scholarly journals Suppression of nbe-miR1919c-5p Expression in Nicotiana benthamiana Enhances Tobacco Curly Shoot Virus and Its Betasatellite Co-Infection

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 392
Author(s):  
Jiang Du ◽  
Rui Wu ◽  
Zhuoying Liu ◽  
Miao Sun ◽  
Hussein Ghanem ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Biological Processes ◽  
Symptom Development ◽  
Rna Molecules ◽  
Leaf Curling ◽  
Tobacco Curly Shoot Virus ◽  
The Relationship ◽  
Diverse Plant ◽  
Short Tandem ◽  
Functional Rna

MicroRNAs (miRNAs) are non-coding but functional RNA molecules of 21–25 nucleotides in length. MiRNAs play significant regulatory roles in diverse plant biological processes. In order to decipher the relationship between nbe-miR1919c-5p and the accumulations of tobacco curly shoot virus (TbCSV) and its betasatellite (TbCSB) DNAs, as well as viral symptom development, we investigated the function of nbe-miR1919c-5p during TbCSV and TbCSB co-infection in plants using a PVX-and a TRV-based short tandem target mimic (STTM) technology. Suppression of nbe-miR1919c-5p expression using these two technologies enhanced TbCSV and TbCSB co-infection-induced leaf curling symptoms in Nicotiana benthamiana plants. Furthermore, suppression of nbe-miR1919c-5p expression enhanced TbCSV and TbCSB DNA accumulations in the infected plants. Our results can advance our knowledge on the nbe-miR1919c-5p function during TbCSV and TbCSB co-infection.

scholarly journals Tobacco curly shoot virus Down-Regulated the Expression of nbe-miR167b-3p to Facilitate Its Infection in Nicotiana benthamiana

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Wu ◽  
Gentu Wu ◽  
Lyuxin Wang ◽  
Xu Wang ◽  
Zhuoying Liu ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Leaf Curling ◽  
The Family ◽  
Tobacco Curly Shoot Virus ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
The Relationship ◽  
Short Tandem

Tobacco curly shoot virus (TbCSV) belongs to the genus Begomovirus of the family Geminiviridae, and causes leaf curling and curly shoot symptoms in tobacco and tomato crops. MicroRNAs (miRNAs) are pivotal modulators of plant development and host-virus interactions. However, the relationship between TbCSV infection and miRNAs accumulation has not been well investigated. The present study was conducted to analyze different expressions of miRNAs in Nicotiana benthamiana in response to the infection of TbCSV via small RNAs sequencing. The results showed that 15 up-regulated miRNAs and 12 down-regulated miRNAs were differentially expressed in TbCSV infected N. benthamiana, and nbe-miR167b-3p was down-regulated. To decipher the relationship between nbe-miR167b-3p expression and the accumulations of TbCSV DNA, pCVA mediation of miRNA overexpression and PVX based short tandem target mimic (STTM) were used in this study. It was found that overexpression of nbe-miR167b-3p attenuated leaf curling symptom of TbCSV and decreased viral DNA accumulation, but suppression of nbe-miR167b-3p expression enhanced the symptoms and accumulation of TbCSV. PRCP, the target gene of nbe-miR167b-3p, was silenced in plants using VIGS and this weakened the viral symptoms and DNA accumulation of TbCSV in the plants. Overall, this study clarified the effect of nbe-miR167b-3p on plant defense during TbCSV infection, and provided a framework to reveal the molecular mechanisms of miRNAs between plants and viruses.

scholarly journals Roles of Small RNAs in Virus-Plant Interactions

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 827 ◽  
Author(s):  
Baogang Zhang ◽  
Wenji Li ◽  
Jialin Zhang ◽  
Lu Wang ◽  
Jianguo Wu
Keyword(s):  
Small Rnas ◽  
Function Analysis ◽  
Plant Viruses ◽  
Control Measures ◽  
Biological Processes ◽  
Plant Interactions ◽  
Rna Molecules ◽  
New Findings ◽  
Underlying Mechanisms ◽  
Diverse Plant

Small RNAs (sRNAs), including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are non-coding but powerful RNA molecules of 20–30 nucleotides in length. sRNAs play crucial regulatory roles in diverse plant biological processes. Recently, many studies on sRNAs have been reported. We summarize new findings of sRNAs in virus-plant interactions to accelerate the function analysis of sRNAs. The main content of this review article includes three parts: virus-responsive sRNAs, function analysis of sRNAs in virus pathogenicity or host resistance, and some sRNAs-mediated underlying mechanisms in virus-plant interactions. New findings of sRNAs deepen our understanding about sRNAs’ roles, which might contribute to the design of novel control measures against plant viruses.

