: 10.2174/1874091x00903010014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 12/05/2008] [Accepted: 01/20/2009] [Indexed: 11/22/2022] Open
Abstract
Ependymins are secretory, calcium-binding sialoproteins which are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these regeneration-responsive glycoproteins is associated with collagen fibrils of the extracellular matrix. Here, the tryptophan fluorescence of ependymins was monitored at various Ca(2+) concentrations. Two distinct states were identified with a relatively sharp transition at about 1 mM Ca(2+). In agreement with previous circular dichroism measurements, this strongly supports the hypothesis that a calcium-induced conformational change is important for the interaction of ependymins with components of the extracellular matrix. Such interactions with constituents of various basal laminae would also explain the important roles of piscine ependymins as well as invertebrate and mammalian ependymin-related proteins for cell adhesion processes and cell migration.
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Affiliation(s)
- Bernhard Ganss
- Max-Planck-Institute for Psychiatry, Department of Neurochemistry, D-82152 Martinsried, Germany
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ZHOU ZC. MYP gene expressions at transcription level in different stages of gonad of sea urchin Strongylocentrotus intermedius and hybrids. YI CHUAN = HEREDITAS 2009; 30:1453-8. [PMID: 19073555 DOI: 10.3724/sp.j.1005.2008.01453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rojas-Cartagena C, Ortíz-Pineda P, Ramírez-Gómez F, Suárez-Castillo EC, Matos-Cruz V, Rodríguez C, Ortíz-Zuazaga H, García-Arrarás JE. Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima. Physiol Genomics 2007; 31:203-15. [PMID: 17579180 PMCID: PMC2866185 DOI: 10.1152/physiolgenomics.00228.2006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Repair and regeneration are key processes for tissue maintenance, and their disruption may lead to disease states. Little is known about the molecular mechanisms that underline the repair and regeneration of the digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model to dissect and characterize the molecular events during intestinal regeneration. To study the gene expression profile, cDNA libraries were constructed from normal, 3-day, and 7-day regenerating intestines of H. glaberrima. Clones were randomly sequenced and queried against the nonredundant protein database at the National Center for Biotechnology Information. RT-PCR analyses were made of several genes to determine their expression profile during intestinal regeneration. A total of 5,173 sequences from three cDNA libraries were obtained. About 46.2, 35.6, and 26.2% of the sequences for the normal, 3-days, and 7-days cDNA libraries, respectively, shared significant similarity with known sequences in the protein database of GenBank but only present 10% of similarity among them. Analysis of the libraries in terms of functional processes, protein domains, and most common sequences suggests that a differential expression profile is taking place during the regeneration process. Further examination of the expressed sequence tag dataset revealed that 12 putative genes are differentially expressed at significant level (R > 6). Experimental validation by RT-PCR analysis reveals that at least three genes (unknown C-4677-1, melanotransferrin, and centaurin) present a differential expression during regeneration. These findings strongly suggest that the gene expression profile varies among regeneration stages and provide evidence for the existence of differential gene expression.
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Dupont S, Thorndyke M. Bridging the regeneration gap: insights from echinoderm models. Nat Rev Genet 2007. [DOI: 10.1038/nrg1923-c1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Suárez-Castillo EC, García-Arrarás JE. Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol 2007; 7:23. [PMID: 17302986 PMCID: PMC1805737 DOI: 10.1186/1471-2148-7-23] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 02/15/2007] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. RESULTS Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the ependymin paralog groups is well supported and several amino acid positions are predicted to be critical for this divergence. CONCLUSION Ependymin proteins are present in vertebrates, invertebrate deuterostomes, and protostomes. Overall, our analyses suggest that the ependymin protein family is a suitable target to experimentally test subfunctionalization in gene copies that originated after gene or genome duplication events.
