scholarly journals Identification and regulation of host genes related to Rice stripe virus symptom production

2015 ◽  
Vol 209 (3) ◽  
pp. 1106-1119 ◽  
Author(s):  
Bingbin Shi ◽  
Lin Lin ◽  
Shihui Wang ◽  
Qin Guo ◽  
Hong Zhou ◽  
...  
Keyword(s):  
Rice Stripe Virus ◽  
Virus Symptom ◽  
Host Genes

Improving the Resistance of Wuyunjing 8 to Rice Stripe Virus via Molecular Marker-assisted Selection

2011 ◽  
Vol 37 (5) ◽  
pp. 745-754 ◽  
Author(s):  
Hong-Gen ZHANG ◽  
Zuo-Peng XU ◽  
Peng LI ◽  
Bo LI ◽  
Chao LIU ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Marker Assisted Selection ◽  
Rice Stripe Virus

scholarly journals A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Annikka Polster ◽  
Lena Öhman ◽  
Julien Tap ◽  
Muriel Derrien ◽  
Boris Le Nevé ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Complex Variable ◽  
16S Rrna Gene Sequencing ◽  
Integrative Analysis ◽  
Rrna Gene ◽  
Analysis Pipeline ◽  
Host Interactions ◽  
Functional Relationships ◽  
Irritable Bowel ◽  
Host Genes

AbstractAlthough incompletely understood, microbiota-host interactions are assumed to be altered in irritable bowel syndrome (IBS). We, therefore, aimed to develop a novel analysis pipeline tailored for the integrative analysis of microbiota-host interactions and association to symptoms and prove its utility in a pilot cohort. A multilayer stepwise integrative analysis pipeline was developed to visualize complex variable associations. Application of the pipeline was demonstrated on a dataset of IBS patients and healthy controls (HC), using the R software package to analyze colonic host mRNA and mucosal microbiota (16S rRNA gene sequencing), as well as gastrointestinal (GI) and psychological symptoms. In total, 42 IBS patients (57% female, mean age 33.6 (range 18–58)) and 20 HC (60% female, mean age 26.8 (range 23–41)) were included. Only in IBS patients, mRNA expression of Toll-like receptor 4 and genes associated with barrier function (PAR2, OCLN, TJP1) intercorrelated closely, suggesting potential functional relationships. This host genes-based “permeability cluster” was associated to mucosa-adjacent Chlamydiae and Lentisphaerae, and furthermore associated to satiety as well as to anxiety, depression and fatigue. In both IBS patients and HC, chromogranins, secretogranins and TLRs clustered together. In IBS patients, this host genes-based “immune-enteroendocrine cluster” was associated to specific members of Firmicutes, and to depression and fatigue, whereas in HC no significant association to microbiota was identified. We have developed a stepwise integrative analysis pipeline that allowed identification of unique host-microbiota intercorrelation patterns and association to symptoms in IBS patients. This analysis pipeline may aid in advancing the understanding of complex variable associations in health and disease.

The Processing and Regulation of Intronic miRNAs Are Independent of Their Host Genes in Arabidopsis

2021 ◽  
Author(s):  
Ying Li ◽  
Qianhuan Guo ◽  
Meng Wang ◽  
Chengchao Zheng ◽  
Kang Yan
Keyword(s):  
Intronic Mirnas ◽  
Host Genes

scholarly journals The nucleocapsid protein of rice stripe virus in cell nuclei of vector insect regulates viral replication

2021 ◽  
Author(s):  
Wan Zhao ◽  
Junjie Zhu ◽  
Hong Lu ◽  
Jiaming Zhu ◽  
Fei Jiang ◽  
...  
Keyword(s):  
Viral Replication ◽  
Nucleocapsid Protein ◽  
Brown Planthopper ◽  
Rice Stripe Virus ◽  
Host Cells ◽  
Cell Nuclei ◽  
Nuclear Entry ◽  
Genomic Rnas ◽  
Importin Α ◽  
Vector Insect