CASC15：A tumor-associated long non-coding RNA

2020 ◽  
Vol 26 ◽  
Author(s):  
Bei Wang ◽  
Wen Xu ◽  
Yuxuan Cai ◽  
Chong Guo ◽  
Gang Zhou ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Therapeutic Target ◽  
Cancer Colorectal ◽  
Tumor Development ◽  
Pathophysiological Mechanism ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Cancer Côlon ◽  
The Relationship ◽  
Long Non Coding Rna

Background: CASC15, one of long non-coding RNA, is involved in the regulation of many tumor biological processes, and is expected to become a new biological therapeutic target. This paper aims to elucidate the pathophysiological function of CASC15 in various tumors. Methods: The relationship between CASC15 and tumors was analyzed by searching references, and summarizes the specific pathophysiological mechanism of CASC15. Results: LncRNA CASC15 is closely related to tumor development, and has been shown to be abnormally high expressed in all kinds of tumors, including breast cancer, cervical cancer, lung cancer, hepatocellular carcinoma, gastric cancer, bladder cancer, colon cancer, colorectal cancer, cardiac hypertrophy, intrahepatic cholangiocarcinoma, leukemia, melanoma, tongue squamous cell carcinoma, nasopharyngeal carcinoma. However, CASC15 has been found to be downexpressed abnormally in ovarian cancer, glioma and neuroblastoma. Besides, it is identified that CASC15 can affect the proliferation, invasion and apoptosis of tumors. Conclusion: LncRNA CASC15 has the potential to become a new therapeutic target or marker for a variety of tumors.

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

The Relationship of Undifferentiated Mesenchymal Cells to TMJ Articular Tissue Thickness

1992 ◽  
Vol 71 (11) ◽  
pp. 1816-1821 ◽  
Author(s):  
C.A. Bibb ◽  
A.G. Pullinger ◽  
F. Baldioceda
Keyword(s):  
Soft Tissue ◽  
Inverse Relationship ◽  
Biological Processes ◽  
Spearman Correlation ◽  
Articular Eminence ◽  
Tissue Thickness ◽  
Cartilage Layer ◽  
Soft Tissue Thickness ◽  
Relationship Of ◽  
The Relationship

Undifferentiated mesenchymal (UM) cells, the progenitor cells of the cartilage layer, have been assigned a significant role in TMJ articular tissue maintenance. This was based on reports of UM cell reduction with increased soft-tissue thickness for the condyle and temporal component. However, the strength of this inverse relationship was not presented and remained unclear. The purpose of the present study was to assess the strength of the correlation between UM cell presence and soft-tissue thickness in young adult TMJs at autopsy. Sagittal histological sections from the central thirds of 50 joints were evaluated with respect to articular soft-tissue thickness, histological character, and UM cell presence in the condyle and temporal component. The superior sector ofthe condyle and the articular eminence showed the greatest variability in soft-tissue thickness and were the only areas to show localized UM cell absence. The eminence was the only location to show an inverse relationship between soft-tissue thickness and UM cell presence, and this was consistent in both an ANOVA (p = 0.0016) and a Spearman correlation analysis. However, the strength of this correlation was only moderate (rho = -0.52), and no such relationship was observed in any other location. This study suggests that the relationship between UM cell presence and soft-tissue thickness is more complex than previously hypothesized and that the contribution of UM cells to articular tissue maintenance has been overstated, while other biological processes were overlooked.

Research progress in predicting DNA methylation modifications and the relation with human diseases

2021 ◽  
Vol 28 ◽  
Author(s):  
Chunyan Ao ◽  
Lin Gao ◽  
Liang Yu
Keyword(s):  
Dna Methylation ◽  
Eukaryotic Cell ◽  
Machine Learning Algorithms ◽  
Research Progress ◽  
Epigenetic Mechanisms ◽  
Biological Processes ◽  
Prediction Tools ◽  
Transformation Mechanisms ◽  
The Relationship ◽  
Treatment And Diagnosis

: DNA methylation is an important mode of regulation in epigenetic mechanisms, and it is one of the research foci in the field of epigenetics. DNA methylation modification affects a series of biological processes, such as eukaryotic cell growth, differentiation and transformation mechanisms, by regulating gene expression. In this review, we systematically summarized the DNA methylation databases, prediction tools for DNA methylation modification, machine learning algorithms for predicting DNA methylation modification, and the relationship between DNA methylation modification and diseases such as hypertension, Alzheimer's disease, diabetic nephropathy, and cancer. An in-depth understanding of DNA methylation mechanisms can promote accurate prediction of DNA methylation modifications and the treatment and diagnosis of related diseases.