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Affiliation(s)
- Edna C Suárez-Castillo
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
| | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 00931, Puerto Rico
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Rossi F, Chini V, Cattaneo AG, Bernardini G, Terova G, Saroglia M, Gornati R. EST-based identification of genes expressed in perch (Perca fluviatilis, L.). Gene Expr 2007; 14:117-27. [PMID: 18257394 PMCID: PMC6042039 DOI: 10.3727/105221607783417600] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Perch are promising species for freshwater aquaculture and, differently from other fish, have not yet been domesticated through artificial selection; therefore, they show a wide genetic variability that is undesirable for aquaculture. In addition to the more traditional methods of aquatic biotechnology, the most recently developed molecular biological techniques can augment the overall efficiency of aquaculture. To help these new molecular techniques find their place in the everyday management of fish farming, we should make an effort to reduce the gap in genomic resources that separates farming species from "model organisms." We performed single-pass sequencing on 1237 randomly selected clones from a perch liver cDNA expression library, 350 clones of a brain-minus-liver, and 639 clones of a liver-minus-brain subtraction library. The sequences were deposited in the NCBI Expressed Sequence Tags database (www.ncbi.nlm.nih.gov/projects/dbEST). In the three libraries we identified 108, 46, and 104 genes, respectively. EST cataloguing and profiling of perch will provide a basis for functional genomic research in this species, but will also promote studies in comparative and environmental genomics, for identifying polymorphic markers that are useful, for example, to survey the disease resistance of fish and for discovering of new molecular markers of exposure. Using these genomic resources, micro- and macroarrays can be produced that will give immediate and practical benefits in the field of aquaculture, allowing early diagnosis of the fish conditions and helping in the generation of new mechanistic data on the nature of fish responses to different farming conditions.
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Affiliation(s)
- Federica Rossi
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Valentina Chini
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Anna Giulia Cattaneo
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Giovanni Bernardini
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Genciana Terova
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Marco Saroglia
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
| | - Rosalba Gornati
- Dipartimento di Biotecnologie e Scienze Molecolari, Università dell’Insubria, I-21100 Varese, Italy
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Burke RD, Angerer LM, Elphick MR, Humphrey GW, Yaguchi S, Kiyama T, Liang S, Mu X, Agca C, Klein WH, Brandhorst BP, Rowe M, Wilson K, Churcher AM, Taylor JS, Chen N, Murray G, Wang D, Mellott D, Olinski R, Hallböök F, Thorndyke MC. A genomic view of the sea urchin nervous system. Dev Biol 2006; 300:434-60. [PMID: 16965768 PMCID: PMC1950334 DOI: 10.1016/j.ydbio.2006.08.007] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 07/29/2006] [Accepted: 08/02/2006] [Indexed: 10/24/2022]
Abstract
The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains before gastrulation indicating that they may operate near the top of a conserved neural gene regulatory network. A family of genes encoding voltage-gated ion channels is present but, surprisingly, genes encoding gap junction proteins (connexins and pannexins) appear to be absent. Genes required for synapse formation and function have been identified and genes for synthesis and transport of neurotransmitters are present. There is a large family of G-protein-coupled receptors, including 874 rhodopsin-type receptors, 28 metabotropic glutamate-like receptors and a remarkably expanded group of 161 secretin receptor-like proteins. Absence of cannabinoid, lysophospholipid and melanocortin receptors indicates that this group may be unique to chordates. There are at least 37 putative G-protein-coupled peptide receptors and precursors for several neuropeptides and peptide hormones have been identified, including SALMFamides, NGFFFamide, a vasotocin-like peptide, glycoprotein hormones and insulin/insulin-like growth factors. Identification of a neurotrophin-like gene and Trk receptor in sea urchin indicates that this neural signaling system is not unique to chordates. Several hundred chemoreceptor genes have been predicted using several approaches, a number similar to that for other animals. Intriguingly, genes encoding homologues of rhodopsin, Pax6 and several other key mammalian retinal transcription factors are expressed in tube feet, suggesting tube feet function as photosensory organs. Analysis of the sea urchin genome presents a unique perspective on the evolutionary history of deuterostome nervous systems and reveals new approaches to investigate the development and neurobiology of sea urchins.
