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Dr. Eva Varallyay
National Agriculture Research and Innovation Center

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0 Virus
0 agricultural biotechnology
0 high-throughput sequencing

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plant
small RNA
high-throughput sequencing
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Communication
Published: 10 June 2021 in Viruses
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Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection.

ACS Style

Emese Demian; Aliz Holczbauer; Zsuzsanna Galbacs; Nikoletta Jaksa-Czotter; Mihaly Turcsan; Robert Olah; Eva Varallyay. Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary. Viruses 2021, 13, 1119 .

AMA Style

Emese Demian, Aliz Holczbauer, Zsuzsanna Galbacs, Nikoletta Jaksa-Czotter, Mihaly Turcsan, Robert Olah, Eva Varallyay. Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary. Viruses. 2021; 13 (6):1119.

Chicago/Turabian Style

Emese Demian; Aliz Holczbauer; Zsuzsanna Galbacs; Nikoletta Jaksa-Czotter; Mihaly Turcsan; Robert Olah; Eva Varallyay. 2021. "Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary." Viruses 13, no. 6: 1119.

Journal article
Published: 16 December 2020 in Plants
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Meristem culture and somatic embryogenesis are effective tools for virus elimination of vegetatively propagated crops including grapevine (Vitis vinifera L.). While both have been shown to be useful to eliminate the main grapevine viruses, their efficiency differs depending on the virus and grapevine variety. In our work, we investigated the efficiency of these two virus elimination methods using small RNA high-throughput sequencing (HTS) and RT-PCR as virus diagnostics. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids, were selected for elimination via somatic embryogenesis (SE) and meristem culture (ME). Our results show for the first time that using SE, elimination in mother plants was effective for all viruses, i.e., grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), Grapevine virus T (GVT) and grapevine Pinot gris virus (GPGV). This study also confirms previous studies showing that SE is a possible strategy for the elimination of GFkV, GRSPaV, HSVd, and GYSVd-1. Our results demonstrate that the efficacy of virus elimination via SE is relatively high while the purging of viroids is lower. Our work provides evidence that the efficiency of SE is comparable to that of the technically difficult ME technique, and that SE will offer a more effective strategy for the production of virus-free grapevine in the future.

ACS Style

Mihaly Turcsan; Emese Demian; Tunde Varga; Nikoletta Jaksa-Czotter; Erno Szegedi; Robert Olah; Eva Varallyay. HTS-Based Monitoring of the Efficiency of Somatic Embryogenesis and Meristem Cultures Used for Virus Elimination in Grapevine. Plants 2020, 9, 1782 .

AMA Style

Mihaly Turcsan, Emese Demian, Tunde Varga, Nikoletta Jaksa-Czotter, Erno Szegedi, Robert Olah, Eva Varallyay. HTS-Based Monitoring of the Efficiency of Somatic Embryogenesis and Meristem Cultures Used for Virus Elimination in Grapevine. Plants. 2020; 9 (12):1782.

Chicago/Turabian Style

Mihaly Turcsan; Emese Demian; Tunde Varga; Nikoletta Jaksa-Czotter; Erno Szegedi; Robert Olah; Eva Varallyay. 2020. "HTS-Based Monitoring of the Efficiency of Somatic Embryogenesis and Meristem Cultures Used for Virus Elimination in Grapevine." Plants 9, no. 12: 1782.

Journal article
Published: 05 November 2020 in Scientific Reports
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Nowadays, one of the main challenges is moving towards an eco-sustainable agriculture, able to preserve the food production through a reduced use of pesticides. Current global food sustenance by intensive agriculture is mainly based on economic crop monocultures and drastically reduces the biodiversity, increasing the yield losses due to the presence of biotic and abiotic stresses. A technology based on plasma activated water (PAW), characterized by the presence in liquid of reactive oxygen and nitrogen species, was tested to try to ensure yield stability also enhancing the plant resistance responses and to promote an eco-sustainable management of plant diseases. In PAW-treated micropropagated periwinkle shoots, periwinkle and grapevine plants, qRT-PCR and small RNAs high-throughput sequencing were used to analyse the differential expression of genes involved in the major plant defence pathways. The results indicate that PAW treatment enhances the plant defence responses and provide an encouraging framework for future applications in plant disease management programs.

ACS Style

Yuri Zambon; Nicoletta Contaldo; Romolo Laurita; Eva Várallyay; Alessandro Canel; Matteo Gherardi; Vittorio Colombo; Assunta Bertaccini. Plasma activated water triggers plant defence responses. Scientific Reports 2020, 10, 1 -10.

