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Oxylipin Diversity in the Diatom Family Leptocylindraceae Reveals DHA Derivatives in Marine Diatoms
No full textMarine planktonic organisms, such as diatoms, are prospective sources of novel bioactive metabolites. Oxygenated derivatives of fatty acids, generally referred to as oxylipins, in diatoms comprise a highly diverse and complex family of secondary metabolites. These molecules have recently been implicated in several biological processes including intra- and inter-cellular signaling as well as in defense against biotic stressors and grazers. Here, we analyze the production and diversity of C-20 and C-22 non-volatile oxylipins in five species of the family Leptocylindraceae, which constitute a basal clade in the diatom phylogeny. We report the presence of species-specific lipoxygenase activity and oxylipin patterns, providing the first demonstration of enzymatic production of docosahexaenoic acid derivatives in marine diatoms. The differences observed in lipoxygenase pathways among the species investigated broadly reflected the relationships observed with phylogenetic markers, thus providing functional support to the taxonomic diversity of the individual species
Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus
Get PDFBackground: Flagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce. Results: In the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world's seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes. Conclusion: Our analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment
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
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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Genetic, physiological and ecological diversity of the diatom genus <i>Leptocylindrus</i>
Get PDFDiatoms are among the most productive photoautotrophic organisms on Earth. Within the diatom genus Leptocylindrus, two species, L. danicus and L. minimus, are reported as abundant in coastal waters worldwide and in the Gulf of Naples (GoN). This thesis aimed at a closer characterisation of Leptocylindrus species through different approaches, including the study of their morphology, molecular phylogeny, metagenomics and biochemistry. Eighty-three strains from the GoN and one strain (CCMP 1856) from the Atlantic US coast were analysed. Based on the morphological, molecular and life cycle differences, the taxonomy of the genus was revised. The GoN species previously identified as L. minimus was in fact identified as L. belgicus Meunier and was placed in a new genus, Tenuicylindrus Nanjappa and Zingone which, along with Leptocylindrus Cleve, belongs to the family Leptocylindraceae. Five species in all were included in the genus Leptocylindrus: L. danicus Cleve and L. minimus Gran, two novel species L. hargravesii and L. convexus, and L. aporus (Hargraves) Nanjappa & Zingone, which was raised from the variety to the species status. The real Leptocylindrus minimus was not found in the GoN. To address the distribution of the 6 species outside the GoN, two metagenomic databases, BioMarKs (Europe) and Tara Oceans (worldwide) were explored. Sequences of L. aporus, L. convexus and L. danicus were recovered at many sites in European waters and across the world's seas, while those of L. minimus were retrieved only in the Oslo fjord and those of T. belgicus were only found in the GoN and Oslo fjord. Additional diversity was observed in the Tara Oceans dataset but, in lack of morphological information, whether this diversity is real remains to be clarified. All species except L. minimus were also categorised based on the diversity in their oxylipins pathways. Leptocylindrus danicus and L. hargravesii shared common lipoxygenase pathways, different from the ones shared by the species L. aporus and L. convexus. Tenuicylindrus belgicus exhibits a pathway distinct from that of Leptocylindrus species. Species-specific compounds produced in minor quantities were also observed. Physiological experiments show that L. aporus can withstand higher (26 "C) temperature but not lower (12 CC) temperature, while L. danicus can withstand low temperature but not high temperature. This corresponds to the species occurrence in the natural environment, where L. aporus blooms during summer and L. danicus is found in all seasons except summer. Altogether, through an interdisciplinary approach, the studies described in this thesis provide substantial information that may have important implications in the field of ecology, evolution, conservation biology and biotechnology
Genetic, physiological and ecological diversity of the diatom genus Leptocylindrus
No full textDiatoms are among the most productive photoautotrophic organisms on Earth. Within the diatom genus Leptocylindrus, two species, L. danicus and L. minimus, are reported as abundant in coastal waters worldwide and in the Gulf of Naples (GoN). This thesis aimed at a closer characterisation of Leptocylindrus species through different approaches, including the study of their morphology, molecular phylogeny, metagenomics and biochemistry. Eighty-three strains from the GoN and one strain (CCMP 1856) from the Atlantic US coast were analysed. Based on the morphological, molecular and life cycle differences, the taxonomy of the genus was revised. The GoN species previously identified as L. minimus was in fact identified as L. belgicus Meunier and was placed in a new genus, Tenuicylindrus Nanjappa and Zingone which, along with Leptocylindrus Cleve, belongs to the family Leptocylindraceae. Five species in all were included in the genus Leptocylindrus: L. danicus Cleve and L. minimus Gran, two novel species L. hargravesii and L. convexus, and L. aporus (Hargraves) Nanjappa & Zingone, which was raised from the variety to the species status. The real Leptocylindrus minimus was not found in the GoN. To address the distribution of the 6 species outside the GoN, two metagenomic databases, BioMarKs (Europe) and Tara Oceans (worldwide) were explored. Sequences of L. aporus, L. convexus and L. danicus were recovered at many sites in European waters and across the world's seas, while those of L. minimus were retrieved only in the Oslo fjord and those of T. belgicus were only found in the GoN and Oslo fjord. Additional diversity was observed in the Tara Oceans dataset but, in lack of morphological information, whether this diversity is real remains to be clarified. All species except L. minimus were also categorised based on the diversity in their oxylipins pathways. Leptocylindrus danicus and L. hargravesii shared common lipoxygenase pathways, different from the ones shared by the species L. aporus and L. convexus. Tenuicylindrus belgicus exhibits a pathway distinct from that of Leptocylindrus species. Species-specific compounds produced in minor quantities were also observed. Physiological experiments show that L. aporus can withstand higher (26 "C) temperature but not lower (12 CC) temperature, while L. danicus can withstand low temperature but not high temperature. This corresponds to the species occurrence in the natural environment, where L. aporus blooms during summer and L. danicus is found in all seasons except summer. Altogether, through an interdisciplinary approach, the studies described in this thesis provide substantial information that may have important implications in the field of ecology, evolution, conservation biology and biotechnology.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
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