AbstractRice stripe virus (RSV) transmitted by the small brown planthopper causes severe rice yield losses in Asian countries. Although viral nuclear entry promotes viral replication in host cells, whether this phenomenon occurs in vector cells remains unknown. Therefore, in this study, we systematically evaluated the presence and roles of RSV in the nuclei of vector insect cells. We observed that the nucleocapsid protein (NP) and viral genomic RNAs were partially transported into vector cell nuclei by utilizing the importin α nuclear transport system. When blocking NP nuclear localization, cytoplasmic RSV accumulation significantly increased. In the vector cell nuclei, NP bound the transcription factor YY1 and affected its positive regulation to FAIM. Subsequently, decreased FAIM expression triggered an antiviral caspase-dependent apoptotic reaction. Our results reveal that viral nuclear entry induces completely different immune effects in vector and host cells, providing new insights into the balance between viral load and the immunity pressure in vector insects.

scholarly journals Genetic diversity and population structure of rice stripe virus in China

2009 ◽  
Vol 90 (4) ◽  
pp. 1025-1034 ◽  
Author(s):  
Tai-Yun Wei ◽  
Jin-Guang Yang ◽  
Fu-Long Liao ◽  
Fang-Luan Gao ◽  
Lian-Ming Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Yunnan Province ◽  
Southwest China ◽  
Eastern China ◽  
Rice Stripe Virus ◽  
Genetic Distances ◽  
Geographical Regions ◽  
Strong Negative Selection ◽  
Recent Outbreak

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

Small nucleolar RNA host genes promoting epithelial–mesenchymal transition lead cancer progression and metastasis

IUBMB Life ◽  
2021 ◽  
Author(s):  
Alessio Biagioni ◽  
Shima Tavakol ◽  
Nooshin Ahmadirad ◽  
Masoumeh Zahmatkeshan ◽  
Lucia Magnelli ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Epithelial Mesenchymal Transition ◽  
Small Nucleolar Rna ◽  
Mesenchymal Transition ◽  
Nucleolar Rna ◽  
Host Genes

scholarly journals Methylation of Host Genes Associated with Coronavirus Infection from Birth of 26 Years

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1198
Author(s):  
Rutu Patel ◽  
Aniruddha Rathod ◽  
Parnian Kheirkhah Rahimabad ◽  
Jiasong Duan ◽  
Hongmei Zhang ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Mixed Models ◽  
Age Groups ◽  
Repeated Measurements ◽  
Epigenetic Alterations ◽  
Time Effects ◽  
Children And Young Adults ◽  
Coronavirus Infection ◽  
And Cluster Analysis ◽  
Host Genes

DNA methylation (DNAm) patterns over time at 1146 CpGs on coronavirus-related genes were assessed to understand whether the varying differences in susceptibility, symptoms, and the outcomes of the SARS-CoV-2 infection in children and young adults could be explained through epigenetic alterations in a host cell’s transcriptional apparatus to coronaviruses. DNAm data from the Isle of Wight birth cohort (IOWBC) at birth, 10, 18, and 26 years of age were included. Linear mixed models with repeated measurements stratified by sex were used to examine temporal patterns, and cluster analysis was performed to identify CpGs following similar patterns. CpGs on autosomes and sex chromosomes were analyzed separately. The association of identified CpGs and expression of their genes were evaluated. Pathway enrichment analyses of the genes was conducted at FDR = 0.05. DNAm at 635 of the 1146 CpGs on autosomes showed statistically significant time effects (FDR = 0.05). The 635 CpGs were classified into five clusters with each representing a unique temporal pattern of DNAm. Of the 29 CpGs on sex chromosomes, DNAm at seven CpGs in males and eight CpGs in females showed time effects (FDR = 0.05). Sex-specific and non-specific associations of DNAm with gene expression were found at 24 and 93 CpGs, respectively. Genes which mapped the 643 CpGs represent 460 biological processes. We suggest that the observed variability in DNAm with advancing age may partially explain differing susceptibility, disease severity, and mortality of coronavirus infections among different age groups.

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