1,721,065 research outputs found
FIGURE 3 in MIDTAL (Microarrays for the Detection of Toxic Algae)
No full textFIGURE 3: Hybridization of fragmented RNA to 16 probes (x axis) on the microarray with increasing hybridisation temperature as compared to non fragmented RNA hybridised at 37°C. Probes with low signals are enhanced by fragmentation. The signal to noise ratio values above the background cut-off of 1 are shown.Published as part of Medlin, Linda K., Montresor, Marina, Graneli, Edna, Reugera, Beatrix, Raine, Robin, Edvardsen, Bente, Lewis, Jane, Elliott, Chris, Pazos, Yolanda & Maranda, Lucie, 2013, MIDTAL (Microarrays for the Detection of Toxic Algae), pp. 201-210 in Phytotaxa 127 (1) on page 206, DOI: 10.11646/phytotaxa.127.1.19, http://zenodo.org/record/508541
FIGURE 5 in MIDTAL (Microarrays for the Detection of Toxic Algae)
No full textFIGURE 5: Comparison of RNA yields extracted from three filters of field material collected at eight stations in the Irish Sea at Galway, Ireland by PTR 5 NUIG with (av spiked = red) and without (av crudeblue = blue) the addition of cells of Dunaliella as the internal control prior to the extraction.Published as part of Medlin, Linda K., Montresor, Marina, Graneli, Edna, Reugera, Beatrix, Raine, Robin, Edvardsen, Bente, Lewis, Jane, Elliott, Chris, Pazos, Yolanda & Maranda, Lucie, 2013, MIDTAL (Microarrays for the Detection of Toxic Algae), pp. 201-210 in Phytotaxa 127 (1) on page 207, DOI: 10.11646/phytotaxa.127.1.19, http://zenodo.org/record/508541
Selection and validation of reference genes for qPCR analysis in the pennate diatoms Pseudo-nitzschia multistriata and P. arenysensis
No full textDiatoms are eukaryotic microalgae broadly present in freshwater and marine ecosystems. The great ecological interest about diatoms has recently led to increased efforts towards the exploration of the molecular properties of these organisms and the development of molecular tools to study the function of genes. We are using as model system two pennate diatoms, Pseudo-nitzschia multistriata and Pseudo-nitzschia arenysensis. In order to enable molecular investigations in these two species, we have made use of sequence information from transcriptomic data to identify genes that can be used as reference genes in quantitative PCR (qPCR). We have analyzed the expression of a set of genes commonly used as reference genes: histone H4, TBP (TATA binding protein), RPS (30 S ribosomal protein), GAPDH (glyceraldehyde 3-phosphate dehydrogenase), TUB A and TUB B (tubulin alpha and tubulin beta), ACT (actin), CDK A (cyclin dependent kinase A) and COPA (coatomer protein complex, subunit alpha). The suitability of these genes as references in qPCR has been tested in different conditions and among different strains. We have found that only TUB A, TUB B and CDK A are stable in all the conditions analyzed. These three genes, in addition to ACT and COPA, are good reference genes for P. multistriata, while GAPDH appears to be differentially expressed in the tested conditions in this species. In P. arenysensis, instead, TUB A, TUB B, CDK A, GAPDH, H4 and RPS show the highest levels of stability and can be considered reliable reference genes. (C) 2013 Elsevier B.V. All rights reserved
Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms
Get PDFDiatoms are among the most diverse eukaryotic microorganisms on Earth, they are responsible for a large fraction of primary production in the oceans and can be found in different habitats. Pseudo-nitzschia are marine planktonic diatoms responsible for blooms in coastal and oceanic waters. We analyzed the transcriptome of three species, Pseudo-nitzschia arenysensis, Pseudo-nitzschia delicatissima and Pseudo-nitzschia multistriata, with different levels of genetic relatedness. These species have a worldwide distribution and the last one produces the neurotoxin domoic acid. We were able to annotate about 80% of the sequences in each transcriptome and the analysis of the relative functional annotations allowed comparison of the main metabolic pathways, pathways involved in the biosynthesis of isoprenoids (MAV and MEP pathways), and pathways putatively involved in domoic acid synthesis. The search for homologous transcripts among the target species and other congeneric species resulted in the discovery of a sequence annotated as Nitric Oxide Synthase (NOS), found uniquely in Pseudo-nitzschia multistriata. The predicted protein product contained all the domains of the canonical metazoan sequence. Putative NOS sequences were found in other available diatom datasets, supporting a role for nitric oxide as signaling molecule in this group of microalgae
Selection and validation of reference genes for qPCR analysis in the pennate diatoms Pseudo-nitzschia multistriata and P. arenysensis