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Affiliation(s)
- R D Burke
- Department of Biology, University of Victoria, Victoria, POB 3020, STN CSC, Victoria, BC, Canada V8W 3N5.
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Jackson DJ, McDougall C, Green K, Simpson F, Wörheide G, Degnan BM. A rapidly evolving secretome builds and patterns a sea shell. BMC Biol 2006; 4:40. [PMID: 17121673 PMCID: PMC1676022 DOI: 10.1186/1741-7007-4-40] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 11/22/2006] [Indexed: 11/29/2022] Open
Abstract
Background Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and design, and as such must contribute to the variety of adaptive architectures and colors found in mollusk shells. The composition of this novel mantle-specific secretome suggests that there are significant molecular differences in the ways in which gastropods synthesize their shells.
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Affiliation(s)
- Daniel J Jackson
- School of Integrative Biology, University of Queensland, Brisbane Qld 4072, Australia
- Department of Geobiology, Geoscience Centre, University of Göttingen, Goldschmidtstr.3, 37077 Göttingen, Germany
| | - Carmel McDougall
- School of Integrative Biology, University of Queensland, Brisbane Qld 4072, Australia
- Department of Zoology, University of Oxford, Tinbergen Bldg., South Parks Road, Oxford OX1 3PS, UK
| | - Kathryn Green
- School of Integrative Biology, University of Queensland, Brisbane Qld 4072, Australia
| | - Fiona Simpson
- Institute of Molecular Biosciences, University of Queensland, Brisbane Qld 4072, Australia
| | - Gert Wörheide
- Department of Geobiology, Geoscience Centre, University of Göttingen, Goldschmidtstr.3, 37077 Göttingen, Germany
| | - Bernard M Degnan
- School of Integrative Biology, University of Queensland, Brisbane Qld 4072, Australia
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Kouznetsova I, Chwieralski CE, Bälder R, Hinz M, Braun A, Krug N, Hoffmann W. Induced trefoil factor family 1 expression by trans-differentiating Clara cells in a murine asthma model. Am J Respir Cell Mol Biol 2006; 36:286-95. [PMID: 16990615 DOI: 10.1165/rcmb.2006-0008oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Asthma is a chronic inflammatory disease of the airways that is accompanied by goblet cell metaplasia and mucus hypersecretion. Trefoil factor family (TFF) peptides represent major secretory products of the respiratory tract and are synthesized together with mucins. In the murine lung, TFF2 is mainly expressed, whereas TFF1 transcripts represent only a minor species. TFF peptides are well known for their motogenic and anti-apoptotic effects, and they modulate the inflammatory response of bronchial epithelial cells. Here, an established mouse model of asthma was investigated (i.e., exposure to Aspergillus fumigatus [AF] antigens). RT-PCR analysis of lung tissue showed elevated levels particularly of TFF1 transcripts in AF-sensitized/challenged animals. In contrast, transcripts encoding Clara cell secretory protein (CCSP/CC10) were strongly diminished in these animals. For comparison, the expression of the goblet cell secretory granule marker mCLCA3/Gob-5, the mucins Muc1-Muc6 and Muc19, and the secretoglobins ScgB3A1 and ScgB3A2, as well as the mammalian ependymin-related gene MERP2, were monitored. Immunohistochemistry localized TFF1 mainly in cells with a mixed phenotype (e.g., TFF1-positive cells stain with the lectin wheat germ agglutinin (WGA), which recognizes mucins characteristic of goblet cells). In addition, these cells express CCSP/CC10, a Clara cell marker. When compared with mucins or CCSP/CC10, TFF1 was stored in a different population of secretory granules localized at the more basolateral portion of these cells. Thus, the results presented indicate for the first time that allergen exposure leads to the trans-differentiation of Clara cells toward a TFF1-expressing mucous phenotype.
