scholarly journals RNASeq analysis ofAedes albopictusmosquitoes during chikungunya virus infection

2018 ◽  
Author(s):  
Ravikiran Vedururu ◽  
Matthew J. Neave ◽  
Mary Tachedjian ◽  
Paul R. Gorry ◽  
Jean-Bernard Duchemin ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Aedes Albopictus ◽  
Post Infection ◽  
Viral Genome ◽  
Chikungunya Virus ◽  
Differentially Expressed ◽  
Single Amino Acid ◽  
The World ◽  
Whole Transcriptome ◽  
Mosquito Infection

AbstractChikungunya virus (CHIKV), preferentially transmitted byAedesmosquitoes, is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to shift in vector preference towardsAedes albopictus, an invasive mosquito. Previous studies have shown that after infection, mosquitoes mount an antiviral immune response. However, molecular interactions during the course of infection at different tissues and time-points remain largely uncharacterised. Here we performed whole transcriptome analysis on dissected midguts and head/thorax of CHIKV (Indian Ocean strain) infectedAedes albopictusto identify differentially expressed genes compared with uninfected controls. For this, RNA was extracted at two days post-infection (D2) from pooled midguts and eight days post-infection (D8) from heads and the anterior 1/3rdof the thorax. We identified 25 and 96 differentially expressed genes from the D2 and D8 samples respectively (p-value <0.05). Customde novotranscriptomes were assembled for the reads that did not align with the reference genome and an additional 225 and 4771 differentially expressed genes from D2 and D8, respectively, were identified. Twenty-two of the identified transcripts, possibly involved in immunity, were validated by qRT-PCR. Interestingly, we also detected changes in viral diversity, as shown by number of mutations in the viral genome, with increase in number of mutations in the midgut compared with mammalian host (Vero cell culture), followed by reduction in the number of mutations in head and thorax at D8, indicating a possible genomic bottleneck. Taken together, these results will help in understanding AedesAlbopictusinteractions with CHIKV and can be utilised to reduce the impact of this viral infection.Author SummaryChikungunya virus has caused several outbreaks around the world in the last decade. Once a relatively unknown virus, it now causes seasonal infections in tropical and some temperate regions. This change in epidemiology is attributed to vector switch fromAedes aegyptitoAedes albopictus, an invasive pest leading to spread and causing infections in temperate regions. Although recent research has identified mosquito factors influencing infections, our understanding of interaction between chikungunya virus and its vector is limited. Using whole transcriptome sequencing of chikungunya infected mosquitoes, we identified differentially expressed genes in the midgut and head and thorax, over the course of mosquito infection. We also detected changes in the viral genome during mosquito infection and a possible genetic bottleneck event with reduction in viral variants at the head and thorax region of mosquito in the later stages of infection. These results will lead to improving our understanding of mosquito-virus interactions withAedes albopictusas a vector and in turn lead to development of novel disease control strategies.

scholarly journals RNASeq Analysis of Aedes albopictus Mosquito Midguts after Chikungunya Virus Infection

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 513 ◽  
Author(s):  
Ravi kiran Vedururu ◽  
Matthew J. Neave ◽  
Mary Tachedjian ◽  
Melissa J. Klein ◽  
Paul R. Gorry ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Aedes Albopictus ◽  
Post Infection ◽  
Chikungunya Virus ◽  
De Novo ◽  
Differentially Expressed ◽  
Single Amino Acid ◽  
P Value ◽  
Antiviral Immune Response ◽  
The Impact

Chikungunya virus (CHIKV) is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to a shift in vector preference towards Aedes albopictus. While mosquitoes are known to mount an antiviral immune response post-infection, molecular interactions during the course of infection at the tissue level remain largely uncharacterised. We performed whole transcriptome analysis on dissected midguts of Aedes albopictus infected with CHIKV to identify differentially expressed genes. For this, RNA was extracted at two days post-infection (2-dpi) from pooled midguts. We initially identified 25 differentially expressed genes (p-value < 0.05) when mapped to a reference transcriptome. Further, multiple differentially expressed genes were identified from a custom de novo transcriptome, which was assembled using the reads that did not align with the reference genome. Thirteen of the identified transcripts, possibly involved in immunity, were validated by qRT-PCR. Homologues of seven of these genes were also found to be significantly upregulated in Aedes aegypti midguts 2 dpi, indicating a conserved mechanism at play. These results will help us to characterise the molecular interaction between Aedes albopictus and CHIKV and can be utilised to reduce the impact of this viral infection.

scholarly journals Whole Transcriptome Analysis of Aedes albopictus Mosquito Head and Thorax Post-Chikungunya Virus Infection

Pathogens ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 132 ◽  
Author(s):  
Ravi kiran Vedururu ◽  
Matthew J. Neave ◽  
Vinod Sundaramoorthy ◽  
Diane Green ◽  
Jennifer A. Harper ◽  
...  
Keyword(s):  
Viral Infection ◽  
Aedes Albopictus ◽  
Post Infection ◽  
Chikungunya Virus ◽  
Quantitative Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Inhibitor ◽  
Significant Difference ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Infectivity Titer

