Ontology highlight
ABSTRACT:
PROVIDER: PRJNA398984 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5945870_1.fastq.gz | Fastqsanger.gz | |||
| SRR5945870_2.fastq.gz | Fastqsanger.gz | |||
| SRR5945880_1.fastq.gz | Fastqsanger.gz | |||
| SRR5945880_2.fastq.gz | Fastqsanger.gz | |||
| SRR5945890_1.fastq.gz | Fastqsanger.gz |
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Project description:In this project we have applied palaeoproteomics to study archaeological shell beads dating back to the beginning of the 7th mill. cal BCE and recovered from a prehistoric site in Jordan (Ba'ja). These beads were made of mollusc shells and were of unknown origin, but suspected to be made of larger bivalves such as Tridacna or Spondylus sp. The aim of the study was to analyse ancient proteins extracted from these beads in order to infer their biological origin. Tiny amounts of ancient samples were used and the extracted proteins were analysed by high resolution liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). In order to identify obtained peptides, we have created an ‘in-house’ molluscan protein database, by gathering molluscan sequences (proteins and transcriptomes), which were downloaded from publicly available databases in NCBI. Searching against this comprehensive database, we were able to identify a number of shell proteins from Tridacna sp., the giant clam shells. Our study reports the oldest molluscan protein sequences ever recovered that come from a very warm environment.
2024-11-04 | PXD041082 | Pride
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
2010-02-05 | GSE14305 | GEO
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.
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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.
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Project description:Schistosomiasis is one of the most socioeconomically harmful neglected tropical diseases in the world. It occurs following infection from parasites of the Schistosoma genus, such as Schistosoma mansoni, which must transition within a molluscan and mammalian host to survive. Previous chemical analyses of schistosome-molluscan interactions indicate that schistosomes orientate towards potential hosts partially through chemosensation, displaying a preference for naïve (uninfected) hosts. Recent advances in proteomic techniques enable sophisticated comparative analyses between infected and naïve snail host proteins. This study aimed to compare the snail-conditioned water (SCW) released by F1 resistant, infected and naïve Biomphalaria glabrata to identify potential attractants and deterrents.
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