AMA Style

Yuri Zambon, Nicoletta Contaldo, Romolo Laurita, Eva Várallyay, Alessandro Canel, Matteo Gherardi, Vittorio Colombo, Assunta Bertaccini. Plasma activated water triggers plant defence responses. Scientific Reports. 2020; 10 (1):1-10.

Chicago/Turabian Style

Yuri Zambon; Nicoletta Contaldo; Romolo Laurita; Eva Várallyay; Alessandro Canel; Matteo Gherardi; Vittorio Colombo; Assunta Bertaccini. 2020. "Plasma activated water triggers plant defence responses." Scientific Reports 10, no. 1: 1-10.

Journal article
Published: 28 July 2020 in Plants
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Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

ACS Style

György Pasztor; Zsuzsanna Galbacs N.; Tamas Kossuth; Emese Demian; Erzsebet Nadasy; Andras P. Takacs; Eva Varallyay. Millet Could Be Both a Weed and Serve as a Virus Reservoir in Crop Fields. Plants 2020, 9, 954 .

AMA Style

György Pasztor, Zsuzsanna Galbacs N., Tamas Kossuth, Emese Demian, Erzsebet Nadasy, Andras P. Takacs, Eva Varallyay. Millet Could Be Both a Weed and Serve as a Virus Reservoir in Crop Fields. Plants. 2020; 9 (8):954.

Chicago/Turabian Style

György Pasztor; Zsuzsanna Galbacs N.; Tamas Kossuth; Emese Demian; Erzsebet Nadasy; Andras P. Takacs; Eva Varallyay. 2020. "Millet Could Be Both a Weed and Serve as a Virus Reservoir in Crop Fields." Plants 9, no. 8: 954.

Journal article
Published: 31 May 2020 in Viruses
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Grapevine line pattern virus (GLPV) was first described 30 years ago in Hungary. The lack of its genomic sequences and of an available antiserum made its detection impossible in other parts of the world. Three different high-throughput sequencing (HTS) protocols applied on a GLPV-infected vine allowed the construction of the full genome sequence of this virus. It includes three RNA segments, encoding four proteins: methyltransferase-helicase (1a), RNA-dependent RNA polymerase (2a), movement protein (3a) and coat protein (3b). The obtained sequences were used to design specific primers for its detection by RT-PCR and Northern blot hybridization, respectively. These diagnostic methods were used to test the presence of GLPV in graft-inoculated plants and in 220 grapevine accessions of different Mediterranean origins. The three RNAs-encoding proteins of GLPV shared a very high amino acid identity with those of hop yellow virus, a tentative member of the Anulavirus genus, leaving no doubt that both are two isolates of the same viral species. A circular RNA originating from the RNA2 was found, for which an alternative silencing suppressor role is hypothesized. Further investigation is needed to determine this possibility and also the host range and pathological significance of the virus.

ACS Style

Toufic Elbeaino; Levente Kontra; Emese Demian; Nikoletta Jaksa-Czotter; Amani Ben Slimen; Richard Fabian; Janos Lazar; Lucie Tamisier; Michele Digiaro; Sebastien Massart; Eva Varallyay. Complete Sequence, Genome Organization and Molecular Detection of Grapevine Line Pattern Virus, a New Putative Anulavirus Infecting Grapevine. Viruses 2020, 12, 1 .

AMA Style

Toufic Elbeaino, Levente Kontra, Emese Demian, Nikoletta Jaksa-Czotter, Amani Ben Slimen, Richard Fabian, Janos Lazar, Lucie Tamisier, Michele Digiaro, Sebastien Massart, Eva Varallyay. Complete Sequence, Genome Organization and Molecular Detection of Grapevine Line Pattern Virus, a New Putative Anulavirus Infecting Grapevine. Viruses. 2020; 12 (6):1.

Chicago/Turabian Style

Toufic Elbeaino; Levente Kontra; Emese Demian; Nikoletta Jaksa-Czotter; Amani Ben Slimen; Richard Fabian; Janos Lazar; Lucie Tamisier; Michele Digiaro; Sebastien Massart; Eva Varallyay. 2020. "Complete Sequence, Genome Organization and Molecular Detection of Grapevine Line Pattern Virus, a New Putative Anulavirus Infecting Grapevine." Viruses 12, no. 6: 1.

