Metagenomic approaches used for virus diagnostics allow for rapid and accurate detection of all viral pathogens in the plants. In order to investigate the occurrence of viruses and virus-like ...organisms infecting grapevine from the Ampelographic collection Kromberk in Slovenia, we used Ion Torrent small RNA sequencing (sRNA-seq) and the VirusDetect pipeline to analyze the sRNA-seq data. The used method revealed the presence of:
(GLRaV-1),
(GLRaV-2),
(GLRaV-3),
(GRSPaV),
(GFLV) and its satellite RNA (satGFLV),
(GFkV),
(GRVFV),
(GPGV),
(GV-Sat),
(HSVd), and
(GYSVd-1). Multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for validation of sRNA-seq predicted infections, including various combinations of viruses or viroids and satellite RNA. mRT-PCR could further be used for rapid and cost-effective routine molecular diagnosis, including widespread, emerging, and seemingly rare viruses, as well as viroids which testing is usually overlooked.
The issue of distributivity of aggregation operations is crucial for many different areas such as utility theory and integration theory. Of special interest are aggregation operations with ...annihilator. This paper is focused on the problem of distributivity for some so called associative, commutative aggregation operations with annihilator
a
, known as associative a-CAOA, and uninorms. The full characterization of distributive pairs for
T
-uninorms,
S
-uninorms and bi-uninorms is given.
Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in ...several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery.
(hop) plants are hosts to several viroids among which
(HLVd) and
(CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.
•In the model precipitation system a mixture of calcite and vaterite precipitate.•The amino acids with charged side groups strongly change the precipitate.•The influence of amino acids with non-polar ...side groups is weak.•The effect of amino acids with polar side groups is similar to effect of charged AA.
Spontaneous precipitation of CaCO3 polymorphs in the presence of selected amino acids (AA) has been investigated. The l-aspartic acid (Asp), l-lysine (Lys), l-asparagine (Asn), l-tyrosine (Tyr), l-phenylalanine (Phe), l-serine (Ser) and l-alanine (Ala) were selected because of different charge and polarity of their side chains at applied experimental conditions. The investigated AA are building units of soluble macromolecules, putatively responsible for biomineralization of molluscs’ exoskeletons. It was assumed that not only the acidic, but also the polar (hydrogen bonding) AA might contribute to macromolecules’ interactions with the mineral surfaces. The mineralogical composition, structure and morphology of precipitates formed in the presence of wide range of concentrations of AA have been determined by XRD, FT-IR and EPR spectroscopy, HPLC-MS and SEM. In the reference system, without AA addition, a mixture of typical calcite rhombohedral crystals and vaterite spherulites has been observed, while AA with negatively charged or polar side chains (Asp, Tyr, Lys, Asn, Ser) significantly changed the morphology, phase composition and crystal structure of the precipitates. The effects of nonpolar AA (Phe, Ala) on the structural and morphological properties of precipitates are less pronounced. The stronger impact observed for polar AA and particularly negatively charged Asp, may be correlated with the additional electrostatic interactions of side-chain groups with mineral surfaces.
The issue of conditional distributivity, which is also known as restricted distributivity, is crucial for many different areas such as utility theory and integration theory. In the present study, we ...focus on this specific form of distributivity for continuous semi-t-operators with respect to disjunctive uninorms with continuous underlying t-norms and t-conorms. This study extends previous research by focusing on a much wider class of uninorms.
Global viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that ...still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.
Herein, upgraded chloroquine (CQ) derivatives capable of overcoming Plasmodium resistance and, at the same time, suppressing excessive immune response and risk of concurrent bacteremia were ...developed. Twelve new ferrocene–CQ hybrids tethered with a small azathia heterocycle (1,3-thiazolidin-4-one, 1,3-thiazinan-4-one, or 5-methyl-1,3-thiazolidin-4-one) were synthesized and fully characterized. All hybrids were evaluated for their in vitro antiplasmodial, antimicrobial, and immunomodulatory activities. Additional assays were performed on selected hybrids to gain insights into their mode of action. Although only hybrid 4a was more potent than the parent drug toward CQ-resistant Dd2 Plasmodium falciparum strain, several other hybrids (such as 6b, 6c, and 6d) manifested substantially improved antimicrobial and immunomodulatory properties. Interesting structure–activity relationship data were obtained, hinting at future research for the development of new multitarget chemotherapies for malaria and other infectious diseases complicated by drug resistance, bacterial co-infection, and immune-driven pathology issues.
RNA interference is an evolutionary conserved mechanism by which organisms regulate the expression of genes in a sequence-specific manner to modulate defense responses against various abiotic or ...biotic stresses. Hops are grown for their use in brewing and, in recent years, for the pharmaceutical industry. Hop production is threatened by many phytopathogens, of which
, the causal agent of Verticillium wilt, is a major contributor to yield losses. In the present study, we performed identification, characterization, phylogenetic, and expression analyses of three Argonaute, two Dicer-like, and two RNA-dependent RNA polymerase genes in the susceptible hop cultivar Celeia and the resistant cultivar Wye Target after infection with
. Phylogeny results showed clustering of hop RNAi proteins with their orthologues from the closely related species
,
and
which form a common cluster with species of the Rosaceae family. Expression analysis revealed downregulation of argonaute 2 in both cultivars on the third day post-inoculation, which may result in reduced AGO2-siRNA-mediated posttranscriptional gene silencing. Both cultivars may also repress ta-siRNA biogenesis at different dpi, as we observed downregulation of argonaute 7 in the susceptible cultivar on day 1 and downregulation of RDR6 in the resistant cultivar on day 3 after inoculation.
(
) is one of the most problematic hop (
L.) pathogens, as the highly virulent fungal pathotypes cause severe annual yield losses due to infections of entire hop fields. In recent years, the RNA ...interference (RNAi) mechanism has become one of the main areas of focus in plant-fungal pathogen interaction studies and has been implicated as one of the major contributors to fungal pathogenicity. MicroRNA-like RNAs (milRNAs) have been identified in several important plant pathogenic fungi; however, to date, no milRNA has been reported in the
species. In the present study, using a high-throughput sequencing approach and extensive bioinformatics analysis, a total of 156 milRNA precursors were identified in the annotated
genome, and 27 of these milRNA precursors were selected as true milRNA candidates, with appropriate microRNA hairpin secondary structures. The stem-loop RT-qPCR assay was used for milRNA validation; a total of nine
milRNAs were detected, and their expression was confirmed. The milRNA expression patterns, determined by the absolute quantification approach, imply that milRNAs play an important role in the pathogenicity of highly virulent
pathotypes. Computational analysis predicted milRNA targets in the
genome and in the host hop transcriptome, and the activity of milRNA-mediated RNAi target cleavage was subsequently confirmed for two selected endogenous fungal target gene models using the 5' RLM-RACE approach.
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