Comparative analysis of microarray data in Arabidopsis transcriptome during compatible interactions with plant viruses.

Abstract:

BACKGROUND:At the moment, there are a number of publications describing gene expression profiling in virus-infected plants. Most of the data are limited to specific host-pathogen interactions involving a given virus and a model host plant - usually Arabidopsis thaliana. Even though several summarizing attempts have been made, a general picture of gene expression changes in susceptible virus-host interactions is lacking. METHODS:To analyze transcriptome response to virus infection, we have assembled currently available microarray data on changes in gene expression levels in compatible Arabidopsis-virus interactions. We used the mean r (Pearson's correlation coefficient) for neighboring pairs to estimate pairwise local similarity in expression in the Arabidopsis genome. RESULTS:Here we provide a functional classification of genes with altered expression levels. We also demonstrate that responsive genes may be grouped or clustered based on their co-expression pattern and chromosomal location. CONCLUSIONS:In summary, we found that there is a greater variety of upregulated genes in the course of viral pathogenesis as compared to repressed genes. Distribution of the responsive genes in combined viral databases differed from that of the whole Arabidopsis genome, thus underlining a role of the specific biological processes in common mechanisms of general resistance against viruses and in physiological/cellular changes caused by infection. Using integrative platforms for the analysis of gene expression data and functional profiling, we identified overrepresented functional groups among activated and repressed genes. Each virus-host interaction is unique in terms of the genes with altered expression levels and the number of shared genes affected by all viruses is very limited. At the same time, common genes can participate in virus-, fungi- and bacteria-host interaction. According to our data, non-homologous genes that are located in close proximity to each other on the chromosomes, and whose expression profiles are modified as a result of the viral infection, occupy 12% of the genome. Among them 5% form co-expressed and co-regulated clusters.

journal_name

Virol J

journal_title

Virology journal

authors

Postnikova OA,Nemchinov LG

doi

10.1186/1743-422X-9-101

subject

Has Abstract

pub_date

2012-05-29 00:00:00

pages

101

issn

1743-422X

pii

1743-422X-9-101

journal_volume

9

pub_type

杂志文章
  • Orf virus DNA vaccines expressing ORFV 011 and ORFV 059 chimeric protein enhances immunogenicity.

    abstract:BACKGROUND:ORFV attenuated live vaccines have been the main prophylactic measure against contagious ecthyma in sheep and goats in the last decades, which play an important role in preventing the outbreak of the disease. However, the available vaccines do not induce lasting immunity in sheep and goats. On the other hand...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-8-562

    authors: Zhao K,He W,Gao W,Lu H,Han T,Li J,Zhang X,Zhang B,Wang G,Su G,Zhao Z,Song D,Gao F

    更新日期:2011-12-29 00:00:00

  • All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity.

    abstract:BACKGROUND:The recent 2009 (H1N1) influenza A pandemic saw a rapid spread of the virus to essentially all parts of the world. In the course of its evolution, the virus acquired many mutations, some of which have been investigated in the context of increased severity due to high occurrences in fatal cases. For example, ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-7-297

    authors: Lee RT,Santos CL,de Paiva TM,Cui L,Sirota FL,Eisenhaber F,Maurer-Stroh S

    更新日期:2010-11-01 00:00:00

  • Characterization of Farmington virus, a novel virus from birds that is distantly related to members of the family Rhabdoviridae.

    abstract:BACKGROUND:Farmington virus (FARV) is a rhabdovirus that was isolated from a wild bird during an outbreak of epizootic eastern equine encephalitis on a pheasant farm in Connecticut, USA. FINDINGS:Analysis of the nearly complete genome sequence of the prototype CT AN 114 strain indicates that it encodes the five canoni...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-10-219

    authors: Palacios G,Forrester NL,Savji N,Travassos da Rosa AP,Guzman H,Detoy K,Popov VL,Walker PJ,Lipkin WI,Vasilakis N,Tesh RB

    更新日期:2013-07-01 00:00:00

  • Inhibition of G1P3 expression found in the differential display study on respiratory syncytial virus infection.

    abstract:BACKGROUND:Respiratory syncytial virus (RSV) is the leading viral pathogen associated with bronchiolitis and lower respiratory tract disease in infants and young children worldwide. The respiratory epithelium is the primary initiator of pulmonary inflammation in RSV infections, which cause significant perturbations of ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-5-114

    authors: Zhao D,Peng D,Li L,Zhang Q,Zhang C

    更新日期:2008-10-06 00:00:00

  • Phylogenetic analysis of Torque Teno Virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients.