Article
Published: 06 February 2020 in European Journal of Plant Pathology
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Grapevine can be infected by several viruses and viroids, the presence of which can lead to yield losses and vineyard decline. Our previous survey of vineyards in Hungary suggested that viral infection originates from infected propagation material. To investigate whether rootstocks can be a source of virus infections, we surveyed seventeen rootstock vineyards and two rootstock collections in Hungary to determine the virome by high-throughput sequencing of small RNAs. The presence of the viruses was also tested by RT-PCR. The results showed that viruses whose presence is routinely checked were almost absent in rootstock vineyards but were present in rootstock genotype collections. Moreover, first the time in Hungary, we detected the presence of Australian grapevine viroid in the rootstock genotype collection at Pecs. In contrast, viruses that are not regulated or not routinely tested, namely, grapevine rupestris stem-pitting-associated virus, grapevine Syrah virus-1 and grapevine Pinot gris virus, were detected in almost all locations in most of the varieties. The presence and absence of infected rootstock genotypes in the same vineyard together with phylogenetic analysis suggested that viral infections originated from infected propagation material. Moreover, we found the symptomatic variant of grapevine Pinot gris virus in several rootstock vineyards without symptoms, suggesting the possibility for leaf mottling and deformation disease symptoms to manifest on susceptible cultivars following grafting onto these rootstocks.

ACS Style

Emese Demian; Nikoletta Jaksa-Czotter; Janos Molnar; Gabor E. Tusnady; Laszlo Kocsis; Eva Varallyay. Grapevine rootstocks can be a source of infection with non-regulated viruses. European Journal of Plant Pathology 2020, 156, 897 -912.

AMA Style

Emese Demian, Nikoletta Jaksa-Czotter, Janos Molnar, Gabor E. Tusnady, Laszlo Kocsis, Eva Varallyay. Grapevine rootstocks can be a source of infection with non-regulated viruses. European Journal of Plant Pathology. 2020; 156 (3):897-912.

Chicago/Turabian Style

Emese Demian; Nikoletta Jaksa-Czotter; Janos Molnar; Gabor E. Tusnady; Laszlo Kocsis; Eva Varallyay. 2020. "Grapevine rootstocks can be a source of infection with non-regulated viruses." European Journal of Plant Pathology 156, no. 3: 897-912.

Research article
Published: 03 May 2019 in PLOS ONE
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Viruses have different strategies for infecting their hosts. Fast and acute infections result in the development of severe symptoms and may cause the death of the plant. By contrast, in a persistent interaction, the virus can survive within its host for a long time, inducing only mild symptoms. In this study, we investigated the gene expression changes induced in CymRSV-, crTMV-, and TCV-infected Nicotiana benthamiana and in PVX- and TMV-U1-infected Solanum lycopersicum plants after the systemic spread of the virus by two different high-throughput methods: microarray hybridization or RNA sequencing. Using these techniques, we were able to clearly differentiate between acute and persistent infections. We validated the gene expression changes of selected genes by Northern blot hybridization or by qRT-PCR. We show that, in contrast to persistent infections, the drastic shut-off of housekeeping genes, downregulation of photosynthesis-related transcripts and induction of stress genes are specific outcomes with acute infections. We also show that these changes are not a consequence of host necrosis or the presence of a viral silencing suppressor. Thermal imaging data and chlorophyll fluorescence measurements correlated very well with the molecular changes. We believe that the molecular and physiological changes detected during acute infections mostly contribute to virus symptom development. The observed characteristic physiological changes associated with economically more dangerous acute infections could serve as a basis for the elaboration of remote monitoring systems suitable for detecting developing virus infections in crops. Moreover, as molecular and physiological changes are characteristics of different types of virus lifestyles, this knowledge can support risk assessments of recently described novel viruses.

ACS Style

Réka Pesti; Levente Kontra; Kenny Paul; Imre Vass; Tibor Csorba; Zoltán Havelda; Éva Várallyay. Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences. PLOS ONE 2019, 14, e0216618 .

AMA Style

Réka Pesti, Levente Kontra, Kenny Paul, Imre Vass, Tibor Csorba, Zoltán Havelda, Éva Várallyay. Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences. PLOS ONE. 2019; 14 (5):e0216618.

Chicago/Turabian Style

Réka Pesti; Levente Kontra; Kenny Paul; Imre Vass; Tibor Csorba; Zoltán Havelda; Éva Várallyay. 2019. "Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences." PLOS ONE 14, no. 5: e0216618.

