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.

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.

Pituitary adenylate cyclase-activating polypeptide (PACAP), a member of the secretin/glucagon/vasoactive intestinal peptide family, exerts various effects on neuronal development as mediated by the differential expression of PAC1 receptor (PAC1-R) isoforms. The expression changes of PAC1-R isoforms (Hip, Hop1) reported in correlation with retinal development suggest an isoform switch during the second postnatal week. Our aim is to determine the exact period of the isoform shift and to describe the PAC1-R-immunoreactive structures appearing from postnatal day 5 (P5) to P10 in the rat retina. The ratio of Hip and Hop1 receptors was assessed and changes in their expression were followed by Taqman and SybrGreen-based quantitative polymerase chain reaction. For the detection of PAC1-R-expressing retinal structures, anti-PAC1-R, anti-calbindin, anti-protein kinase C, anti-glutamine synthetase, anti-HPC1 and anti-Brn3a antibodies were utilized. At the transcript level, a marked decrease to an undetectable level was measured in Hip mRNA expression from P6 to P9. Hop1 expression appeared to be unchanged from P6 to P9, followed by a significant elevation at P10. A Hip/Hop1 isoform shift occurred between P6 and P7. Immunostaining showed strong PAC1-R labeling from P5 to P10 in ganglion, amacrine, horizontal and rod bipolar neurons and in glial Muller cell processes. The Hop1 isoform was predominantly expressed in various types of retinal cell beginning at P7, because of a dramatic reduction in Hip mRNA level. As the Hop1 receptor is coupled to different signaling cascades, this isoform shift might alter the physiological role of PACAP during this particular period.

Although L-glutamate is the main excitatory neurotransmitter in the retina, excess glutamate level triggers severe neuronal damages. Therefore, monosodium glutamate has been used to probe neurodegenerative mechanisms but precise toxicity schedule is not available in vivo. We report, for the first time, a temporal analysis of apoptotic processes induced by subcutaneously applied monosodium glutamate. We investigated the glutamate triggered subcellular processes over a time scale of 48 h in neonatal retina. We employed immunoblots to measure the level of activated apoptotic factors and immunocytochemistry to reveal the dying cells. Upregulation of active caspase-9 started at 3 h and peaked at 6 h post-injection. Activations of caspase-3, caspase-6 and caspase-7 consistent with their late-phase roles increased at 6 h post-injection. The apoptotic processes were terminated by 24 h post-injection. Caspase 12 and calpain-2 seemed unaffected by subcutaneous monosodium glutamate administration. Uniquely, we found that the ubiquitous calpain-1 is not expressed in newborn rat retina.