scholarly journals Comparative Analysis of miRNA Abundance Revealed the Function of Vvi-miR828 in Fruit Coloring in Root Restriction Cultivation Grapevine (Vitis vinifera L.)

2019 ◽  
Vol 20 (16) ◽  
pp. 4058 ◽  
Author(s):  
Qiuju Chen ◽  
Bohan Deng ◽  
Jie Gao ◽  
Zhongyang Zhao ◽  
Zili Chen ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Small Rna ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Vitis Vinifera L ◽  
Anthocyanin Content ◽  
Early Maturation ◽  
Root Restriction

Root restriction cultivation leads to early maturation and quality improvement, especially in the anthocyanin content in grapevine. However, the molecular mechanisms that underlie these changes have not been thoroughly elucidated. In this study, four small RNA libraries were constructed, which included the green soft stage (GS) and ripe stage (RS) of ‘Muscat’ (Vitis vinifera L.) grape berries that were grown under root restriction (RR) and in traditional cultivation (no root restriction, CK). A total of 162 known miRNAs and 14 putative novel miRNAs were detected from the four small RNA libraries by high-throughput sequencing. An analysis of differentially expressed miRNAs (DEMs) revealed that 13 miRNAs exhibited significant differences in expression between RR and CK at the GS and RS stages, respectively. For different developmental stages of fruit, 23 and 34 miRNAs showed expression differences between the GS and RS stages in RR and CK, respectively. The expression patterns of the eight DEMs and their targets were verified by qRT-PCR, and the expression profiles of target genes were confirmed to be complementary to the corresponding miRNAs in RR and CK. The function of Vvi-miR828, which showed the down regulated expression in the RS stage under root restriction, was identified by gene transformation in Arabidopsis. The anthocyanin content significantly decreased in transgenic lines, which indicates the regulatory capacity of Vvi-miR828 in fruit coloration. The miRNA expression pattern comparison between RR and CK might provide a means of unraveling the miRNA-mediated molecular process regulating grape berry development under root restricted cultivation.

scholarly journals Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2754
Author(s):  
Liuhui Kuang ◽  
Jiahua Yu ◽  
Qiufang Shen ◽  
Liangbo Fu ◽  
Liyuan Wu
Keyword(s):  
Genetic Diversity ◽  
Gene Ontology ◽  
Salt Stress ◽  
Small Rna ◽  
Abiotic Stresses ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Barley Cultivar ◽  
Golden Promise

Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley.

scholarly journals INFLUENCE OF IRRIGATION STRATEGIES ON THE PHYSICOCHEMICAL PROPERTIES OF ‘SYRAH’ WINE PRODUCED IN SÃO FRANCISCO VALLEY

Irriga ◽  
2018 ◽  
Vol 23 (4) ◽  
pp. 818-834 ◽  
Author(s):  
Vanessa De Souza Oliveira ◽  
Giuliano Elias Pereira ◽  
Augusto Miguel Nascimento Lima ◽  
Alessandra Monteiro Salviano ◽  
Russaika Lirio Nascimento ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Vitis Vinifera ◽  
Deficit Irrigation ◽  
Vitis Vinifera L ◽  
Anthocyanin Content ◽  
Regulated Deficit Irrigation ◽  
Total Anthocyanin ◽  
Volatile Acidity ◽  
Total Anthocyanin Content ◽  
Caixa Postal

