The microstructural, mineralogical and transcriptional developments of shell biomineralization of Pinctada maxima
Ontology highlight
ABSTRACT:
ORGANISM(S): Pinctada maxima
PROVIDER: GSE14305 | GEO | 2010/02/05
SECONDARY ACCESSION(S): PRJNA114557
REPOSITORIES: GEO
Similar Datasets
Project description:Molluscan larval ontogeny is a highly conserved process typical of 3 principal developmental stages. A characteristic unique to each of these stages is shell design, termed prodissoconch I, prodissoconch II and dissoconch. These shells vary in morphology, mineralogy and microstructure. The discrete temporal transitions in shell biomineralization between these larval stages are utilized in this study to investigate transcriptional involvement in several distinct biomineralization events. Scanning electron microscopy and X-ray diffraction analysis of P. maxima larvae and juveniles collected throughout post-embryonic ontogenesis, document the mineralogy and microstructure of each shelled stage as well as establishing a timeline for transitions in biomineralization. P. maxima larval samples most representative of these biomineralization distinctions and transitions were analyzed for differential gene expression on the microarray platform PmaxArray 1.0. A number of transcripts are reported as differentially expressed in correlation to the mineralization events of P. maxima larval ontogeny. Some of those isolated are known shell matrix genes while others are novel, these are discussed in relation to potential shell formation roles. This interdisciplinary investigation has married the shell developments of P. maxima larval ontogeny with corresponding gene expression profiles, furthering the elucidation of shell biomineralization. Keywords: Temporal expression profiling by array Microarray is used to examine the temporal differential expression of transcripts from several bivalve larval development stages including 24hrs post fertilization, 3 days, 17 days, 20 days, 23 days, 26 days, 30 days, 35 days, 40 days. Differential expression profiles for transcripts of all the temporal samples was determined based on comparison to a common reference of unfertilized eggs. Each temporal larval sample included in the study has at least 3 replicate hybridizations. Dye flips have been incorporated in the replicates. A total of 46 microarray hybridizations were performed in this investigation for differential expression analysis.
2010-02-04 | E-GEOD-14305 | biostudies-arrayexpress
Project description:The mantle is a thin tissue from which proteins are secreted dictating the mollusk shell construction. As a conserved organ involved in shell formation throughout mollusks, the mantle is an excellent foundation from which to study biomineralization. A P. maxima mantle tissue specific cDNA microarray, termed PmaxArray 1.0, has been developed comprising 5000 cDNA transcripts derived from the mantle tissue of P. maxima. This tool has been used to investigate the spatial functional dynamics of the mantle tissue identifying over 2000 PmaxArray 1.0 spots as differentially expressed spatially within this organ. Gene expression profiles observed for these transcripts indicated 5 major spatial functions for the mantle, 3 of which have been putatively attributed to shell formation roles associated with nacre microstructure, calcite prismatic microstructure and periostracum. These transcripts are further examined with in situ expression localization and comparative sequence analyses in reference to potential shell formation roles. This spatial investigation has expedited the elucidation of functions within the dynamic mantle organ, paying particular attention to of shell biomineralization. Keywords: Spatial expression profiling by array
2010-02-05 | GSE14303 | GEO
Project description:The mantle is a thin tissue from which proteins are secreted dictating the mollusk shell construction. As a conserved organ involved in shell formation throughout mollusks, the mantle is an excellent foundation from which to study biomineralization. A P. maxima mantle tissue specific cDNA microarray, termed PmaxArray 1.0, has been developed comprising 5000 cDNA transcripts derived from the mantle tissue of P. maxima. This tool has been used to investigate the spatial functional dynamics of the mantle tissue identifying over 2000 PmaxArray 1.0 spots as differentially expressed spatially within this organ. Gene expression profiles observed for these transcripts indicated 5 major spatial functions for the mantle, 3 of which have been putatively attributed to shell formation roles associated with nacre microstructure, calcite prismatic microstructure and periostracum. These transcripts are further examined with in situ expression localization and comparative sequence analyses in reference to potential shell formation roles. This spatial investigation has expedited the elucidation of functions within the dynamic mantle organ, paying particular attention to of shell biomineralization. Keywords: Spatial expression profiling by array The mantle tissue from 9 animals was dissected into 5 separate sections: outer fold (OF), middle fold (MF), inner fold (IF), ventral mantle tissue (VM) and dorsal mantle tissue (DM). Total RNA was extracted from these tissues and pooled across subjects in order to reduce the effect of biological variation; such that 3 individuals were pooled together totaling 3 pooled replicate samples for each tissue. All the biologically pooled tissue types were compared against a common reference in which total RNA from all tissues types and all nine animals was equally pooled. A total of 30 dual channel microarrays hybridizations were performed and analyzed.