Journal article
Published: 01 January 2019 in Phytopathogenic Mollicutes
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ACS Style

Yuri Zambon; Nicoletta Contaldo; Assunta Bertaccini; Eva Varallyay. Small RNA profiling of aster yellows infected Catharanthus roseus plants. Phytopathogenic Mollicutes 2019, 9, 131 .

AMA Style

Yuri Zambon, Nicoletta Contaldo, Assunta Bertaccini, Eva Varallyay. Small RNA profiling of aster yellows infected Catharanthus roseus plants. Phytopathogenic Mollicutes. 2019; 9 (1):131.

Chicago/Turabian Style

Yuri Zambon; Nicoletta Contaldo; Assunta Bertaccini; Eva Varallyay. 2019. "Small RNA profiling of aster yellows infected Catharanthus roseus plants." Phytopathogenic Mollicutes 9, no. 1: 131.

Communication
Published: 11 June 2018 in Viruses
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Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.

ACS Style

Dániel Baráth; Nikoletta Jaksa-Czotter; János Molnár; Tünde Varga; Júlia Balássy; Luca Krisztina Szabó; Zoltán Kirilla; Gábor E. Tusnády; Éva Preininger; Eva Varallyay. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses 2018, 10, 318 .

AMA Style

Dániel Baráth, Nikoletta Jaksa-Czotter, János Molnár, Tünde Varga, Júlia Balássy, Luca Krisztina Szabó, Zoltán Kirilla, Gábor E. Tusnády, Éva Preininger, Eva Varallyay. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses. 2018; 10 (6):318.

Chicago/Turabian Style

Dániel Baráth; Nikoletta Jaksa-Czotter; János Molnár; Tünde Varga; Júlia Balássy; Luca Krisztina Szabó; Zoltán Kirilla; Gábor E. Tusnády; Éva Preininger; Eva Varallyay. 2018. "Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary." Viruses 10, no. 6: 318.

Protocol
Published: 01 March 2018 in Methods in Molecular Biology
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Woody perennial plants like grapevine and fruit trees can be infected by several viruses even as multiple infections. Since they are propagated vegetatively, the phytosanitary status of the propagation material (both the rootstock and the variety) can have a profound effect on the lifetime and health of the new plantations. The fast evolution of sequencing techniques provides a new opportunity for metagenomics-based viral diagnostics. Viral derived small RNAs produced by the host immune system during viral infection can be sequenced by next-generation techniques and analyzed for the presence of viruses, revealing the presence of all known viral pathogens in the sample. This method is based on Illumina sequencing of short RNAs and bioinformatics analysis of virus-derived small RNAs in the host. Here we describe a protocol for this challenging technique step by step with notes, in order to ensure success for every user.

ACS Style

Nikoletta Czotter; János Molnár; Réka Pesti; Emese Demián; Dániel Baráth; Tünde Varga; Éva Várallyay. Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections. Methods in Molecular Biology 2018, 1746, 115 -130.

AMA Style

Nikoletta Czotter, János Molnár, Réka Pesti, Emese Demián, Dániel Baráth, Tünde Varga, Éva Várallyay. Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections. Methods in Molecular Biology. 2018; 1746 ():115-130.

Chicago/Turabian Style

Nikoletta Czotter; János Molnár; Réka Pesti; Emese Demián; Dániel Baráth; Tünde Varga; Éva Várallyay. 2018. "Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections." Methods in Molecular Biology 1746, no. : 115-130.

Original research article
Published: 06 February 2018 in Frontiers in Microbiology
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As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

ACS Style

Nikoletta Czotter; Janos Molnar; Emese Szabó; Emese Demian; Levente Kontra; Ivett Baksa; Gyorgy Szittya; Laszlo Kocsis; Tamás Deák; Gyorgy Bisztray; Gabor E. Tusnady; Jozsef Burgyan; Eva Varallyay. NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards. Frontiers in Microbiology 2018, 9, 122 .

AMA Style

Nikoletta Czotter, Janos Molnar, Emese Szabó, Emese Demian, Levente Kontra, Ivett Baksa, Gyorgy Szittya, Laszlo Kocsis, Tamás Deák, Gyorgy Bisztray, Gabor E. Tusnady, Jozsef Burgyan, Eva Varallyay. NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards. Frontiers in Microbiology. 2018; 9 ():122.