    abstract:BACKGROUND:Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the prese...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-9-320

    authors: Hussain T,Manzoor S,Waheed Y,Tariq H,Hanif K

    更新日期:2012-12-28 00:00:00

  • Intracytoplasmic stable expression of IgG1 antibody targeting NS3 helicase inhibits replication of highly efficient hepatitis C Virus 2a clone.

    abstract:BACKGROUND:Hepatitis C virus (HCV) infection is a major public health problem with more than 170 million cases of chronic infections worldwide. There is no protective vaccine currently available for HCV, therefore the development of novel strategy to prevent chronic infection is important. We reported earlier that a re...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-7-118

    authors: Chandra PK,Hazari S,Poat B,Gunduz F,Prabhu R,Liu G,Burioni R,Clementi M,Garry RF,Dash S

    更新日期:2010-06-07 00:00:00

  • Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses.

    abstract:BACKGROUND:A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. METHOD:The microspheres coated with purified recombinant glycop...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-018-1048-x

    authors: Wang H,Cong F,Guan J,Xiao L,Zhu Y,Lian Y,Huang R,Chen M,Guo P

    更新日期:2018-09-21 00:00:00

  • Current status and future directions in the management of chronic hepatitis C.

    abstract::Hepatitis C virus (HCV) is endemic worldwide, and it causes cirrhosis and other complications that often lead to death; nevertheless, our knowledge of the disease and its mechanisms is limited. HCV is most common in underdeveloped nations, including many in Africa and Asia. The virus is usually transmitted by parenter...

    journal_title:Virology journal

    pub_type: 杂志文章,评审

    doi:10.1186/1743-422X-9-57

    authors: Aman W,Mousa S,Shiha G,Mousa SA

    更新日期:2012-03-02 00:00:00

  • Comparison of the efficacy of lamivudine and telbivudine in the treatment of chronic hepatitis B: a systematic review.

    abstract:BACKGROUND:Chronic viral hepatitis B remains a global public health concern. Currently, several drugs, such as lamivudine and telbivudine, are recommended for treatment of patients with chronic hepatitis B. However, there are no conclusive results on the comparison of the efficacy of lamivudine (LAM) and telbivudine (L...

    journal_title:Virology journal

    pub_type: 杂志文章,meta分析,评审

    doi:10.1186/1743-422X-7-211

    authors: Zhao S,Tang L,Fan X,Chen L,Zhou R,Dai X

    更新日期:2010-09-03 00:00:00

  • A neutralization assay for respiratory syncytial virus using a quantitative PCR-based endpoint assessment.

    abstract:BACKGROUND:Few studies have used quantitative polymerase chain reaction (qPCR) as an approach to measure virus neutralization assay endpoints. Its lack of use may not be surprising considering that sample nucleic acid extraction and purification can be expensive, labor-intensive, and rate-limiting. METHODS:Virus/antib...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-10-195

    authors: Varada JC,Teferedegne B,Crim RL,Mdluli T,Audet S,Peden K,Beeler J,Murata H

    更新日期:2013-06-15 00:00:00

  • Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease.

    abstract:BACKGROUND:Citrus sudden death (CSD), a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution and symptomatology it is suspected that the agent may be a new strain of Cit...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-5-9

    authors: Gomes CP,Nagata T,de Jesus WC Jr,Neto CR,Pappas GJ Jr,Martin DP

    更新日期:2008-01-16 00:00:00

  • Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains.

    abstract:BACKGROUND:Pseudorabies virus (PRV) of the family Herpesviridae is the causative agent of Aujeszky's disease. Attenuation of PRV by serial passaging in vitro is a well-established method; however, the dynamic variations occurring on viral genome during this process have not been characterized. METHODS:Genome sequencin...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-018-1102-8

    authors: Ye C,Wu J,Tong W,Shan T,Cheng X,Xu J,Liang C,Zheng H,Li G,Tong G

    更新日期:2018-12-29 00:00:00

  • Early detection of Varicella-Zoster virus (VZV)-specific T-cells before seroconversion in primary varicella infection: case report.

    abstract::Here we report the case of a 54-year old, immunocompetent German patient with primary varicella whose Varicella-Zoster Virus (VZV)-specific T-cell responses could be detected early in infection and before the onset of seroconversion. This case demonstrates that the detection of VZV-specific T-cells may under certain c...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-7-54

    authors: Baiker A,Haase R,Eberle J,Vizoso Pinto MG,Pfrepper KI,Petrich A,Deml L,Campe H,Nitschko H,Jaeger G

    更新日期:2010-03-06 00:00:00

  • 18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells.