scholarly journals Current and Emerging Themes in the Structural Analysis of Viral RNA Genomes: Applications for the Development of Novel Therapeutic Drugs

2015 ◽  
Vol 1 (1) ◽  
pp. 15 ◽  
Author(s):  
Cristina Romero-López ◽  
Alfredo Berzal-Herranz
Keyword(s):  
Rna Folding ◽  
Viral Infections ◽  
Genome Structure ◽  
Rna Molecules ◽  
Molecular Virology ◽  
Viral Genomes ◽  
Viral Propagation ◽  
Bioinformatic Tools ◽  
Rna Domains ◽  
Functional Rna

RNA molecules assume different roles in many different biological processes. This functional diversity is intimately related to RNA folding. In recent years, advances in the field of structure analysis by high-throughput methodologies and the development of novel potent bioinformatic tools have enabled the first structural maps of the eukaryotic transcriptome and the further establishment of novel function-structure relationships. This important progress has been of special relevance in the field of molecular virology. Viral genomes are compact entities that require overlapping coding levels to bear all the genetic information required for viral propagation. This is achieved by the acquisition of functional RNA domains, structurally conserved encoding units that perform essential roles for the consecution of the viral cycle. Interfering with the activity of these structural elements offers a potential means of treating viral infections, such as that caused by the hepatitis C virus, HCV. This review summarizes major achievements in the development of emerging methodologies for the analysis of RNA folding and their application to the study of the HCV genome structure. It will also examine the progress toward the design of novel antiviral compounds based in nucleic acids able to interfere with the folding of functional RNA domains.

scholarly journals N6-Methyladenosine and Rheumatoid Arthritis: A Comprehensive Review

2021 ◽  
Vol 12 ◽  
Author(s):  
Sha Wu ◽  
Xiao-Feng Li ◽  
Yuan-Yuan Wu ◽  
Su-Qin Yin ◽  
Cheng Huang ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Immune Cells ◽  
Myeloid Leukemia ◽  
Immune Cell ◽  
Bone Destruction ◽  
Synovial Cell ◽  
Biological Processes ◽  
Cell Life ◽  
History Of ◽  
The Relationship

Rheumatoid arthritis (RA), one of the most common autoimmune diseases, is characterized by immune cell infiltration, fibroblast-like synovial cell hyperproliferation, and cartilage and bone destruction. To date, numerous studies have demonstrated that immune cells are one of the key targets for the treatment of RA. N6-methyladenosine (m6A) is the most common internal modification to eukaryotic mRNA, which is involved in the splicing, stability, export, and degradation of RNA metabolism. m6A methylated-related genes are divided into writers, erasers, and readers, and they are critical for the regulation of cell life. They play a significant role in various biological processes, such as virus replication and cell differentiation by controlling gene expression. Furthermore, a growing number of studies have indicated that m6A is associated with the occurrence of numerous diseases, such as lung cancer, bladder cancer, gastric cancer, acute myeloid leukemia, and hepatocellular carcinoma. In this review, we summarize the history of m6A research and recent progress on RA research concerning m6A enzymes. The relationship between m6A enzymes, immune cells, and RA suggests that m6A modification offers evidence for the pathogenesis of RA, which will help in the development of new therapies for RA.

GEREDB: Gene expression regulation database curated by mining abstracts from literature

2019 ◽  
Vol 17 (04) ◽  
pp. 1950024 ◽  
Author(s):  
Tinghua Huang ◽  
Xiali Huang ◽  
Bomei Shi ◽  
Min Yao
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Expression Regulation ◽  
Biological Database ◽  
Biological Processes ◽  
Expression Data ◽  
Biological Responses ◽  
Human Genes ◽  
The Relationship ◽  
Made In

Understanding how genes are expressed and regulated in different biological processes are fundamental and challenging issues. Considerable progress has been made in studying the relationship between the expression and regulation of human genes. However, it is difficult to use these resources productively to analyze gene expression data. GEREDB ( www.thua45.cn/geredb ) has been developed to facilitate analyses that will provide insights into the regulation of genes that govern specific biological responses. GEREDB is a publicly available, manually curated biological database that stores the data regarding relationships between expression and regulation of human genes. To date, more than 39,000 Links have been contextually annotated by reviewing more than 53,000 abstracts. GEREDB can be searched using the official NCBI gene symbol as a query, and it can be downloaded along with the GEREA software package. GEREDB has the ability to analyze user-supplied gene expression data in a causal analysis oriented manner using the GEREA bioinformatics tool.

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