Pathogenicity Detection and Genome Analysis of Two Different Geographic Strains of BmNPV

The pathogenicity of different concentrations of Bombyx mori nuclear polyhedrosis virus- Zhenjiang strain (BmNPV ZJ) and Yunnan strain (BmNPV YN) was assessed in Baiyu larvae. The structures of the two viral strains were observed by negative-staining electron microscopy, and their proliferation was examined by quantitative polymerase chain reaction (qPCR). The genomic sequences of these two viruses were obtained to investigate the differences in their pathogenicity. The lethal concentration 50 (LC50) of BmNPV ZJ against Baiyu larvae was higher than that of BmNPV YN, indicating a relatively more robust pathogenicity in BmNPV YN. Electron microscopic images showed that the edges of BmNPV YN were clearer than those of BmNPV ZJ. The qPCR analysis demonstrated significantly higher relative expressions of immediately early 1 gene (ie-1), p143, vp39, and polyhedrin genes (polh) in BmNPV ZJ than in BmNPV YN at 12–96 h. The complete genomes of BmNPV ZJ and BmNPV YN were, respectively, 135,895 bp and 143,180 bp long, with 141 and 145 coding sequences and 40.93% and 39.71% GC content. Considering the BmNPV ZJ genome as a reference, 893 SNP loci and 132 InDel mutations were observed in the BmNPV YN genome, resulting in 106 differential gene sequences. Among these differential genes, 76 (including 22 hub genes and 35 non-hub genes) possessed amino acid mutations. Thirty genes may have been related to viral genome replication and transcription and five genes may have been associated with the viral oral infection. These results can help in understanding the mechanisms of pathogenicity of different strains of BmNPV in silkworms.

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Phenotypic diversity of BmNPV isolated from different geographical locations of south India

Research Journal of Chemistry and Environment ◽

10.25303/2511rjce7179 ◽

2021 ◽

Vol 25 (11) ◽

pp. 71-79

Author(s):

Madhuri Sathyanarayana ◽

S.E. Neelagund ◽

Dayanand B. Sajjan ◽

Rajat Hegde

Keyword(s):

World War Ii ◽

South India ◽

Phenotypic Diversity ◽

World War ◽

Electron Microscopic ◽

Study Results ◽

Occlusion Bodies ◽

Different Strains ◽

Nuclear Polyhedrosis ◽

Diameter Of Polyhedra

Viral diseases take the lives of n number of silkworms each year resulting in 30-40% of average crop loss. Grasserie is one of the deadly diseases caused by NPV (Nuclear Polyhedrosis virus) for silkworm. BmNPV was observed throughout the year with increased severity in the summer and autumn crops. During the World War II, accidentally effective pest’s suppression was observed by the introduction of baculovirus into the environment. Morphological parameters of occlusion bodies of BmNPV from different strains were examined to validate detailed structure of these viruses. This examination mainly focused on light microscopic and electron microscopic study. Results in intelligible images of HRH, HSR, KNK, MSI and VKK BmNPV isolates under various magnifications were observed. The diameter of completely formed OBs of HRH, HSR, KNK, MSI, VKK was found to be 1.2 to 2.8 μm, 1.4 to 3.2 μm, 0.8 to 2.6 μm and 1.1 to 2.9 μm, 1.1 to 3.4 μm. Granulated OBs size ranges from 0.5 to 2.4μm. The diameter of polyhedra ranges about 0.6–1.6μm. Thus, uncovering these aspects may help to spell out indetail phenotypic diversity of BmNPV isolates from south India.

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Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

Genes ◽

10.3390/genes12040480 ◽

2021 ◽

Vol 12 (4) ◽

pp. 480

Author(s):

Lin Tao ◽

Xiaoyun He ◽

Yanting Jiang ◽

Yufang Liu ◽

Yina Ouyang ◽

...

Keyword(s):

Signaling Pathway ◽

Litter Size ◽

Luteal Phase ◽

Antigen Processing ◽

Osteoclast Differentiation ◽

Follicular Phase ◽

Comparative Genomic ◽

Genome Replication ◽

Viral Genome Replication ◽

Transcriptomic Level

The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.