INFLUENCE OF IRRIGATION STRATEGIES ON THE PHYSICOCHEMICAL PROPERTIES OF ‘SYRAH’ WINE PRODUCED IN SÃO FRANCISCO VALLEY     VANESSA DE SOUZA OLIVEIRA1; GIULIANO ELIAS PEREIRA2; AUGUSTO MIGUEL NASCIMENTO LIMA1; ALESSANDRA MONTEIRO SALVIANO3; RUSSAIKA LÍRIO NASCIMENTO1 E LUÍS HENRIQUE BASSOI4   1Univasf, Colegiado de Engenharia e Ambienta, Avenida Antonio Carlos Magalhães, 510, 48902-300, Juazeiro - BA, Brasil. [email protected], [email protected], [email protected] 2Embrapa Uva e Vinho, Rua Livramento, 515, Caixa Postal 130, 95701-008, Bento Gonçalves - RS, Brasil. [email protected] 3Embrapa Semiárido, BR 428 km 152, Caixa Postal 23, 56302-970, Petrolina - PE, Brasil. [email protected] 4Embrapa Instrumentação, Rua XV de Novembro, 1452, Caixa Postal 741, 13560-970, São Carlos - SP, Brasil. [email protected]     1 ABSTRACT   Deficit irrigation is used to control grapevine vegetative vigor and the grape composition can be influenced by soil water content. The minerals contained in the grapes are responsible for the physicochemical properties and stability of the wine. Therefore, the aim of this work was to evaluate the effects of irrigation strategies on the properties of ‘Syrah’ wines produced in São Francisco Valley, Brazil. The irrigation treatments used were FI (full irrigation), RDI (regulated deficit irrigation), and DI (deficit irrigation). Winemaking was performed by traditional methods, followed by stabilization and bottling. Density, alcohol content, pH, total and volatile acidity, total and free sulfur dioxide, total polyphenols index, color intensity, and total anthocyanin content were determined, as well as the contents of Ca, Mg, P, K, Na, Mn, Fe, Cu, Zn, Cd, Cr, Ni, and Pb. The properties of wines were influenced by irrigation strategies, except for the content of total anthocyanin, Mg, P, Na, Cu, and Mn. The contents of Cd, Cr, Fe, and Zn were similar in the vines. The wines demonstrated varied properties with different typicalities. Irrigation strategies can be recommended for different products, FI for young and cheap, and DI and RDI for aged and more expensive wines.   Keywords: Vitis vinifera L., grape, water availability, tropical wine.     OLIVEIRA, V. DE S.; PEREIRA, G. E.; LIMA, A. M. N.; SALVIANO, A. M.; NASCIMENTO, R. L. E BASSOI, L. H. INFLUÊNCIA DE ESTRATÉGIAS DE IRRIGAÇÃO NAS PROPRIEDADES FÍSICO-QUÍMICAS DO VINHO ‘SYRAH’ PRODUZIDO NO VALE DO SÃO FRANCISCO           2 RESUMO   A irrigação com déficit é utilizada para controlar o vigor vegetativo da videira, e a composição da uva pode ser influenciada pela umidade do solo. Os minerais presentes nas uvas são responsáveis pelas propriedades físico-químicas e pela estabilidade do vinho. Portanto, o objetivo deste trabalho foi avaliar os efeitos de estratégias de irrigação sobre as propriedades do vinho ‘Syrah’ produzido no Vale do São Francisco, Brasil. As estratégias de irrigação utilizadas foram IP (irrigação plena), IDC (irrigação com déficit controlado) e ID (irrigação com déficit). A elaboração de vinhos foi realizada por métodos tradicionais, seguido de estabilização e engarrafamento. A densidade, teor de álcool, pH, acidez total e volátil, dióxido de total e livre de enxofre, o índice total de polifenóis, a intensidade da cor, conteúdo total de antocianina e concentrações de Ca, Mg, P, K, Na, Mn, Fe, Cu e Zn, Cd, Cr, Ni e Pb foram determinadas. As propriedades dos vinhos foram influenciadas pelas estratégias de irrigação, exceto os teores totais de antocianinas, e de Mg, P, Na, Cu e Mn. Os níveis de Cd, Cr, Fe e Zn foram semelhantes nos vinhos. Os vinhos demonstraram propriedades variadas com diferentes tipicidades. As estratégias de irrigação podem ser recomendadas para a obtenção de diferentes produtos, sendo a IP para vinhos jovens e baratos, e o ID e IDC para vinhos envelhecidos e mais caros.   Palavras chave: Vitis vinifera L., uva, disponibilidade de água, vinho tropical.

scholarly journals Insecticide Exposure Triggers a Modulated Expression of ABC Transporter Genes in Larvae of Anopheles gambiae s.s.

Insects ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 66 ◽  
Author(s):  
Valentina Mastrantonio ◽  
Marco Ferrari ◽  
Agata Negri ◽  
Tommaso Sturmo ◽  
Guido Favia ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Abc Transporter ◽  
Abc Transporters ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Larval Mortality ◽  
Expression Patterns ◽  
Main Tool ◽  
Gene Expression Response ◽  
Abc Transporter Genes

Insecticides remain a main tool for the control of arthropod vectors. The urgency to prevent the insurgence of insecticide resistance and the perspective to find new target sites, for the development of novel molecules, are fuelling the study of the molecular mechanisms involved in insect defence against xenobiotic compounds. In this study, we have investigated if ATP-binding cassette (ABC) transporters, a major component of the defensome machinery, are involved in defence against the insecticide permethrin, in susceptible larvae of the malaria vector Anopheles gambiae sensu stricto. Bioassays were performed with permethrin alone, or in combination with an ABC transporter inhibitor. Then we have investigated the expression profiles of five ABC transporter genes at different time points following permethrin exposure, to assess their expression patterns across time. The inhibition of ABC transporters increased the larval mortality by about 15-fold. Likewise, three genes were up-regulated after exposure to permethrin, showing different patterns of expression across the 48 h. Our results provide the first evidences of ABC transporters involvement in defence against a toxic in larvae of An. gambiae s.s. and show that the gene expression response is modulated across time, being continuous, but stronger at the earliest and latest times after exposure.

scholarly journals Differential Expression of Maize and Teosinte microRNAs under Submergence, Drought, and Alternated Stress

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1367
Author(s):  
Edgar Baldemar Sepúlveda-García ◽  
José Francisco Pulido-Barajas ◽  
Ariana Arlene Huerta-Heredia ◽  
Julián Mario Peña-Castro ◽  
Renyi Liu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Zea Mays ◽  
High Throughput ◽  
Small Rna ◽  
Abiotic Stresses ◽  
Crop Production ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Evolutionary Divergence ◽  
Rna Profiling

Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.