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Affiliation(s)
- Irina Kouznetsova
- Institut für Molekularbiologie und Medizinische Chemie, Otto-von-Guericke-Universität, Magdeburg; and Fraunhofer-Institut für Toxikologie und Experimentelle Medizin, Hannover, Germany
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Bradley SP, Pahari M, Uknis ME, Rastellini C, Cicalese L. Gene Expression Profiles Characterize Early Graft Response in Living Donor Small Bowel Transplantation: A Case Report. Transplant Proc 2006; 38:1742-3. [PMID: 16908269 DOI: 10.1016/j.transproceed.2006.05.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The cellular and histological events that occur during the regeneration process in invertebrates have been studied in the field of visceral regeneration. We would like to explore the molecular aspects of the regeneration process in the small intestine. The aim of this study was to characterize the gene expression profiles of the intestinal graft to identify which genes may have a role in regeneration of graft tissue posttransplant. METHODS In a patient undergoing living related small bowel transplantation (LRSBTx) in our institution, mucosal biopsies were obtained from the recipient intestine and donor graft at the time of transplant and at weeks 1, 2, 3, and 6 posttransplant. Total RNA was isolated from sample biopsies followed by gene expression profiles determined from the replicate samples (n = 3) for each biopsy using the Affymetrix U133 Plus 2.0 Human GeneChip set. RESULTS Two profiles were obtained from the data. One profile showed rapid increase of 45 genes immediately after transplant by week 1 with significant changes (P < .05) greater than threefold including the chemokine CXC9 and glutathione-related stress factors, GPX2 and GSTA4. The second profile identified 133 genes that were significantly decreased by threefold or greater immediately after transplant week 1, including UCC1, the human homolog of the Ependymin gene. CONCLUSION We have identified two gene expression profiles representing early graft responses to small bowel transplantation. These profiles will serve to identify and study those genes whose products may play a role in accelerating tissue regeneration following segmental LRSBTx.
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Affiliation(s)
- S P Bradley
- Division of Organ Transplantation, Department of Surgery, University of Massachusetts Medical School-UMass/Memorial Healthcare, 55 Lake Avenue North, Worcester, MA 01655, USA
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Volz DC, Hinton DE, Law JM, Kullman SW. Dynamic gene expression changes precede dioxin-induced liver pathogenesis in medaka fish. Toxicol Sci 2005; 89:524-34. [PMID: 16267337 DOI: 10.1093/toxsci/kfj033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A major challenge for environmental genomics is linking gene expression to cellular toxicity and morphological alteration. Herein, we address complexities related to hepatic gene expression responses after a single injection of the aryl hydrocarbon receptor (AHR) agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) and illustrate an initial stress response followed by cytologic and adaptive changes in the teleost fish medaka. Using a custom 175-gene array, we find that overall hepatic gene expression and histological changes are strongly dependent on dose and time. The most pronounced dioxin-induced gene expression changes occurred early and preceded morphologic alteration in the liver. Following a systematic search for putative Ah response elements (AHREs) (5'-CACGCA-3') within 2000 bp upstream of the predicted transcriptional start site, the majority (87%) of genes screened in this study did not contain an AHRE, suggesting that gene expression was not solely dependent on AHRE-mediated transcription. Moreover, in the highest dosage, we observed gene expression changes associated with adaptation that persisted for almost two weeks, including induction of a gene putatively identified as ependymin that may function in hepatic injury repair. These data suggest that the cellular response to dioxin involves both AHRE- and non-AHRE-mediated transcription, and that coupling gene expression profiling with analysis of morphologic pathogenesis is essential for establishing temporal relationships between transcriptional changes, toxicity, and adaptation to hepatic injury.
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Affiliation(s)
- David C Volz
- Integrated Toxicology Program and Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina 27708, USA
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