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Electron Microscopic Studies on the Nuclear-Polyhedrosis Viruses of Several Lepidoptera

Japanese Journal of Applied Entomology and Zoology ◽

10.1303/jjaez.8.222 ◽

1964 ◽

Vol 8 (3) ◽

pp. 222-226 ◽

Cited By ~ 2

Author(s):

Hisao ARUGA ◽

Tosihiko HUKUHARA ◽

Shôichi FUKUDA ◽

Sigeo TANAKA

Keyword(s):

Electron Microscopic ◽

Microscopic Studies ◽

Nuclear Polyhedrosis

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Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing

10.32469/10355/45905 ◽

2014 ◽

Author(s):

◽

Olufemi Fasina

Keyword(s):

Gene Expression ◽

Rna Processing ◽

Viral Genome ◽

Transcription Initiation ◽

Alternative Polyadenylation ◽

Open Reading Frames ◽

Genome Replication ◽

University Of Missouri ◽

Diverse Range ◽

Viral Genome Replication

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3ï¿½-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome.

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Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat

PLoS ONE ◽

10.1371/journal.pone.0243507 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243507

Author(s):

Zhihong Wu ◽

Erhan Hai ◽

Zhengyang Di ◽

Rong Ma ◽

Fangzheng Shang ◽

...

Keyword(s):

Network Analysis ◽

Hair Follicle ◽

Quantitative Polymerase Chain Reaction ◽

Correlation Coefficients ◽

Hair Follicles ◽

Functional Enrichment ◽

Follicle Development ◽

Hub Genes ◽

Cashmere Goats ◽

Hair Follicle Development

Objective Mature hair follicles represent an important stage of hair follicle development, which determines the stability of hair follicle structure and its ability to enter the hair cycle. Here, we used weighted gene co-expression network analysis (WGCNA) to identify hub genes of mature skin and hair follicles in Inner Mongolian cashmere goats. Methods We used transcriptome sequencing data for the skin of Inner Mongolian cashmere goats from fetal days 45–135 days, and divided the co expressed genes into different modules by WGCNA. Characteristic values were used to screen out modules that were highly expressed in mature skin follicles. Module hub genes were then selected based on the correlation coefficients between the gene and module eigenvalue, gene connectivity, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The results were confirmed by quantitative polymerase chain reaction (qPCR). Results Ten modules were successfully defined, of which one, with a total of 3166 genes, was selected as a specific module through sample and gene expression pattern analyses. A total of 584 candidate hub genes in the module were screened by the correlation coefficients between the genes and module eigenvalue and gene connectivity. Finally, GO/KEGG functional enrichment analyses detected WNT10A as a key gene in the development and maturation of skin hair follicles in fetal Inner Mongolian cashmere goats. qPCR showed that the expression trends of 13 genes from seven fetal skin samples were consistent with the sequencing results, indicating that the sequencing results were reliable.n

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Integrated Transcriptomic Analysis Revealed Hub Genes and Pathways Involved in Sorafenib Resistance in Hepatocellular Carcinoma

Pathology & Oncology Research ◽

10.3389/pore.2021.1609985 ◽

2021 ◽

Vol 27 ◽

Author(s):

Xili Jiang ◽

Wei Zhang ◽

Lifeng Li ◽

Shucai Xie

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Pearson Correlation ◽

Acquired Resistance ◽

Rank Aggregation ◽

Health Concern ◽

Hub Genes ◽

Multikinase Inhibitor

Hepatocellular carcinoma (HCC), a high mortality malignancy, has become a worldwide public health concern. Acquired resistance to the multikinase inhibitor sorafenib challenges its clinical efficacy and the survival benefits it provides to patients with advanced HCC. This study aimed to identify critical genes and pathways associated with sorafenib resistance in HCC using integrated bioinformatics analysis. Differentially expressed genes (DEGs) were identified using four HCC gene expression profiles (including 34 sorafenib-resistant and 29 sorafenib-sensitive samples) based on the robust rank aggregation method and R software. Gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. A protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING), and small molecules reversing sorafenib resistance were searched for using the connectivity map (CMAP) database. Pearson correlation and survival analyses of hub genes were performed using cBioPortal and Gene Expression Profiling and Interactive Analysis (GEPIA). Finally, the expression levels of hub genes in sorafenib-resistant HCC cells were verified using quantitative polymerase chain reaction (q-PCR). A total of 165 integrated DEGs (66 upregulated and 99 downregulated in sorafenib resistant samples compared sorafenib sensitive ones) primarily enriched in negative regulation of endopeptidase activity, extracellular exosome, and protease binding were identified. Some pathways were commonly shared between the integrated DEGs. Seven promising therapeutic agents and 13 hub genes were identified. These findings provide a strategy and theoretical basis for overcoming sorafenib resistance in HCC patients.