Chikungunya virus (CHIKV) is transmitted by Aedes mosquitoes and causes prolonged arthralgia in patients. After crossing the mosquito midgut barrier, the virus disseminates to tissues including the head and salivary glands. To better understand the interaction between Aedes albopictus and CHIKV, we performed RNASeq analysis on pools of mosquito heads and parts of the thorax 8 days post infection, which identified 159 differentially expressed transcripts in infected mosquitos compared to uninfected controls. After validation using RT-qPCR (reverse transcriptase-quantitative polymerase chain reaction), inhibitor of Bruton’s tyrosine kinase (BTKi), which has previously been shown to be anti-inflammatory in mammals after viral infection, was further evaluated for its functional significance. Knockdown of BTKi using double-stranded RNA in a mosquito cell line showed no significant difference in viral RNA or infectivity titer. However, BTKi gene knocked-down cells showed increased apoptosis 24 hours post-infection compared with control cells, suggesting involvement of BTKi in the mosquito response to viral infection. Since BTK in mammals promotes an inflammatory response and has been shown to be involved in osteoclastogenesis, a hallmark of CHIKV pathogenesis, our results suggest a possible conserved mechanism at play between mosquitoes and mammals. Taken together, these results will add to our understanding of Aedes Albopictus interactions with CHIKV.

scholarly journals RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

2021 ◽  
Vol 8 ◽  
Author(s):  
Kirsten E. McLoughlin ◽  
Carolina N. Correia ◽  
John A. Browne ◽  
David A. Magee ◽  
Nicolas C. Nalpas ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Mycobacterium Bovis ◽  
Peripheral Blood ◽  
Post Infection ◽  
Time Course ◽  
De Novo ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Infection Time ◽  
Time Point

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

scholarly journals mRNA transcriptome analysis of bone in a mouse model of implant-associated Staphylococcus aureus osteomyelitis

2021 ◽  
Author(s):  
Yihuang Lin ◽  
Jianwen Su ◽  
Yutian Wang ◽  
Daorong Xu ◽  
Xianrong Zhang ◽  
...  
Keyword(s):  
Mouse Model ◽  
Differentially Expressed Genes ◽  
Post Infection ◽  
Early Stage ◽  
Molecular Pathogenesis ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Receptor Interaction ◽  
Pathological Changes ◽  
Ifn Γ

To investigate the molecular pathogenesis of bone with osteomyelitis, we developed implant-associated osteomyelitis (IAOM) models in mice. An orthopedic stainless pin was surgically placed in the right femoral mid-shaft of mice followed by an inoculation of S. aureus into the medullary cavity. Typical characteristics of IAOM, like periosteal reaction and intra-osseous abscess, occurred by day 14 post-infection. By day 28 post-infection, necrotic abscess, sequestrum formation and deformity of the whole femur were observed. Transcriptional analysis identified 101 and 1,702 differentially expressed genes (DEGs) between groups by days 3 and 14 post-infection, respectively. Analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed the enrichment of pathways in response to bacterium, receptor-ligand activity and chemokine signaling by day 3 post-infection. However, by day 14 post-infection, the enrichment switched to angiogenesis, positive regulation of cell motility and migration, skeletal system development and cytokine-cytokine receptor interaction. Furthermore, protein-protein interaction network analysis identified 4 cytokines (Il6, Cxcl10, IFN-γ and Cxcl9) associated with IAOM at an early stage of infection. Overall, as the pathological changes in this mouse model were consistent with those in human IAOM, our model may be used to investigate the mechanism and treatment of IAOM. Furthermore, the data of transcriptome sequencing and bioinformatic analysis will be an important resource for dissecting the molecular pathogenesis of bone with IAOM. Highlights 1. An implant-associated osteomyelitis (IAOM) mice model was developed. 2. The pathological changes in this mouse model were consistent with those in human IAOM. 3. 101 and 1,702 differentially expressed genes (DEGs) were identified between groups by days 3 and 14 post-infection, respectively. 4. Il6, Cxcl10, IFN-γ and Cxcl9 were screened out as the most important genes associated with early stage IAOM

scholarly journals PSVI-36 Transcriptome analysis of porcine tonsils following PRRS virus infection

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 202-203
Author(s):  
Haesu Ko ◽  
Won-Il Kim ◽  
Han-Hwa Chae ◽  
Won-Chul Park ◽  
Jong-Eun Park ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Post Infection ◽  
Cellular Response ◽  
Interleukin 1 ◽  
Clinical Signs ◽  
Negative Regulation ◽  
Differentially Expressed ◽  
Genome Replication ◽  
Go Terms

