1,720,963 research outputs found
Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution
Get PDFDNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation
Orchid NAC Transcription Factors: A Focused Analysis of CUPULIFORMIS Genes
Get PDFPlant transcription factors are involved in different developmental pathways. NAC transcription factors (No Apical Meristem, Arabidopsis thaliana Activating Factor, Cup-shaped Cotyledon) act in various processes, e.g., plant organ formation, response to stress, and defense mechanisms. In Antirrhinum majus, the NAC transcription factor CUPULIFORMIS (CUP) plays a role in determining organ boundaries and lip formation, and the CUP homologs of Arabidopsis and Petunia are involved in flower organ formation. Orchidaceae is one of the most species-rich families of angiosperms, known for its extraordinary diversification of flower morphology. We conducted a transcriptome and genome-wide analysis of orchid NACs, focusing on the No Apical Meristem (NAM) subfamily and CUP genes. To check whether the CUP homologs could be involved in the perianth formation of orchids, we performed an expression analysis on the flower organs of the orchid Phalaenopsis aphrodite at different developmental stages. The expression patterns of the CUP genes of P. aphrodite suggest their possible role in flower development and symmetry establishment.
In addition, as observed in other species, the orchid CUP1 and CUP2 genes seem to be regulated by the microRNA, miR164. Our results represent a preliminary study of NAC transcription factors in orchids to understand the role of these genes during orchid flower formation
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
Comparative genomics and transcriptomics to identify key regulators of orchid flower symmetry and organ identity
Get PDFThe Orchidaceae are a monocot angiosperm family with an extraordinary diversification of flower architecture and unique ecological characteristics. In addition to the scientific interest, orchids have a considerable economic value, representing the most commercialized ornamental plants. For these reasons, a complete understanding of the complex molecular network that regulates orchid flower development is an interesting challenge.
The class B MADS-box AP3/DEF genes lead to orchid perianth morphogenesis together with other MADS-box genes (AGL6 and SEP-like). This work aims to identify novel candidates that may be part of the genetic program at the base of orchid flower symmetry and organ identity determination.
The in silico differential expression analysis on RNA-seq data of wild-type and peloric Phalaenopsis orchids suggested that the YABBY DROOPING LEAF-like gene PeDL2 could be a novel regulator of the orchid lip specification. In wild-type Phalaenopsis, PeDL2 is differentially expressed in lip and lateral inner tepals, while in the perianth organs of the peloric mutant it is expressed at similar levels. This is the first evidence of the expansion of a DL-like gene expression domain to the perianth, since it is generally involved in reproductive organs and leaf development. The regulatory relationship between DL-like and class B MADS-box genes of other angiosperms, together with the central role of the MADS-box genes in orchid perianth development, supports the hypothesis that DL2 can be involved in the regulatory network underlying the orchid flower development. These premises prompted me to focus my Ph.D. research project on the orchid DL-like genes.
Genomics and transcriptomics revealed that the orchids with zygomorphic flowers have two DL genes, whereas the ancestral orchids with actinomorphic flowers have only one. These observations and the expression pattern of the Phalaenopsis DL genes suggest that the DL paralogs conserved their function in the development of the reproductive organs; however, after a duplication event, the neofunctionalization of the DL2 gene could explain its acquisition of a role in orchid lip development and bilateral symmetry determination.
The PeDL2 expression pattern is similar to that of the AP3/DEF genes belonging to clades 3 and 4 and opposite to that of the AP3/DEF genes belonging to clades 1 and 2, suggesting a possible regulatory link.
To support the hypothesis of the orchid DL2 neofunctionalization, I evaluated the expression of the DL- and DEF-like genes outside the Phalaenopsis genus (Vanilla planifolia, Phragmipedium logifolium, and Rhyncholaeliocattleya). The obtained results led to a reformulation of the initial hypothesis, suggesting that DL2 could have acquired a specific role in lip development only in evolutionarily more recent orchids. In the basal zygomorphic orchids, DL2 is expressed at similar levels in all the perianth organs. Possibly, after gene duplication, DL2 acquired a new function in the perianth specification, and later assumed a specific role in the lip.
To characterize PeDL2, I performed intracellular protein localization experiments, confirming its nuclear localization. In addition, I predicted the DLs structure and interactions by computational approach and confirmed the results by yeast two-hybrid analysis.
Finally, I evaluated the DL2 transcriptional regulation by in silico screening of possible promoter interactors. I validated these results through yeast one-hybrid assay and protoplasts dsRNAi experiments. According to these analyses, DL2 transcription could be modulated by different transcription factors; in particular, the Phalaenopsis clade 1 DEF-like protein MADS2 could repress DL2 expression
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
Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development
Get PDFThe molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene
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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