scholarly journals Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season Through Complex Regulation of mRNA and Small RNA Transcriptomes

2021 ◽  
Vol 22 (7) ◽  
pp. 3531
Author(s):  
Marina Dermastia ◽  
Blaž Škrlj ◽  
Rebeka Strah ◽  
Barbara Anžič ◽  
Špela Tomaž ◽  
...  
Keyword(s):  
Small Rnas ◽  
Interaction Network ◽  
Growing Season ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Bois Noir ◽  
Growing Seasons ◽  
New Genes ◽  
Causal Pathogen

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.

Kaolin impacts on hormonal balance, polyphenolic composition and oenological parameters in red grapevine berries during ripening

2021 ◽  
pp. 1-15
Author(s):  
Sara Bernardo ◽  
Lia-Tânia Dinis ◽  
Nelson Machado ◽  
Ana Barros ◽  
Marta Pitarch-Bielsa ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Growing Season ◽  
Growing Seasons ◽  
Polyphenolic Composition ◽  
Berry Ripening ◽  
Hormonal Balance ◽  
Summer Stress ◽  
Fruit Damage ◽  
Stress Signals

BACKGROUND: Kaolin particle-film application is a well-known strategy to avoid fruit damage. However, its putative role in balancing berry ripening under a changing climate remains poorly explored. OBJECTIVE: We assessed kaolin treatment effect on several ripening berry components, hormonal balance and oenological parameters of the field-grown Touriga-Franca (TF) and Touriga–Nacional (TN) grapevine varieties at veraison (EL35) and ripening (EL38) during two growing seasons (2017 and 2018). RESULTS: Under the adverse summer conditions (two heatwave events) of 2017, kaolin application increased 211.2 %and 51.4 %the salicylic acid (SA) and abscisic acid (ABA) levels in TF berries at EL38, while no significant differences were observed in TN. Conversely, TF, and TN kaolin treated berries showed lower SA and ABA accumulation in 2018, respectively. Tartaric acid content increased about 17.2 %, and 24.2 %in TF and TN treated berries at stage EL35 in the 2017 growing season. Though kaolin treatment had no consistent effect on anthocyanins accumulation, flavonoids, ortho-diphenols and tannins increased in kaolin treated grapevines in 2017. CONCLUSIONS: This study highlights the key role of climate in triggering ripening related processes and fruit quality potential. Nevertheless, kaolin treated grapevines displayed an improved response to oxidative stress signals by increasing secondary metabolites accumulation in warm vintages. Kaolin application promoted different varietal responses, with a possible ripening delaying effect in TF, reinforcing its efficiency in alleviating severe summer stress impacts.

scholarly journals Epiphytic Microbiome of Grapes Berries Varies Between Phenological Timepoints, Growing Seasons and Regions

2019 ◽  
Author(s):  
Megan E. Hall ◽  
Isabelle O’Bryon ◽  
Wayne F. Wilcox ◽  
Michael V. Osier ◽  
Lance Cadle-Davidson
Keyword(s):  
New York ◽  
Growing Season ◽  
Phenological Stage ◽  
Phenological Stages ◽  
Growing Seasons ◽  
Single Region ◽  
Finger Lakes ◽  
Primary Focus ◽  
One Year

AbstractExtensive research into the microbial ecology of grapes near harvest, with a primary focus on yeasts, has improved our understanding of some components of variation that influence grapevine terroir. Metagenomic tools enable a broader exploration of the plant microbiome and components of variability due to such factors as year, location, management, and phenological stage. In 2014, to characterize the microbial changes of the grape surface over the course of the growing season in the Finger Lakes region of New York, we examined the epiphytic microbiome of grapes at five key phenological stages: pea-sized, bunch closure, Veraison, 15 Brix and harvest. This experiment was repeated in two subsequent years in the Finger Lakes, New York in 2015, and in Tasmania, Australia in 2016, to examine variability of regional terroir. We found significant shifts in taxa presence and relative taxa abundance between phenological timepoints, and determined that the epiphytic microbiome differed significantly not just between regions but also within a single region from one year to the next. These findings call into question the role of the phytobiome in the expression of terroir, as the phytobiome is dynamically responding to its environment, within and between years and locations. On the berry surface in particular, these dynamics are complicated by weather and management. Understanding that the grape surface microbiome is consistently changing may influence how we manage the berry epiphytic microbiome, potentially affecting disease management and vinification decisions.

scholarly journals The functional role of microRNAs in laryngeal carcinoma

2017 ◽  
Vol 12 (1) ◽  
pp. 460-464
Author(s):  
Jinzhang Cheng ◽  
Junjun Chen ◽  
Zonggui Wang ◽  
Dan Yu ◽  
Yuanzhang Zu
Keyword(s):  
Laryngeal Cancer ◽  
Cancer Diagnosis ◽  
Small Rnas ◽  
Tumor Suppressor Genes ◽  
Functional Role ◽  
Recent Progress ◽  
Transcriptional Level ◽  
Diagnosis And Prognosis ◽  
Potential Use