Chicago/Turabian Style

Nikoletta Czotter; Janos Molnar; Emese Szabó; Emese Demian; Levente Kontra; Ivett Baksa; Gyorgy Szittya; Laszlo Kocsis; Tamás Deák; Gyorgy Bisztray; Gabor E. Tusnady; Jozsef Burgyan; Eva Varallyay. 2018. "NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards." Frontiers in Microbiology 9, no. : 122.

Published erratum
Published: 01 June 2017 in The EMBO Journal
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ACS Style

Eva Varallyay; Anna Válóczi; Ákos Ágyi; József Burgyán; Zoltan Havelda. Plant virus‐mediated induction of miR168 is associated with repression of ARGONAUTE 1 accumulation. The EMBO Journal 2017, 36, 1641 -1642.

AMA Style

Eva Varallyay, Anna Válóczi, Ákos Ágyi, József Burgyán, Zoltan Havelda. Plant virus‐mediated induction of miR168 is associated with repression of ARGONAUTE 1 accumulation. The EMBO Journal. 2017; 36 (11):1641-1642.

Chicago/Turabian Style

Eva Varallyay; Anna Válóczi; Ákos Ágyi; József Burgyán; Zoltan Havelda. 2017. "Plant virus‐mediated induction of miR168 is associated with repression of ARGONAUTE 1 accumulation." The EMBO Journal 36, no. 11: 1641-1642.

Journal article
Published: 09 June 2016 in Archives of Virology
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Virus-induced gene silencing (VIGS) uses recombinant viruses to study gene function; however, the effect of the virus vector itself on the gene expression of the host is not always considered. In our work, we investigated non-targeted gene expression changes of the host in order to see how often these changes appear. Effects of various VIGS vector infections were analysed by monitoring gene expression levels of housekeeping genes by Northern blot analysis in four different hosts. We found that non-targeted changes happens very often. More importantly, these non-targeted effects can cause drastic changes in the gene-expression pattern of host genes that are usually used as references in these studies. We have also found that in a tobacco rattle virus (TRV)-based VIGS, the presence of foreign sequences in the cloning site of the vector can also have a non-targeted effect, and even the use of an internal control can lead to unpredicted changes. Our results show that although VIGS is a very powerful technique, the VIGS vector, as a pathogen of the host, can cause unwanted changes in its gene-expression pattern, highlighting the importance of careful selection of both the genes to be tested and those to be used as references in the planned experiments.

ACS Style

Enikő Oláh; Réka Pesti; Dénes Taller; Zoltán Havelda; Éva Várallyay. Non-targeted effects of virus-induced gene silencing vectors on host endogenous gene expression. Archives of Virology 2016, 161, 2387 -2393.

AMA Style

Enikő Oláh, Réka Pesti, Dénes Taller, Zoltán Havelda, Éva Várallyay. Non-targeted effects of virus-induced gene silencing vectors on host endogenous gene expression. Archives of Virology. 2016; 161 (9):2387-2393.

Chicago/Turabian Style

Enikő Oláh; Réka Pesti; Dénes Taller; Zoltán Havelda; Éva Várallyay. 2016. "Non-targeted effects of virus-induced gene silencing vectors on host endogenous gene expression." Archives of Virology 161, no. 9: 2387-2393.

Journal article
Published: 31 May 2016 in Genome Medicine
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IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which primarily occurs during inflammatory responses. The signaling pathways defining the genome-wide microRNA expression profile as well as the cellular functions controlled by microRNAs during alternative macrophage activation are largely unknown. Hence, in the current work we examined the regulation and function of IL-4-regulated microRNAs in human and mouse alternative macrophage activation. We utilized microarray-based microRNA profiling to detect the dynamic expression changes during human monocyte-macrophage differentiation and IL-4-mediated alternative macrophage activation. The expression changes and upstream regulatory pathways of selected microRNAs were further investigated in human and mouse in vitro and in vivo models of alternative macrophage activation by integrating small RNA-seq, ChIP-seq, ChIP-quantitative PCR, and gene expression data. MicroRNA-controlled gene networks and corresponding functions were identified using a combination of transcriptomic, bioinformatic, and functional approaches. The IL-4-controlled microRNA expression pattern was identified in models of human and mouse alternative macrophage activation. IL-4-dependent induction of miR-342-3p and repression of miR-99b along with miR-125a-5p occurred in both human and murine macrophages in vitro. In addition, a similar expression pattern was observed in peritoneal macrophages of Brugia malayi nematode-implanted mice in vivo. By using IL4Rα- and STAT6-deficient macrophages, we were able to show that IL-4-dependent regulation of miR-342-3p, miR-99b, and miR-125a-5p is mediated by the IL-4Rα-STAT6 signaling pathway. The combination of gene expression studies and chromatin immunoprecipitation experiments demonstrated that both miR-342-3p and its host gene, EVL, are coregulated directly by STAT6. Finally, we found that miR-342-3p is capable of controlling macrophage survival through targeting an anti-apoptotic gene network including Bcl2l1. Our findings identify a conserved IL-4/STAT6-regulated microRNA signature in alternatively activated human and mouse macrophages. Moreover, our study indicates that miR-342-3p likely plays a pro-apoptotic role in such cells, thereby providing a negative feedback arm to IL-4-dependent macrophage proliferation.