"Terroir" effect, as a result of enviromental stess, depends more on soil depth than on soil type (Vitis vinifera L. cv. Grenache Noir, Côtes du Rhône, France, 2000)

OENO One ◽  
2006 ◽  
Vol 40 (4) ◽  
pp. 177 ◽  
Author(s):  
Jacques Coipel ◽  
Begoña Rodriguez Lovelle ◽  
Catherine Sipp ◽  
Cornelis Van Leeuwen
Keyword(s):  
Vitis Vinifera ◽  
Soil Type ◽  
Soil Depth ◽  
Soil Types ◽  
Vitis Vinifera L ◽  
Anthocyanin Content ◽  
Nitrogen Status ◽  
Grape Quality ◽  
Shallow Soils ◽  
Berry Composition

<p style="text-align: justify;">Among other elements of the natural environment, soil greatly influences vine behaviour and berry composition. Its influence is complex, because soil affects vine water and mineral uptake, as well as temperature in the root zone. In this research, investigations were undertaken to assess whether vine development and grape quality potentiel could be linked to specific soil types. 15 dry farmed plots planted with Vitis vinifera L. cv. Grenache noir were studied in 2000 on five soil types of the Southern Côtes du Rhône (France). No clear relationship could be established between soil type, vine growth, yield and berry composition. However, vine water and nitrogen status were related to soil depth. On shallow soils, vine water and nitrogen status were low, which resulted in early shoot growth cessation and moderate yield, as well as high berry sugar and anthocyanin content. Severe water stress is known for affecting negatively berry ripening. Nevertheless, although this study was carried out under dry, Mediterranean conditions, the grapes with the highest potential for making quality red wines were obtained on the soils with the lowest water holding capacity.</p>

Circulating melanoma cells isolated from clinical blood samples and characterized by full-length mRNA sequencing at single-cell level.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10539-10539 ◽  
Author(s):  
Yu-Chieh Wang ◽  
Daniel Ramskold ◽  
Shujun Luo ◽  
Robin Li ◽  
Qiaolin Deng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Melanoma Cells ◽  
Clinical Samples ◽  
Single Cell Level ◽  
Cell Level ◽  
Blood Samples

10539 Background: Melanoma is the most aggressive type of skin cancer. Late-stage melanoma is highly metastatic and currently lacks effective treatment. This discouraging clinical observation highlights the need for a better understanding of the molecular mechanisms underlying melanoma initiation and progression and for developing new therapeutic approaches based on novel targets. Although genome-wide transcriptome analyses have been frequently used to study molecular alterations in clinical samples, it has been technically challenging to obtain the transcriptomic profiles at single-cell level. Methods: Using antibody-mediated magnetic activated cell separation (MACS), we isolated and individualized putative circulating melanoma cells (CMCs) from the blood samples of the melanoma patients at advance stages. The transcriptomic analysis based on a novel and robust mRNA-Seq protocol (Smart-Seq) was established and applied to the putative CMCs for single-cell profiling. Results: We have discovered distinct gene expression patterns, including new putative markers for CMCs. Meanwhile, the gene expression profiles derived of the CMC candidates isolated from the patient’s blood samples are closely-related to the expression profiles of other cells originated from human melanocytes, including normal melanocytes in primary culture and melanoma cell lines. Compared with existing methods, Smart-Seq has improved read coverage across transcripts, which provides advantage for better analyzing transcript isoforms and SNPs. Conclusions: Our results suggest that the techniques developed in this research for cell isolation and transcriptomic analyses can potentially be used for addressing many biological and clinical questions requiring genomewide transcriptome profiling in rare cells.

scholarly journals Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yani Dong ◽  
Likang Lyu ◽  
Haishen Wen ◽  
Bao Shi
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Interaction ◽  
Cynoglossus Semilaevis ◽  
Rna Seq ◽  
Tongue Sole ◽  
Gene Interaction Networks ◽  
Half Smooth Tongue Sole ◽  
The Brain

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.

scholarly journals Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yuan Li ◽  
Yun Ren ◽  
Ying Zhao ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Putative Target ◽  
Genome Wide ◽  
Ginger Rhizome ◽  
Rhizome Development

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

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