scholarly journals Peer Review #1 of "Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid (v0.1)"

2015 ◽  
Author(s):  
M Gerdol
Keyword(s):  
Peer Review ◽  
High Throughput ◽  
Okadaic Acid ◽  
Transcriptomic Responses ◽  
Sublethal Concentrations

scholarly journals Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1429 ◽  
Author(s):  
Victoria Suarez-Ulloa ◽  
Juan Fernandez-Tajes ◽  
Vanessa Aguiar-Pulido ◽  
M. Veronica Prego-Faraldo ◽  
Fernanda Florez-Barros ◽  
...  
Keyword(s):  
Digestive Gland ◽  
Okadaic Acid ◽  
Algal Blooms ◽  
Molecular Transport ◽  
Shellfish Poisoning ◽  
Transcriptomic Response ◽  
Custom Made ◽  
Transcriptomic Responses ◽  
Sublethal Concentrations

Background.Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the primary cause of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom.Methods.Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellateProrocentrum limafor 24 h). The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues.Results.Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the musselMytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of this tissue for future biomonitoring studies.Discussion.Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of tools for the monitoring of OA pollution.

scholarly journals Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid

2015 ◽  
Author(s):  
Victoria Suarez-Ulloa ◽  
Juan Fernandez-Tajes ◽  
Vanessa Aguiar-Pulido ◽  
M. Veronica Prego-Faraldo ◽  
Fernanda Florez-Barros ◽  
...  
Keyword(s):  
Digestive Gland ◽  
Okadaic Acid ◽  
Algal Blooms ◽  
Molecular Transport ◽  
Shellfish Poisoning ◽  
Transcriptomic Response ◽  
Custom Made ◽  
Transcriptomic Responses ◽  
Sublethal Concentrations

Background: Diarrhetic Shellfish Poisoning (DSP) Harmful Algal Blooms (HABs) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the main responsible of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom. Methods: Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellate Prorocentrum lima for 24 hours). Modifications in the expression of environmentally relevant transcripts were initially assessed using qPCR. The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues. Results: Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the mussel Mytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of this tissue for future biomonitoring studies. Discussion: Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of OA biomarkers.

scholarly journals Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid

2015 ◽  
Author(s):  
Victoria Suarez-Ulloa ◽  
Juan Fernandez-Tajes ◽  
Vanessa Aguiar-Pulido ◽  
M. Veronica Prego-Faraldo ◽  
Fernanda Florez-Barros ◽  
...  
Keyword(s):  
Digestive Gland ◽  
Okadaic Acid ◽  
Algal Blooms ◽  
Molecular Transport ◽  
Shellfish Poisoning ◽  
Transcriptomic Response ◽  
Custom Made ◽  
Transcriptomic Responses ◽  
Sublethal Concentrations

Background: Diarrhetic Shellfish Poisoning (DSP) Harmful Algal Blooms (HABs) represent a major threat for human consumers of shellfish. The biotoxin Okadaic Acid (OA), a well-known phosphatase inhibitor and tumor promoter, is the main responsible of acute DSP intoxications. Although several studies have described the molecular effects of high OA concentrations on sentinel organisms (e.g., bivalve molluscs), the effect of prolonged exposures to low (sublethal) OA concentrations is still unknown. In order to fill this gap, this work combines Next-Generation sequencing and custom-made microarray technologies to develop an unbiased characterization of the transcriptomic response of mussels during early stages of a DSP bloom. Methods: Mussel specimens were exposed to a HAB episode simulating an early stage DSP bloom (200 cells/L of the dinoflagellate Prorocentrum lima for 24 hours). Modifications in the expression of environmentally relevant transcripts were initially assessed using qPCR. The unbiased characterization of the transcriptomic responses triggered by OA was carried out using two complementary methods of cDNA library preparation: normalized and Suppression Subtractive Hybridization (SSH). Libraries were sequenced and read datasets were mapped to Gene Ontology and KEGG databases. A custom-made oligonucleotide microarray was developed based on these data, completing the expression analysis of digestive gland and gill tissues. Results: Our findings show that exposure to sublethal concentrations of OA is enough to induce gene expression modifications in the mussel Mytilus. Transcriptomic analyses revealed an increase in proteasomal activity, molecular transport, cell cycle regulation, energy production and immune activity in mussels. Oppositely, a number of transcripts hypothesized to be responsive to OA (notably the Serine/Threonine phosphatases PP1 and PP2A) failed to show substantial modifications. Both digestive gland and gill tissues responded similarly to OA, although expression modifications were more dramatic in the former, supporting the choice of this tissue for future biomonitoring studies. Discussion: Exposure to OA concentrations within legal limits for safe consumption of shellfish is enough to disrupt important cellular processes in mussels, eliciting sharp transcriptional changes as a result. By combining the study of cDNA libraries and a custom-made OA-specific microarray, our work provides a comprehensive characterization of the OA-specific transcriptome, improving the accuracy of the analysis of expresion profiles compared to single-replicated RNA-seq methods. The combination of our data with related studies helps understanding the molecular mechanisms underlying molecular responses to DSP episodes in marine organisms, providing useful information to develop a new generation of OA biomarkers.

Combinatorial Fabrication and High-Throughput Characterization of Thin Film Metal Oxide Libraries for Solar water Splitting

2018 ◽  
Author(s):  
Alfred Ludwig ◽  
Mona Nowak ◽  
Swati Kumari ◽  
Helge S. Stein ◽  
Ramona Gutkowski ◽  
...  
Keyword(s):  
Thin Film ◽  
Metal Oxide ◽  
Water Splitting ◽  
High Throughput ◽  
Solar Water ◽  
Solar Water Splitting

scholarly journals Database of ab initio L-edge X-ray absorption near edge structure

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yiming Chen ◽  
Chi Chen ◽  
Chen Zheng ◽  
Shyam Dwaraknath ◽  
Matthew K. Horton ◽  
...  
Keyword(s):  
High Throughput ◽  
Scattering Theory ◽  
Research Community ◽  
Metal Compounds ◽  
Edge Structure ◽  
X Ray ◽  
Initial Release ◽  
Computational Workflow ◽  
X Ray Absorption

AbstractThe L-edge X-ray Absorption Near Edge Structure (XANES) is widely used in the characterization of transition metal compounds. Here, we report the development of a database of computed L-edge XANES using the multiple scattering theory-based FEFF9 code. The initial release of the database contains more than 140,000 L-edge spectra for more than 22,000 structures generated using a high-throughput computational workflow. The data is disseminated through the Materials Project and addresses a critical need for L-edge XANES spectra among the research community.

High-Throughput Synthesis and Characterization of a Combinatorial Materials Library in Bulk Alloys

2021 ◽  
Vol 52 (4) ◽  
pp. 1159-1168
Author(s):  
Lei Zhao ◽  
Yuanxun Zhou ◽  
Hui Wang ◽  
Xuebin Chen ◽  
Lixia Yang ◽  
...  
Keyword(s):  
High Throughput ◽  
Synthesis And Characterization ◽  
Combinatorial Materials ◽  
Bulk Alloys

High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins

2019 ◽  
Vol 60 (5) ◽  
pp. 1082-1097 ◽  
Author(s):  
Panneerselvam Krishnamurthy ◽  
Yukiko Fujisawa ◽  
Yuya Takahashi ◽  
Hanako Abe ◽  
Kentaro Yamane ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
High Density ◽  
Biosynthesis Pathway ◽  
Mutant Library ◽  
Triterpenoid Saponins
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