ACS Style

Zsolt Czimmerer; Tamas Varga; Máté Kiss; Cesaré Ovando Vázquez; Quang Minh Doan-Xuan; Minik Rückerl; Sudhir Gopal Tattikota; Xin Yan; Zsuzsanna S. Nagy; Bence Dániel; Szilard Poliska; Attila Horváth; Gergely Nagy; Eva Varallyay; Matthew N. Poy; Judith Allen; Zsolt Bacsó; Cei Abreu-Goodger; Laszlo Nagy. The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p. Genome Medicine 2016, 8, 63 .

AMA Style

Zsolt Czimmerer, Tamas Varga, Máté Kiss, Cesaré Ovando Vázquez, Quang Minh Doan-Xuan, Minik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna S. Nagy, Bence Dániel, Szilard Poliska, Attila Horváth, Gergely Nagy, Eva Varallyay, Matthew N. Poy, Judith Allen, Zsolt Bacsó, Cei Abreu-Goodger, Laszlo Nagy. The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p. Genome Medicine. 2016; 8 (1):63.

Chicago/Turabian Style

Zsolt Czimmerer; Tamas Varga; Máté Kiss; Cesaré Ovando Vázquez; Quang Minh Doan-Xuan; Minik Rückerl; Sudhir Gopal Tattikota; Xin Yan; Zsuzsanna S. Nagy; Bence Dániel; Szilard Poliska; Attila Horváth; Gergely Nagy; Eva Varallyay; Matthew N. Poy; Judith Allen; Zsolt Bacsó; Cei Abreu-Goodger; Laszlo Nagy. 2016. "The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p." Genome Medicine 8, no. 1: 63.

Journal article
Published: 01 December 2015 in BMC Genomics
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Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.

ACS Style

Ivett Baksa; Tibor Nagy; Endre Barta; Zoltán Havelda; Éva Várallyay; Dániel Silhavy; József Burgyán; György Szittya. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics 2015, 16, 1 -21.

AMA Style

Ivett Baksa, Tibor Nagy, Endre Barta, Zoltán Havelda, Éva Várallyay, Dániel Silhavy, József Burgyán, György Szittya. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics. 2015; 16 (1):1-21.

Chicago/Turabian Style

Ivett Baksa; Tibor Nagy; Endre Barta; Zoltán Havelda; Éva Várallyay; Dániel Silhavy; József Burgyán; György Szittya. 2015. "Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis." BMC Genomics 16, no. 1: 1-21.

Journal article
Published: 30 July 2015 in Molecular Plant Pathology
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Infection of Wheat dwarf virus (WDV) strains on barley results in dwarf disease, imposing severe economic losses on crop production. As the natural resistance resources against this virus are limited, it is imperative to elaborate a biotechnological approach that will provide effective and safe immunity to a wide range of WDV strains. Because vector insect‐mediated WDV infection occurs during cool periods in nature, it is important to identify a technology which is effective at lower temperature. In this study, we designed artificial microRNAs (amiRNAs) using a barley miRNA precursor backbone, which target different conservative sequence elements of the WDV strains. Potential amiRNA sequences were selected to minimize the off‐target effects and were tested in a transient sensor system in order to select the most effective constructs at low temperature. On the basis of the data obtained, a polycistronic amiRNA precursor construct (VirusBuster171) was built expressing three amiRNAs simultaneously. The construct was transformed into barley under the control of a constitutive promoter. The transgenic lines were kept at 12–15 °C to mimic autumn and spring conditions in which major WDV infection and accumulation take place. We were able to establish a stable barley transgenic line displaying resistance to insect‐mediated WDV infection. Our study demonstrates that amiRNA technology can be an efficient tool for the introduction of highly efficient resistance in barley against a DNA virus belonging to the Geminiviridae family, and this resistance is effective at low temperature where the natural insect vector mediates the infection process.