    abstract:BACKGROUND:One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-9-230

    authors: Kuchipudi SV,Tellabati M,Nelli RK,White GA,Perez BB,Sebastian S,Slomka MJ,Brookes SM,Brown IH,Dunham SP,Chang KC

    更新日期:2012-10-08 00:00:00

  • Intracellular localization of Crimean-Congo Hemorrhagic Fever (CCHF) virus glycoproteins.

    abstract:BACKGROUND:Crimean-Congo Hemorrhagic Fever virus (CCHFV), a member of the genus Nairovirus, family Bunyaviridae, is a tick-borne pathogen causing severe disease in humans. To better understand the CCHFV life cycle and explore potential intervention strategies, we studied the biosynthesis and intracellular targeting of ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-2-42

    authors: Haferkamp S,Fernando L,Schwarz TF,Feldmann H,Flick R

    更新日期:2005-04-25 00:00:00

  • Torque teno virus dynamics during the first year of life.

    abstract:BACKGROUND:Torque teno virus is a small chronically persisting circular negative ssDNA virus reaching near 100% prevalence. It is reported to be a marker for immune function in immunocompromised patients. The possibility of vertical maternal-fetal transmission remains controversial but incidence rate of TTV DNA in chil...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-018-1007-6

    authors: Tyschik EA,Rasskazova AS,Degtyareva AV,Rebrikov DV,Sukhikh GT

    更新日期:2018-05-30 00:00:00

  • A novel protein-coding ORF72.2 gene was identified from Marek's disease virus strain CVI988.

    abstract::Marek's disease is a highly contagious disease of poultry characterized by rapid-on set of T-cell lymphomas, which is caused by Marek's disease virus (MDV), but its pathogenic mechanism is still not very clear. Recently, some new progress were achieved in molecular character of MDV. Along with the genomic sequencing o...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-7-371

    authors: Tian M,Zhao Y,Shi M,Lin Y,Zou N,Liu P,Wen X,Cao S,Huang Y

    更新日期:2010-12-23 00:00:00

  • Rapid detection of anti-Vaccinia virus neutralizing antibodies.

    abstract::Increasing infections with Monkeypox and Cowpox viruses pose a continuous and growing threat to human health. The standard method for detecting poxvirus neutralizing antibodies is the plaque-reduction neutralization test that is specific but also time-consuming and laborious. Therefore, a rapid and reliable method was...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-8-139

    authors: Kramski M,Drozd A,Lichtfuss GF,Dabrowski PW,Ellerbrok H

    更新日期:2011-03-25 00:00:00

  • Agnoprotein of polyomavirus BK interacts with proliferating cell nuclear antigen and inhibits DNA replication.

    abstract:BACKGROUND:The human polyomavirus BK expresses a 66 amino-acid peptide referred to as agnoprotein. Though mutants lacking agnoprotein are severely reduced in producing infectious virions, the exact function of this peptide remains incompletely understood. To elucidate the function of agnoprotein, we searched for novel ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-014-0220-1

    authors: Gerits N,Johannessen M,Tümmler C,Walquist M,Kostenko S,Snapkov I,van Loon B,Ferrari E,Hübscher U,Moens U

    更新日期:2015-02-01 00:00:00

  • Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene.

    abstract:BACKGROUND:The genus Orbivirus includes several species that infect livestock - including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. RESULTS:Bioinformatic evidence is p...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-5-48

    authors: Firth AE

    更新日期:2008-04-14 00:00:00

  • Origin of measles virus: divergence from rinderpest virus between the 11th and 12th centuries.

    abstract::Measles, caused by measles virus (MeV), is a common infection in children. MeV is a member of the genus Morbillivirus and is most closely related to rinderpest virus (RPV), which is a pathogen of cattle. MeV is thought to have evolved in an environment where cattle and humans lived in close proximity. Understanding th...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-7-52

    authors: Furuse Y,Suzuki A,Oshitani H

    更新日期:2010-03-04 00:00:00

  • A predominance of R5-like HIV genotypes in vaginal secretions is associated with elevated plasma HIV-1 RNA levels and the absence of anti-retroviral therapy.

    abstract::HIV expressed in genital secretions provides the inoculum from which transmitting variants are selected, both in sexual transmission and mother-to-infant transmission during partuition. Characterization of HIV levels and genotypes found in vaginal secretions and the impact of anti-retroviral therapy (ART) on this viru...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-5-87

    authors: Randolph TC,Kissinger PJ,Clark RA,Lacour N,Amedee AM

    更新日期:2008-07-29 00:00:00

  • Acute flaccid myelitis associated with enterovirus-D68 infection in an otherwise healthy child.