No full textDiatoms are eukaryotic microalgae broadly present in freshwater and marine ecosystems. The great ecological interest about diatoms has recently led to increased efforts towards the exploration of the molecular properties of these organisms and the development of molecular tools to study the function of genes. We are using as model system two pennate diatoms, Pseudo-nitzschia multistriata and Pseudo-nitzschia arenysensis. In order to enable molecular investigations in these two species, we have made use of sequence information from transcriptomic data to identify genes that can be used as reference genes in quantitative PCR (qPCR). We have analyzed the expression of a set of genes commonly used as reference genes: histone H4, TBP (TATA binding protein), RPS (30. S ribosomal protein), GAPDH (glyceraldehyde 3-phosphate dehydrogenase), TUB A and TUB B (tubulin α and tubulin β), ACT (actin), CDK A (cyclin dependent kinase A) and COPA (coatomer protein complex, subunit α). The suitability of these genes as references in qPCR has been tested in different conditions and among different strains. We have found that only TUB A, TUB B and CDK A are stable in all the conditions analyzed. These three genes, in addition to ACT and COPA, are good reference genes for P. multistriata, while GAPDH appears to be differentially expressed in the tested conditions in this species. In P. arenysensis, instead, TUB A, TUB B, CDK A, GAPDH, H4 and RPS show the highest levels of stability and can be considered reliable reference genes. © 2013 Elsevier B.V
Osservazione del Fitoplancton al microscopio elettronico a scansione (SEM) e a trasmissione (TEM)
No full textQuesto volume rappresenta l’aggiornamento del manuale pubblicato nel 1990 nella rivista Nova Thalassia 11 intitolato “Metodi nell’ecologia del plancton marino” ed è stato curato dal direttivo del comitato plancton della SIBM in carica dal 2007 al 2009. Lo scopo principale del volume è quello di confermare le metodologie ancora valide già proposte nel volume citato e di aggiornare le nuove tecnologie applicate nella moderna oceanografia biologica dedicata all’ambiente di mare aperto ed all’ambiente costiero. Il volume è rivolto alle istituzioni italiane di ricerca che studiano le problematiche legate all’ecologia del plancton marino, ma anche agli enti locali che per legge devono svolgere attività di monitoraggio.
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Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
FIGURE 4 in MIDTAL (Microarrays for the Detection of Toxic Algae)
No full textFIGURE 4: Average RNA amounts (pg/cell) over a three-day period for three different strains of Prymnesium parvum N. Carter (1937: 40) cultures grown under three levels of four environmental stressors: light (top left), nutrients (top right), salinity (bottom left) and temperature (bottom right). In each treatment, the optimal value for the growth of P. parvum is shown in red and the stress conditions tested are in blue and green.Published as part of Medlin, Linda K., Montresor, Marina, Graneli, Edna, Reugera, Beatrix, Raine, Robin, Edvardsen, Bente, Lewis, Jane, Elliott, Chris, Pazos, Yolanda & Maranda, Lucie, 2013, MIDTAL (Microarrays for the Detection of Toxic Algae), pp. 201-210 in Phytotaxa 127 (1) on page 207, DOI: 10.11646/phytotaxa.127.1.19, http://zenodo.org/record/508541
Specificity of Lipoxygenase Pathways Supports Species Delineation in the Marine Diatom Genus Pseudo-nitzschia
No full textOxylipins are low-molecular weight secondary metabolites derived from the incorporation of oxygen into the carbon chains of polyunsaturated fatty acids (PUFAs). Oxylipins are produced in many prokaryotic and eukaryotic lineages where they are involved in a broad spectrum of actions spanning from stress and defense responses, regulation of growth and development, signaling, and innate immunity. We explored the diversity in oxylipin patterns in the marine planktonic diatom Pseudo-nitzschia. This genus includes several species only distinguishable with the aid of molecular markers. Oxylipin profiles of cultured strains were obtained by reverse phase column on a liquid chromatograph equipped with UV photodiode detector and q-ToF mass spectrometer. Lipoxygenase compounds were mapped on phylogenies of the genus Pseudo-nitzschia inferred from the nuclear encoded hyper-variable region of the LSU rDNA and the plastid encoded rbcL. Results showed that the genus Pseudo-nitzschia exhibits a rich and varied lipoxygenase metabolism of eicosapentaenoic acid (EPA), with a high level of specificity for oxylipin markers that generally corroborated the genotypic delineation, even among genetically closely related cryptic species. These results suggest that oxylipin profiles constitute additional identification tools for Pseudo-nitzschia species providing a functional support to species delineation obtained with molecular markers and morphological traits. The exploration of the diversity, patterns and plasticity of oxylipin production across diatom species and genera will also provide insights on the ecological functions of these secondary metabolites and on the selective pressures driving their diversification
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