ACS Style

András Kis; Gergely Tholt; Milán Ivanics; Eva Varallyay; Barnabás Jenes; Zoltán Havelda. Polycistronic artificial miRNA-mediated resistance toWheat dwarf virusin barley is highly efficient at low temperature. Molecular Plant Pathology 2015, 17, 427 -437.

AMA Style

András Kis, Gergely Tholt, Milán Ivanics, Eva Varallyay, Barnabás Jenes, Zoltán Havelda. Polycistronic artificial miRNA-mediated resistance toWheat dwarf virusin barley is highly efficient at low temperature. Molecular Plant Pathology. 2015; 17 (3):427-437.

Chicago/Turabian Style

András Kis; Gergely Tholt; Milán Ivanics; Eva Varallyay; Barnabás Jenes; Zoltán Havelda. 2015. "Polycistronic artificial miRNA-mediated resistance toWheat dwarf virusin barley is highly efficient at low temperature." Molecular Plant Pathology 17, no. 3: 427-437.

Journal article
Published: 01 October 2013 in Genetics
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The first microRNAs were discovered some 20 years ago, but only a small fraction of the microRNA-encoding genes have been described in detail yet. Here we report the molecular analysis of a computationally predicted Drosophila melanogaster microRNA gene, mir-282. We show that the mir-282 gene is the source of a 4.9-kb-long primary transcript with a 5′ cap and a 3′-poly(A) sequence and a mature microRNA of ∼25 bp. Our data strongly suggest the existence of an independent mir-282 gene conserved in holometabolic insects. We give evidence that the mir-282 locus encodes a functional transcript that influences viability, longevity, and egg production in Drosophila. We identify the nervous system-specific adenylate cyclase (rutabaga) as a target of miR-282 and assume that one of the main functions of mir-282 is the regulation of adenylate cyclase activity in the nervous system during metamorphosis.

ACS Style

Péter Vilmos; Ágnes Bujna; Milán Szuperák; Zoltan Havelda; Eva Varallyay; János Szabad; Lucie Kucerova; Kálmán Somogyi; Ildikó Kristó; Tamás Lukácsovich; Ferenc Jankovics; Laszlo Henn; Miklós Erdélyi. Viability, Longevity, and Egg Production of Drosophila melanogaster Are Regulated by the miR-282 microRNA. Genetics 2013, 195, 469 -480.

AMA Style

Péter Vilmos, Ágnes Bujna, Milán Szuperák, Zoltan Havelda, Eva Varallyay, János Szabad, Lucie Kucerova, Kálmán Somogyi, Ildikó Kristó, Tamás Lukácsovich, Ferenc Jankovics, Laszlo Henn, Miklós Erdélyi. Viability, Longevity, and Egg Production of Drosophila melanogaster Are Regulated by the miR-282 microRNA. Genetics. 2013; 195 (2):469-480.

Chicago/Turabian Style

Péter Vilmos; Ágnes Bujna; Milán Szuperák; Zoltan Havelda; Eva Varallyay; János Szabad; Lucie Kucerova; Kálmán Somogyi; Ildikó Kristó; Tamás Lukácsovich; Ferenc Jankovics; Laszlo Henn; Miklós Erdélyi. 2013. "Viability, Longevity, and Egg Production of Drosophila melanogaster Are Regulated by the miR-282 microRNA." Genetics 195, no. 2: 469-480.

Journal article
Published: 20 September 2013 in Nucleic Acids Research
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Plant viruses ubiquitously mediate the induction of miR168 trough the activities of viral suppressors of RNA silencing (VSRs) controlling the accumulation of ARGONAUTE1 (AGO1), one of the main components of RNA silencing based host defence system. Here we used a mutant Tombusvirus p19 VSR (p19-3M) disabled in its main suppressor function, small interfering RNA (siRNA) binding, to investigate the biological role of VSR-mediated miR168 induction. Infection with the mutant virus carrying p19-3M VSR resulted in suppressed recovery phenotype despite the presence of free virus specific siRNAs. Analysis of the infected plants revealed that the mutant p19-3M VSR is able to induce miR168 level controlling the accumulation of the antiviral AGO1, and this activity is associated with the enhanced accumulation of viral RNAs. Moreover, saturation of the siRNA-binding capacity of p19 VSR mediated by defective interfering RNAs did not influence the miR168-inducing activity. Our data indicate that p19 VSR possesses two independent silencing suppressor functions, viral siRNA binding and the miR168-mediated AGO1 control, both of which are required to efficiently cope with the RNA-silencing based host defence. This finding suggests that p19 VSR protein evolved independent parallel capacities to block the host defence at multiple levels.

