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Transcriptional and posttranscriptional regulatory networks controlling leaf cell differentiation during drought stress in Brachypodium distachyon
No full textLED streetlamps alter tree architecture, downregulate the photosynthetic process and alter the sugar metabolism of Populus alba L
No full textThe escalating issue of light pollution in urban environments poses multifaceted challenges, affecting not only the nocturnal sky but also exerting intricate influences on plant physiology. This study delves into the physiological responses of an urban ornamental tree, Populus alba L. clone DI-1, to varying intensities of streetlamp LED night lighting (NL), a shift from traditional High-Pressure Sodium lamps. The investigation "sheds light " on the molecular pathways underlying observed physiological regulations, aiming to offer a comprehensive understanding of the manifold effects of NL on this tree species. NL altered tree architecture, i.e. increased branch length and diameters, underscoring the dynamic response of trees to nocturnal artificial lighting conditions. Regarding tree physiology, the NL-triggered net CO 2 assimilation (P n ) during the night resulted in limitations in stomatal conductance during daylight hours. This led to a reduction in P n , particularly during dawn, hindering the quantum yield for the reduction of end acceptors of PSI. Changes in chlorophyll a-to-b proportion and overall concentration, electron transport chain, and gene expression further highlight the intricate interplay between NL and plant metabolic regulation. Notably, the increased gene expression of sugar transporters in both NL trees suggested a responsive shift in sugar and starch metabolism. This was reflected in the absence of a starch accumulation during daylight hours in NL leaves. The study emphasizes the need for a holistic approach to urban lighting, considering its profound impact on photosynthesizing citizens. These findings highlight the pressing need for the development of innovative lighting spectra with reduced impact on plant physio-chemistry while ensuring visibility for citizen safety
Molecular networks controlling leaf cell differentiation during drought stress in Brachypodium distachyon
No full textAn important challenge for today agriculture is to intensify worldwide cereal production in a sustainable manner in order to respond to the increasing food demand.
Food production is limited mainly by biotic and abiotic stress and in particular by drought stress, the most common environmental factor affecting plant growth worldwide. For these reasons, the understanding of the complex molecular mechanisms involved in plant response during drought stresses is crucial for developing improved crop varieties better adapted to limiting environments.
Brachypodium distachyon (Bd), a drought-tolerant wild grass, is an interesting model species to deeply study the molecular mechanisms involved in drought-stress response. With this aim, in this study a reproducible soil assay to subject Bd to drought stress was applied, which resulted in a drastically leaf size reduction. This effect was mainly caused by a reduction in cell expansion instead of a reduction of cell proliferation, underlining the insensitivity of the meristem to drought stress.
Starting from this drastic phenotypic effect, the project, using Next Generation Sequencing (NGS) data provides a description of the molecular networks activated in response to drought, focusing on three different developmental zones (proliferation, expansion, and mature cells) of the third young developing Brachypodium leaf. More specifically, in order to investigate the mechanisms controlling leaf growth reduction during drought, the third emerging leaf was dissected in the three developmental zones and each zone was subjected to whole transcriptome analysis based on NGS. Eighteen libraries were sequenced, i.e. 3 cell types of leaf grown in control and drought condition, considering 3 biological replicates. Bioinformatics tools and statistical analyses were applied to NGS data, showing that distinct leaf cell zones respond differently to drought treatment. Moreover, the integration of mRNA-Seq data with small RNA-Seq data, previously produced by the lab, allowed to investigate the link between microRNAs and their putative target genes
AGO2-RIP-Seq reveals miR-34/miR-449 cluster targetome in sinonasal cancers
No full textSinonasal tumours are heterogeneous malignancies, presenting different histological features and clinical behaviour. Many studies emphasize the role of specific miRNA in the development and progression of cancer, and their expression profiles could be used as prognostic biomarkers to predict the survival. Recently, using the next-generation sequencing (NGS)-based miRNome analysis the miR-34/miR-449 cluster was identified as miRNA superfamily involved in the pathogenesis of sinonasal cancers (SNCs). In the present study, we established an Argonaute-2 (AGO2): mRNA immunoprecipitation followed by high-throughput sequencing to analyse the regulatory role of miR-34/miR-449 in SNCs. Using this approach, we identified direct target genes (targetome), which were involved in regulation of RNA-DNA metabolic, transcript and epigenetic processes. In particular, the STK3, C9orf78 and STRN3 genes were the direct targets of both miR-34c and miR-449a, and their regulation are predictive of tumour progression. This study provides the first evidence that miR-34/miR-449 and their targets are deregulated in SNCs and could be proposed as valuable prognostic biomarkers
A Possible Cause for the Differential Expression of a Subset of miRNAs in Mesenchymal Stem Cells Derived from Myometrium and Leiomyoma
Get PDFThe aetiology of leiomyoma is debated; however, dysregulated progenitor cells or miRNAs appear to be involved. Previous profiling analysis of miRNA in healthy myometrium- (M-MSCs) and leiomyoma- (L-MSCs) derived mesenchymal stem cells (MSCs) identified 15 miRNAs differentially expressed between M-MSCs and L-MSCs. Here, we try to elucidate whether these differentially regulated 15 miRNAs arise as a conversion of M-MSCs along the differentiation process or whether they may originate from divergent cell commitment. To trace the origin of the dysregulation, a comparison was made of the expression of miRNAs previously identified as differentially regulated in M-MSCs and L-MSCs with that detected in MSCs from amniotic fluid (considered as a substitute for embryonic cells). The results do not allow for a foregone conclusion: the miRNAs converging to the adherens junction pathway showed a gradual change along the differentiation process, and the miRNAs which coincided with the other three pathways (ECM-receptor interaction, TGFβ and cell cycle) showed a complex, not linear, regulation and, therefore, a trend along the hypothetical differentiation process was not deduced. However, the role of miRNAs appears to be predominant in the onset of leiomyoma and may follow two different mechanisms (early commitment; exacerbation); furthermore, miRNAs can support the observed (epigenetic) predisposition
Brachypodium distachyon long noncoding RNAs: Genome-wide identification and expression analysis
No full textRecent advances in high throughput sequencing technology have revealed a pervasive and complex transcriptional activity of all eukaryotic genomes and have allowed the identification and characterization of several classes of noncoding RNAs (ncRNAs) with key roles in various biological processes. Among ncRNAs, long ncRNAs (lncRNAs) are transcripts typically longer than 200 nucleotides whose members tend to be expressed at low levels, show a lack of phylogenetic conservation and exhibit tissue-specific, cell-specific, or stress-responsive expression profiles. Although a large set of lncRNAs has been identified both in animal and plant systems, the regulatory roles of lncRNAs are only beginning to be recognized and the molecular basis of lncRNA mediated gene regulation remains largely unexplored, particularly in plants. Here, we describe an efficient methodology to identify long noncoding RNAs using next-generation sequencing data
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
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