AbstractMicroRNAs are a class of non-coding, small RNAs, which modulate gene expression at the post-transcriptional level. Numerous studies have showed microRNAs are involved in the pathogenesis of laryngeal cancer through regulating tumor-related genes such as oncogenes or tumor suppressor genes. In this review, we summarize recent progress on the function of microRNAs in laryngeal cancer. We focus on potential use of microRNAs in laryngeal cancer diagnosis and prognosis.

scholarly journals Neutrophil Involvement in Covid-19

2020 ◽  
Author(s):  
Athanasios Didangelos
Keyword(s):  
Interaction Network ◽  
Lavage Fluid ◽  
Lung Epithelial Cells ◽  
Organ Injury ◽  
Rna Seq ◽  
Protein Protein Interaction ◽  
Associated Proteins ◽  
Infected Cells ◽  
Neutrophil Response

Covid-19 is often related to hyperinflammation that drives lung or multi-organ injury. The immunopathological mechanisms that cause excessive inflammation following SARS-Cov-2 infection are under investigation while different approaches to limit hyperinflammation in affected patients are being proposed. Here, a computational protein-protein interaction network approach was used on recently available data to identify possible Covid-19 inflammatory mechanisms and bioactive genes. First, network analysis of putative SARS-Cov-2 cellular receptors and their directly associated proteins, led to the mining of a robust neutrophil response signature and multiple relevant inflammatory genes. Second, analysis of RNA-seq datasets of lung epithelial cells infected with SARS-Cov-2 revealed that infected cells specifically expressed neutrophil-attracting chemokines, further supporting the likely role of neutrophils in Covid-19 inflammation. Third, analysis of RNA-seq datasets of bronchoalveolar lavage fluid from Covid-19 patients, identified neutrophil-specific genes and chemokines. Different immunoregulatory and neutrophil-relevant molecules mined here such as, TNFR, IL8, CXCR1, CXCR2, ADAM10, GPR84, MME-neprilysin, ANPEP and LAP3 are druggable and might be therapeutic targets in efforts to limit SARS-Cov-2 inflammation in severe clinical cases. The role of neutrophils in Covid-19 needs to be studied further.

scholarly journals Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

2022 ◽  
Author(s):  
Elliott Chapman ◽  
Francesca Taglini ◽  
Elizabeth H Bayne
Keyword(s):  
Transposable Elements ◽  
Fission Yeast ◽  
Transcriptional Repression ◽  
Small Rnas ◽  
Transcriptional Silencing ◽  
Transcriptional Level ◽  
Genome Maintenance ◽  
Repeat Sequences ◽  
Heterochromatin Assembly

RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhanching RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.

scholarly journals Germline silencing of UASt depends on the piRNA pathway

2018 ◽  
Author(s):  
Yi-Chun Huang ◽  
Henry Moreno ◽  
Sarayu Row ◽  
Dongyu Jia ◽  
Wu-Min Deng
Keyword(s):  
Binary System ◽  
Small Rnas ◽  
Transgene Expression ◽  
Rna Seq ◽  
Somatic Tissues ◽  
Germline Expression ◽  
Germline Cells ◽  
Pirna Pathway ◽  
Nonsense Mediated Rna Decay

AbstractOne of the most extensively used techniques in Drosophila is the Gal4/UAS binary system, which allows tissue-specific misexpression or knockdown of specific genes of interest. The original UAS vector, UASt, can only be activated for transgene expression in somatic tissues and not in the germline cells. Rørth (1998) generated UASp, a modified UAS vector that is responsive to Gal4 in both somatic and germline tissues, by replacing both the hsp70 promoter and the SV40 3’UTR with the P transposase promoter and the K10 3’UTR respectively. At present, the mechanisms by which UASt is silenced in germline cells are not fully understood. Here, we report that the piRNA pathway is involved in suppressing UASt expression in ovarian germline cells. Individually knocking down or mutating components of the piRNA biogenesis pathway (e.g., Piwi, AGO3, Aub, Spn-E, and Vasa) resulted in the expression of the UASt-reporter (GFP or RFP) in the germline. An RNA-seq analysis of small RNAs revealed that the hsp70 promoter of UASt is targeted by piRNAs, and in the aub mutant ovary, the amount of piRNAs targeting the hsp70 promoter is reduced by around 40 folds. In contrast, the SV40 3’UTR of the UASt, which happens to be targeted by the Nonsense-mediated RNA decay (NMD) pathway, is not responsible for germline UASt suppression, as UASt-reporters with NMD-insensitive 3’UTRs fail to show germline expression. Taken together, our studies reveal a crucial role of the piRNA pathway, potentially via the suppression of the hsp70 promoter, in germline UASt silencing in Drosophila ovaries.

scholarly journals The long noncoding RNA MALAT1 modulates adipose loss in cancer-associated cachexia by suppressing adipogenesis through PPAR-γ