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Dimerisation of the influenza virus RNA polymerase during viral genome replication

Access Microbiology ◽

10.1099/acmi.ac2019.po0145 ◽

2019 ◽

Vol 1 (1A) ◽

Author(s):

Alexander Walker ◽

Haitian Fan ◽

Loic Carrique ◽

Jeremy Keown ◽

David Bauer ◽

...

Keyword(s):

Influenza Virus ◽

Rna Polymerase ◽

Viral Genome ◽

Genome Replication ◽

Virus Rna ◽

Viral Genome Replication

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The formation and modification of chromatin-like structure of human parvovirus B19 regulate viral genome replication and RNA processing

Virus Research ◽

10.1016/j.virusres.2017.03.001 ◽

2017 ◽

Vol 232 ◽

pp. 134-138 ◽

Cited By ~ 1

Author(s):

Huanzhou Xu ◽

Sujuan Hao ◽

Junmei Zhang ◽

Zhen Chen ◽

Hanzhong Wang ◽

...

Keyword(s):

Rna Processing ◽

Viral Genome ◽

Parvovirus B19 ◽

Genome Replication ◽

Human Parvovirus B19 ◽

Viral Genome Replication

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Mosquito metabolomics reveal that dengue virus replication requires phospholipid reconfiguration via the remodeling cycle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015095117 ◽

2020 ◽

Vol 117 (44) ◽

pp. 27627-27636

Author(s):

Thomas Vial ◽

Wei-Lian Tan ◽

Eric Deharo ◽

Dorothée Missé ◽

Guillaume Marti ◽

...

Keyword(s):

Dengue Virus ◽

Viral Genome ◽

De Novo ◽

Genome Replication ◽

Mosquito Vector ◽

Phospholipid Biosynthesis ◽

Replication Complex ◽

Mosquito Cells ◽

Viral Genome Replication ◽

Blood Meals

Dengue virus (DENV) subdues cell membranes for its cellular cycle by reconfiguring phospholipids in humans and mosquitoes. Here, we determined how and why DENV reconfigures phospholipids in the mosquito vector. By inhibiting and activating the de novo phospholipid biosynthesis, we demonstrated the antiviral impact of de novo–produced phospholipids. In line with the virus hijacking lipids for its benefit, metabolomics analyses indicated that DENV actively inhibited the de novo phospholipid pathway and instead triggered phospholipid remodeling. We demonstrated the early induction of remodeling during infection by using isotope tracing in mosquito cells. We then confirmed in mosquitoes the antiviral impact of de novo phospholipids by supplementing infectious blood meals with a de novo phospholipid precursor. Eventually, we determined that phospholipid reconfiguration was required for viral genome replication but not for the other steps of the virus cellular cycle. Overall, we now propose that DENV reconfigures phospholipids through the remodeling cycle to modify the endomembrane and facilitate formation of the replication complex. Furthermore, our study identified de novo phospholipid precursor as a blood determinant of DENV human-to-mosquito transmission.

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Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles

Viruses ◽

10.3390/v11030288 ◽

2019 ◽

Vol 11 (3) ◽

pp. 288 ◽

Cited By ~ 7

Author(s):

Raquel Tenorio ◽

Isabel Fernández de Castro ◽

Jonathan J. Knowlton ◽

Paula F. Zamora ◽

Danica M. Sutherland ◽

...

Keyword(s):

Protein Complexes ◽

Host Cells ◽

Genome Replication ◽

Nonstructural Proteins ◽

Particle Assembly ◽

The Matrix ◽

Viral Genome Replication ◽

Pathogenic Viruses ◽

Infected Cells ◽

Reovirus Replication

Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA–protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.

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