ACS Style

Éva Várallyay; Enikő Oláh; Zoltán Havelda. Independent parallel functions of p19 plant viral suppressor of RNA silencing required for effective suppressor activity. Nucleic Acids Research 2013, 42, 599 -608.

AMA Style

Éva Várallyay, Enikő Oláh, Zoltán Havelda. Independent parallel functions of p19 plant viral suppressor of RNA silencing required for effective suppressor activity. Nucleic Acids Research. 2013; 42 (1):599-608.

Chicago/Turabian Style

Éva Várallyay; Enikő Oláh; Zoltán Havelda. 2013. "Independent parallel functions of p19 plant viral suppressor of RNA silencing required for effective suppressor activity." Nucleic Acids Research 42, no. 1: 599-608.

Journal article
Published: 11 April 2013 in Molecular Plant Pathology
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Various plant viruses ubiquitously mediate the induction of miR168, resulting in the control of ARGONAUTE 1 (AGO1), which is the pivotal component of the microRNA (miRNA) regulation pathway and can also exhibit antiviral function. Here, we demonstrate that miR168-driven control of AGO1 can persist for a long time in virus-infected plants and can be an important component of symptom development. We also show that infection of RNA viruses belonging to various genera is associated with the transcriptional induction of the MIR168 precursor gene. Moreover, in a transient expression study, we reveal that different unrelated viral suppressors of RNA silencing (VSRs) are responsible for the enhanced accumulation of miR168. The induction of miR168 accumulation is an early function of VSRs and this activity is associated with the control of the endogenous AGO1 protein level. The common ability of unrelated VSRs to induce the miR168 level implies that this activity might be a component of the host defence suppression in plant-virus interactions.

ACS Style

Eva Varallyay; Zoltán Havelda. Unrelated viral suppressors of RNA silencing mediate the control of ARGONAUTE1 level. Molecular Plant Pathology 2013, 14, 567 -575.

AMA Style

Eva Varallyay, Zoltán Havelda. Unrelated viral suppressors of RNA silencing mediate the control of ARGONAUTE1 level. Molecular Plant Pathology. 2013; 14 (6):567-575.

Chicago/Turabian Style

Eva Varallyay; Zoltán Havelda. 2013. "Unrelated viral suppressors of RNA silencing mediate the control of ARGONAUTE1 level." Molecular Plant Pathology 14, no. 6: 567-575.

Research article
Published: 31 January 2013 in PLOS ONE
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Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. These novel findings aim for new detection methods for the individual short regulatory RNA-s in order to be able to confirm the primary data and characterize newly identified subtypes in different biological conditions. We have developed a flexible method to design RT-qPCR assays that are very sensitive and robust. The newly designed assays were tested extensively in samples from plant, mouse and even human formalin fixed paraffin embedded tissues. Moreover, we have shown that these assays are able to quantify endogenously generated shRNA molecules. The assay design method is freely available for anyone who wishes to use a robust and flexible system for the quantitative analysis of matured regulatory RNA-s.

ACS Style

Zsolt Czimmerer; Julianna Hulvely; Zoltan Simandi; Eva Varallyay; Zoltan Havelda; Erzsebet Szabo; Attila Varga; Balazs Dezso; Maria Balogh; Attila Horvath; Balint Domokos; Zsolt Torok; Laszlo Nagy; Balint Balint. A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules. PLOS ONE 2013, 8, e55168 .

AMA Style

Zsolt Czimmerer, Julianna Hulvely, Zoltan Simandi, Eva Varallyay, Zoltan Havelda, Erzsebet Szabo, Attila Varga, Balazs Dezso, Maria Balogh, Attila Horvath, Balint Domokos, Zsolt Torok, Laszlo Nagy, Balint Balint. A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules. PLOS ONE. 2013; 8 (1):e55168.

Chicago/Turabian Style

Zsolt Czimmerer; Julianna Hulvely; Zoltan Simandi; Eva Varallyay; Zoltan Havelda; Erzsebet Szabo; Attila Varga; Balazs Dezso; Maria Balogh; Attila Horvath; Balint Domokos; Zsolt Torok; Laszlo Nagy; Balint Balint. 2013. "A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules." PLOS ONE 8, no. 1: e55168.