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jun Han ◽  
Lei Shen ◽  
Zheng Zhan ◽  
Yuguo Liu ◽  
Chang Zhang ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Reporter Gene ◽  
Noncoding Rna ◽  
Early Stage ◽  
Interaction Network ◽  
Reporter Gene Assay ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Ppar Γ ◽  
Gene Assay

Abstract Background Cancer-associated cachexia is a multifactorial syndrome defined by progressive weight loss with ongoing loss of adipose tissue and skeletal muscle. Adipose loss occurs in the early stage of cachexia and is associated with reduced quality of life and survival time. Although numerous lncRNAs are regarded as novel regulators in adipose metabolism, the role of lncRNAs that selectively modulate the development of adipose loss in cachexia remains limited. Methods In this study, we analyzed microarray data of lncRNAs in adipose loss and further explored the function and mechanism of MALAT1 in adipose loss. First, we explored the expression and function of MALAT1 in adipose cell by quantitative PCR and RNA knockdown. Subsequently, the mechanism of MALAT1 involvement in adipose loss was analyzed via RNA-seq, bioinformatics analysis and reporter gene assay. Finally, we explored the clinical significance of MALAT1 through correlation analysis. Results Cellular experiments revealed that knocking down MALAT1 significantly inhibited the process of adipogenesis. RNA-seq data showed that numerous adipogenic genes were downregulated upon MALAT1 knockdown. A protein–protein interaction network analysis identified PPAR-γ as the central node transcription factor, the inhibition of which explains the downregulation of numerous adipogenic genes. A reporter gene assay suggested that MALAT1 can regulate the gene expression of PPAR-γ at the transcriptional level. Moreover, MALAT1 was weakly expressed in the subcutaneous white adipose tissue of cancer-associated cachexia patients and was related to low fat mass index and poor prognosis in cancer patients. Conclusions This study indicated that MALAT1 is associated with adipose loss in cancer-associated cachexia by regulating adipogenesis through PPAR-γ, which may potentially be a novel target for the diagnosis and treatment of cancer-associated cachexia in the clinic.

scholarly journals Connecting small RNAs and Aging

2015 ◽  
Author(s):  
Joshua Elkington
Keyword(s):  
Cross Talk ◽  
Systems Analysis ◽  
Small Rnas ◽  
Prediction Tools ◽  
New Genes ◽  
Wide Range ◽  
Range Of Functions

Small RNAs have a wide range of functions and recent studies have found connections between these molecules and aging pathways. However, the process to systematically characterize this relationship is slow. Prediction tools can be used to expedite this process by finding new genes and pathways that cross talk with each other. Using phylogenetic and systems analysis, connections between small RNAs and aging were proven and new genes that may be related to aging were identified. This type of analysis can be applied to many different pathways in order to fully characterize the role of small RNAs.

scholarly journals Growth Responses of Boreal Scots Pine, Norway Spruce and Silver Birch Seedlings to Simulated Climate Warming over Three Growing Seasons in a Controlled Field Experiment

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 943
Author(s):  
Katri Nissinen ◽  
Virpi Virjamo ◽  
Antti Kilpeläinen ◽  
Veli-Pekka Ikonen ◽  
Laura Pikkarainen ◽  
...  
Keyword(s):  
Norway Spruce ◽  
Scots Pine ◽  
Root Biomass ◽  
Growing Season ◽  
Silver Birch ◽  
Shoot Biomass ◽  
Growth Responses ◽  
Growing Seasons ◽  
Simulated Climate ◽  
Shoot And Root Biomass

We studied the growth responses of boreal Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies L. Karst.) and silver birch (Betula pendula Roth) seedlings to simulated climate warming of an average of 1.3 °C over the growing season in a controlled field experiment in central Finland. We had six replicate plots for elevated and ambient temperature for each tree species. The warming treatment lasted for the conifers for three growing seasons and for the birch two growing seasons. We measured the height and diameter growth of all the seedlings weekly during the growing season. The shoot and root biomass and their ratios were measured annually in one-third of seedlings harvested from each plot in autumn. After two growing seasons, the height, diameter and shoot biomass were 45%, 19% and 41% larger in silver birch seedlings under the warming treatment, but the root biomass was clearly less affected. After three growing seasons, the height, diameter, shoot and root biomass were under a warming treatment 39, 47, 189 and 113% greater in Scots pine, but the root:shoot ratio 29% lower, respectively. The corresponding responses of Norway spruce to warming were clearly smaller (e.g., shoot biomass 46% higher under a warming treatment). As a comparison, the relative response of height growth in silver birch was after two growing seasons equal to that measured in Scots pine after three growing seasons. Based on our findings, especially silver birch seedlings, but also Scots pine seedlings benefitted from warming, which should be taken into account in forest regeneration in the future.

scholarly journals Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 315
Author(s):  
Hailin Liu ◽  
Xin Han ◽  
Jue Ruan ◽  
Lian Xu ◽  
Bing He
Keyword(s):  
Ginkgo Biloba ◽  
Leaf Development ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Rna Seq ◽  
Final Size ◽  
Dioecious Species ◽  
Related Factors ◽  
New Genes ◽  
Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

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