    abstract:BACKGROUND:Reporting new cases of enterovirus (EV)-D68-associated acute flaccid myelitis (AFM) is essential to understand how the virus causes neurological damage and to characterize EV-D68 strains associated with AFM. CASE PRESENTATION:A previously healthy 4-year-old boy presented with sudden weakness and limited mob...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-016-0678-0

    authors: Esposito S,Chidini G,Cinnante C,Napolitano L,Giannini A,Terranova L,Niesters H,Principi N,Calderini E

    更新日期:2017-01-11 00:00:00

  • Vaccination with dengue virus-like particles induces humoral and cellular immune responses in mice.

    abstract:BACKGROUND:The incidence of dengue, an infectious disease caused by dengue virus (DENV), has dramatically increased around the world in recent decades and is becoming a severe public health threat. However, there is currently no specific treatment for dengue fever, and licensed vaccine against dengue is not available. ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-8-333

    authors: Zhang S,Liang M,Gu W,Li C,Miao F,Wang X,Jin C,Zhang L,Zhang F,Zhang Q,Jiang L,Li M,Li D

    更新日期:2011-06-30 00:00:00

  • Virology on the Internet: the time is right for a new journal.

    abstract::Virology Journal is an exclusively on-line, Open Access journal devoted to the presentation of high-quality original research concerning human, animal, plant, insect bacterial, and fungal viruses. Virology Journal will establish a strategic alternative to the traditional virology communication process. ...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-1-1

    authors: Garry RF

    更新日期:2004-08-26 00:00:00

  • Screening and identification of B-cell epitopes within envelope protein of tembusu virus.

    abstract:BACKGROUND:Tembusu virus is a newly emerging flavivirus that caused egg-drop syndrome in ducks in China. TMUV envelope protein is a major structural protein locates at the surface of tembusu virus particle. During tembusu virus infection, envelope protein plays a pivotal role in induction of neutralizing antibody. Howe...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-018-1052-1

    authors: Zhao D,Han K,Huang X,Zhang L,Wang H,Liu N,Tian Y,Liu Q,Yang J,Liu Y,Li Y

    更新日期:2018-09-17 00:00:00

  • Replicative homeostasis II: influence of polymerase fidelity on RNA virus quasispecies biology: implications for immune recognition, viral autoimmunity and other "virus receptor" diseases.

    abstract::Much of the worlds' population is in active or imminent danger from established infectious pathogens, while sporadic and pandemic infections by these and emerging agents threaten everyone. RNA polymerases (RNApol) generate enormous genetic and consequent antigenic heterogeneity permitting both viruses and cellular pat...

    journal_title:Virology journal

    pub_type: 杂志文章,评审

    doi:10.1186/1743-422X-2-70

    authors: Sallie R

    更新日期:2005-08-22 00:00:00

  • Replicative homeostasis III: implications for antiviral therapy and mechanisms of response and non-response.

    abstract::While improved drug regimens have greatly enhanced outcomes for patients with chronic viral infection, antiviral therapy is still not ideal due to drug toxicities, treatment costs, primary drug failure and emergent resistance. New antiviral agents, alternative treatment strategies and a better understanding of viral p...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-4-29

    authors: Sallie R

    更新日期:2007-03-13 00:00:00

  • Oral vaccination with a recombinant Salmonella vaccine vector provokes systemic HIV-1 subtype C Gag-specific CD4+ Th1 and Th2 cell immune responses in mice.

    abstract:BACKGROUND:Recombinant Salmonella vaccine vectors may potentially be used to induce specific CD4+ T cell responses against foreign viral antigens. Such immune responses are required features of vaccines against pathogens such as human immunodeficiency virus type 1 (HIV-1). The aim of this study was to investigate the i...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/1743-422X-6-87

    authors: Chin'ombe N,Bourn WR,Williamson AL,Shephard EG

    更新日期:2009-06-25 00:00:00

  • Chikungunya virus infection in Cynomolgus macaques following Intradermal and aerosol exposure.

    abstract:BACKGROUND:Chikungunya virus (CHIKV) is transmitted via mosquito bite and potentially by aerosol, causing chikungunya fever and arthritic disease in humans. There are currently no licensed vaccines or antiviral therapeutics to protect against CHIKV infection in humans. Animal models recapitulating human disease, especi...

    journal_title:Virology journal

    pub_type: 杂志文章

    doi:10.1186/s12985-017-0804-7

    authors: Cirimotich CM,Vela EM,Garver J,Barnewall RE,Miller BD,Meister GT,Rogers JV

    更新日期:2017-07-20 00:00:00