Abstract The major concern for the pig industry is disease control and prevention, and porcine reproductive and respiratory syndrome (PRRS) is one of the main threats to it. Tonsil is a part of the immune system and its role is to recognize and reject foreign antigens to prevent them from invading the lungs. Interestingly, porcine tonsil can harbor PRRS viruses over 150 days post infection (dpi) with no clinical signs, causing PRRS re-break. This study was conducted to find out variation in levels of gene expression in tonsils and investigate functional roles of differentially expressed genes in tonsils depending on days post infection. We used porcine tonsils from weaned pigs following experimental infection with PRRSV-2 (JA142 strain) at 3, 10, 21, 28, 35 dpi. Based on RNA-seq analysis pipeline, differentially expressed genes (DEGs) were considered significant at False Discovery Rate (FDR) ≤ 0.05 level and above the two-fold change. Comparative analyses of 3 dpi vs. 10 dpi, 3 dpi vs. 21 dpi, 3 dpi vs. 28 dpi, and 3 dpi vs. 35 dpi produced 368, 315, 754, and 336 DEGs, respectively. Then we annotated the functions of each DEG set using DAVID tool. Significant GO terms of the MF, BP, and CC ontologies and KEGG pathways were selected within the limit of FDR &lt; 0.05. Common overrepresented GO terms of all DEG sets were mainly negative regulation of viral genome replication, defense response to virus, negative regulation of type Ⅰ interferon production, and type Ⅰ interferon signaling pathway. Specific GO terms were found such as cellular response to interleukin-1, interferon-gamma-mediated signaling pathway, growth factor activity, and acute-phase response from each DEG set, respectively. It suggested tonsil responded to protect itself from PRRSV infection but further study is required to understand PRRSV persistence in tonsils.

scholarly journals Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium

2020 ◽  
Author(s):  
Hua Liu ◽  
Chang Luo ◽  
Dongliang Chen ◽  
Yaqin Wang ◽  
Shuang Guo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Floral Organ ◽  
Chrysanthemum Morifolium ◽  
Differentially Expressed ◽  
Vegetative Buds ◽  
Ray Florets ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background: Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils.Results: We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding.Conclusions: The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.

scholarly journals Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium

2020 ◽  
Author(s):  
Hua Liu ◽  
Chang Luo ◽  
Dongliang Chen ◽  
Yaqin Wang ◽  
Shuang Guo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Floral Organ ◽  
Chrysanthemum Morifolium ◽  
Differentially Expressed ◽  
Vegetative Buds ◽  
Ray Florets ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. Results We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds . Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. Conclusions The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.

scholarly journals Chikungunya Virus Transmission at Low Temperature by Aedes albopictus Mosquitoes

Pathogens ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 149 ◽  
Author(s):  
B. M. C. Randika Wimalasiri-Yapa ◽  
Liesel Stassen ◽  
Wenbiao Hu ◽  
Laith Yakob ◽  
Elizabeth A. McGraw ◽  
...  
Keyword(s):  
South African ◽  
Aedes Albopictus ◽  
Post Infection ◽  
Chikungunya Virus ◽  
Virus Transmission ◽  
Early Time ◽  
Vero Cells ◽  
Ambient Temperatures ◽  
Time Points ◽  
Central South

Aedes albopictus is an important vector of chikungunya virus (CHIKV). In Australia, Ae. albopictus is currently only known to be present on the islands of the Torres Strait but, should it invade the mainland, it is projected to spread to temperate regions. The ability of Australian Ae. albopictus to transmit CHIKV at the lower temperatures typical of temperate areas has not been assessed. Ae. albopictus mosquitoes were orally challenged with a CHIKV strain from either Asian or East/Central/South African (ECSA) genotypes (107 pfu/mL), and maintained at a constant temperature of either 18 °C or 28 °C. At 3- and 7-days post-infection (dpi), CHIKV RNA copies were quantified in mosquito bodies, and wings and legs using real time polymerase chain reaction (qRT-PCR), while the detection of virus in saliva (a proxy for transmission) was performed by amplification in cell culture followed by observation of cytopathic effect in Vero cells. Of the ≥95% of Ae. albopictus that survived to 7 dpi, all mosquitoes became infected and showed body dissemination of CHIKV at both temperatures and time points. Both the Asian and ECSA CHIKV genotypes were potentially transmissible by Australian Ae. albopictus at 28 °C within 3 days of oral challenge. In contrast, at 18 °C none of the mosquitoes showed evidence of ability to transmit either genotype of CHIKV at 3 dpi. Further, at 18 °C only Ae. albopictus infected with the ECSA genotype showed evidence of virus in saliva at 7 dpi. Overall, infection with the ECSA CHIKV genotype produced higher virus loads in mosquitoes compared to infection with the Asian CHIKV genotype. Our results suggest that lower ambient temperatures may impede transmission of some CHIKV strains by Ae. albopictus at early time points post infection.

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