2010-05-15 | E-GEOD-14303 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13980: Analysis of the global gene expression profile for pearl oyster, Pinctada maxima, exposed to organotin (tributyltin) GSE14303: Differential expression analysis of genes from the mantle tissue of pearl oyster: Pinctada maxima GSE14305: The microstructural, mineralogical and transcriptional developments of shell biomineralization of Pinctada maxima Refer to individual Series
2010-02-04 | E-GEOD-14306 | biostudies-arrayexpress
Project description:Bivalves are well known sentinel organism in the detection of environmental pollutants. Bioaccumulation of these contaminants in bivalves often manifests as specific alterations of their biological processes, which are used as biomarkers for environmental pollution. Tributyltin (TBT) is one such pollutant previously used as a biocide in marine antifouling paints, it now causes a number deleterious effects in bivalves leaching out of sediments in marine ecosystems. One effect extensively documented is shell abnormalities, including shell thickening and chambering. Changes in amino acid compositions of the shell matrix are associated with these deformations suggesting that TBT mode of action influences the biological control of shell biomineralization. This environmental toxicants effect on shell biomineralization was analyzed in this investigation at a transcriptional level in order to elucidate the normal shell biomineralization process. P. maxima animals were exposed to TBT in laboratory conditions and a concentration range for chronic and acute toxicity has been established. Animals exposed to chronic concentrations were analyzed for differential gene expression using PmaxArray 1.0 microarray platform and compared against control animals. Genes indentified as differentially expressed in association with TBT exposure included up-regulation of immunity and detoxification related genes and down-regulation of several shell matrix genes. A number of novel transcripts were additionally identified. The potential actions of these genes are discussed with reference to TBT toxicity and shell biomineralization. This investigation has used a microarray to determine transcriptional effects of TBT on P. maxima and proposed the involvement of novel components in shell formation, aiding the elucidation of the process. Keywords: Expression profiling by array, stress response
2010-02-05 | GSE13980 | GEO
Project description:Bivalves are well known sentinel organism in the detection of environmental pollutants. Bioaccumulation of these contaminants in bivalves often manifests as specific alterations of their biological processes, which are used as biomarkers for environmental pollution. Tributyltin (TBT) is one such pollutant previously used as a biocide in marine antifouling paints, it now causes a number deleterious effects in bivalves leaching out of sediments in marine ecosystems. One effect extensively documented is shell abnormalities, including shell thickening and chambering. Changes in amino acid compositions of the shell matrix are associated with these deformations suggesting that TBT mode of action influences the biological control of shell biomineralization. This environmental toxicants effect on shell biomineralization was analyzed in this investigation at a transcriptional level in order to elucidate the normal shell biomineralization process. P. maxima animals were exposed to TBT in laboratory conditions and a concentration range for chronic and acute toxicity has been established. Animals exposed to chronic concentrations were analyzed for differential gene expression using PmaxArray 1.0 microarray platform and compared against control animals. Genes indentified as differentially expressed in association with TBT exposure included up-regulation of immunity and detoxification related genes and down-regulation of several shell matrix genes. A number of novel transcripts were additionally identified. The potential actions of these genes are discussed with reference to TBT toxicity and shell biomineralization. This investigation has used a microarray to determine transcriptional effects of TBT on P. maxima and proposed the involvement of novel components in shell formation, aiding the elucidation of the process. Keywords: Expression profiling by array, stress response In order to determine to differential expression profiles for transcripts relevant to TBT exposure, 9 animals treated with TBT 50 ng1-1 were compared to 9 control animals untreated on a dual channel (Cy3 and Cy5) cDNA microarrays. The RNA for the 9 control animals was pooled together for a common reference while the RNA from the 9 treated animals was separated into 3 pooled replicates, each containing RNA from 3 individual animals. Each of the pooled treatment replicates were labeled (Cy3 or Cy5) as was the controls (opposing treatment label) and hybridized to a separate microarray chip, totaling 3 chips. Each chip had duplicate spot grids printed on the left and right of the chip providing technical replication. In total 6 microarrays were challenged and analyzed comprising 3 biological replicates each with 2 technical replicates.
2010-05-14 | E-GEOD-13980 | biostudies-arrayexpress
Project description:Shells of pearl oyster are natural biominerals with remarkable properties and can be repaired after damage, which are regulated by biomacromolcules especially shell matrix proteins (SMPs). Identifying SMPs is critical for further understanding the process. Although proteomic methods have been used to reveal the complex protein mixture in mature shells, the proteomics of repaired shells after shell damage have not been reported before. Here, we studied the SMPs of the repaired shells (prismatic layers) 5-10 days after shell damage in Pinctada fucata by integrating transcriptomics and proteomics and compared the microstructure difference between repaired and mature shells. Although the repaired shells are calcite, similar to mature shells, the microstructure of repaired shells has holes in the center of prisms with irregular and curved edges. In total, we found 49 SMPs from the repaired shells including some proteins only existing in mature nacreous layers. Peroxidase-like protein and beta-N-acetylhexosaminidase may be important players in repaired shells. In addition, they have the capability to affect CaCO3 crystallization process in vitro, altering the packing and reducing the crystallinity of crystals. This study could improve our understanding of shell repair process and lay the foundation for studying SMPs-controlled biomineralization.
2019-03-26 | PXD010130 | Pride
Project description:Background: The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date. Methods: The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing. Results: We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. Conclusions: The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly.
2018-06-18 | PXD009567 | Pride
Project description:The microstructural, mineralogical and transcriptional developments of shell biomineralization of Pinctada maxima
| PRJNA114557 | ENA
Project description:Circulating hemocytes in the hemolymph represent the backbone of innate immunity in bivalves. Hemocytes are also found in the extrapallial fluid (EPF), the space delimited between the shell and the mantle, which is the site of shell biomineralization. This study investigated the transcriptome, proteome, and function of hemocytes found in the EPF and hemolymph in the hard clam Mercenaria mercenaria. Total and differential hemocyte counts were similar between EPF and hemolymph. Overexpressed genes in the EPF were found to have domains previously identified as being part of the biomineralization toolkit and involved in bivalve shell formation. Biomineralization related genes included chitin-metabolism genes, carbonic anhydrase, perlucin, and insoluble shell matrix protein genes. Overexpressed genes in the EPF encoded proteins present at higher abundances in the EPF proteome, specifically those related to shell formation such as carbonic anhydrase and insoluble shell matrix proteins. Genes coding for bicarbonate and ion transporters were also overexpressed, suggesting that EPF hemocytes are involved in regulating the availability of ions critical for biomineralization. Functional assays also showed that Ca2+ content of hemocytes in the EPF were significantly higher than those in hemolymph, supporting the idea that hemocytes serve as a source of Ca2+ during biomineralization. Overexpressed genes and proteins also contained domains such as C1q that have dual functions in biomineralization and immune response. The percent of phagocytic granulocytes was not significantly different between EPF and hemolymph. Together, these findings suggest that hemocytes in EPF have dual functions of biomineralization and immunity.
2022-01-09 | MSV000088664 | MassIVE