Image-based assessment of plant disease progression identifies new genetic loci for resistance to Ralstonia solanacearum in tomato.

A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best strategies to control these losses is through breeding for disease resistance. One barrier to the identification of resistance genes is the quantification of disease severity, which is typically based on the determination of a subjective score by a human observer. We hypothesized that image-based, non-destructive measurements of plant morphology over an extended period after pathogen infection would capture subtle quantitative differences between genotypes, and thus enable identification of new disease resistance loci. To test this, we inoculated a genetically diverse biparental mapping population of tomato (Solanum lycopersicum) with Ralstonia solanacearum, a soilborne pathogen that causes bacterial wilt disease. We acquired over 40 000 time-series images of disease progression in this population, and developed an image analysis pipeline providing a suite of 10 traits to quantify bacterial wilt disease based on plant shape and size. Quantitative trait locus (QTL) analyses using image-based phenotyping for single and multi-traits identified QTLs that were both unique and shared compared with those identified by human assessment of wilting, and could detect QTLs earlier than human assessment. Expanding the phenotypic space of disease with image-based, non-destructive phenotyping both allowed earlier detection and identified new genetic components of resistance.

Development of an IoT-integrated multiplexed digital PCR system for quantitative detection of infectious diseases.

For rapid detection of the COVID-19 infection, the digital polymerase chain reaction (dPCR) with higher sensitivity and specificity has been presented as a promising method of point-of-care testing (POCT). Unlike the conventional real-time PCR (qPCR), the dPCR system allows absolute quantification of the target DNA without a calibration curve. Although a number of dPCR systems have previously been reported, most of these previous assays lack multiplexing capabilities. As different variants of COVID-19 have rapidly emerged, there is an urgent need for highly specific multiplexed detection systems. Additionally, the advances in the Internet of Things (IoT) technology have enabled the onsite detection of infectious diseases. Here, we present an IoT-integrated multiplexed dPCR (IM-dPCR) system involving sample compartmentalization, DNA amplification, fluorescence imaging, and quantitative analysis. This IM-dPCR system comprises three modules: a plasmonic heating-based thermal cycler, a multi-color fluorescence imaging set-up, and a firmware control module. Combined with a custom-developed smartphone application built on an IoT platform, the IM-dPCR system enabled automatic processing, data collection, and cloud storage. Using a self-priming microfluidic chip, 9 RNA groups (e.g., H1N1, H3N2, IFZ B, DENV2, DENV3, DENV4, OC43, 229E, and NL63) associated with three infectious diseases (e.g., influenza, dengue, and human coronaviruses) were analyzed with higher linearity (>98%) and sensitivity (1 copy per µL). The IM-dPCR system exhibited comparable analytical accuracy to commercial qPCR platforms. Therefore, this IM-dPCR system plays a crucial role in the onsite detection of infectious diseases.

Maize Plants Chimeric for an Autoactive Resistance Gene Display a Cell-Autonomous Hypersensitive Response but Non-Cell Autonomous Defense Signaling.

The maize gene Rp1-D21 is a mutant form of the gene Rp1-D that confers resistance to common rust. Rp1-D21 triggers a spontaneous defense response that occurs in the absence of the pathogen and includes a programed cell death called the hypersensitive response (HR). Eleven plants heterozygous for Rp1-D21, in four different genetic backgrounds, were identified that had chimeric leaves with lesioned sectors showing HR abutting green nonlesioned sectors lacking HR. The Rp1-D21 sequence derived from each of the lesioned portions of leaves was unaltered from the expected sequence whereas the Rp1-D21 sequences from nine of the nonlesioned sectors displayed various mutations, and we were unable to amplify Rp1-D21 from the other two nonlesioned sectors. In every case, the borders between the sectors were sharp, with no transition zone, suggesting that HR and chlorosis associated with Rp1-D21 activity was cell autonomous. Expression of defense response marker genes was assessed in the lesioned and nonlesioned sectors as well as in near-isogenic plants lacking and carrying Rp1-D21. Defense gene expression was somewhat elevated in nonlesioned sectors abutting sectors carrying Rp1-D21 compared with near-isogenic plants lacking Rp1-D21. This suggests that, whereas the HR itself was cell autonomous, other aspects of the defense response initiated by Rp1-D21 were not.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize).

The nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here, we report a nonsense mutation in the maize ortholog, aladin1 (ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense allele ali1-2 identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of the ali1-1 mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in maize.

Whole Root Transcriptomic Analysis Suggests a Role for Auxin Pathways in Resistance to Ralstonia solanacearum in Tomato.

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and causes significant crop loss in the Solanaceae family. The pathogen first infects roots, which are a critical source of resistance in tomato (Solanum lycopersicum L.). Roots of both resistant and susceptible plants are colonized by the pathogen, yet rootstocks can provide significant levels of resistance. Currently, mechanisms of this 'root-mediated resistance' remain largely unknown. To identify the molecular basis of this resistance, we analyzed the genome-wide transcriptional response of roots of resistant 'Hawaii 7996' and susceptible 'West Virginia 700' (WV) tomatoes at multiple timepoints after inoculation with R. solanacearum. We found that defense pathways in roots of the resistant Hawaii 7996 are activated earlier and more strongly than roots of susceptible WV. Further, auxin signaling and transport pathways are suppressed in roots of the resistant variety. Functional analysis of an auxin transport mutant in tomato revealed a role for auxin pathways in bacterial wilt. Together, our results suggest that roots mediate resistance to R. solanacearum through genome-wide transcriptomic changes that result in strong activation of defense genes and alteration of auxin pathways.

Ralstonia solanacearum Differentially Colonizes Roots of Resistant and Susceptible Tomato Plants.

Ralstonia solanacearum is the causal agent of bacterial wilt and infects over 200 plant species in 50 families. The soilborne bacterium is lethal to many solanaceous species, including tomato. Although resistant plants can carry high pathogen loads (between 105 and 108 CFU/g fresh weight), the disease is best controlled by the use of resistant cultivars, particularly resistant rootstocks. How these plants have latent infections yet maintain resistance is not clear. R. solanacearum first infects the plant through the root system and, thus, early root colonization events may be key to understanding resistance. We hypothesized that the distribution and timing of bacterial invasion differed in roots of resistant and susceptible tomato cultivars. Here, we use a combination of scanning electron microscopy and light microscopy to investigate R. solanacearum colonization in roots of soil-grown resistant and susceptible tomato cultivars at multiple time points after inoculation. Our results show that colonization of the root vascular cylinder is delayed in resistant 'Hawaii7996' and that, once bacteria enter the root vascular tissues, colonization in the vasculature is spatially restricted. Our data suggest that resistance is due, in part, to the ability of the resistant cultivar to restrict bacterial root colonization in space and time.

BSMV as a Biotemplate for Palladium Nanomaterial Synthesis.

The vast unexplored virus biodiversity makes the application of virus templates to nanomaterial synthesis especially promising. Here, a new biotemplate, Barley stripe mosaic virus (BSMV) was successfully used to synthesize organic-metal nanorods of similarly high quality to those produced with Tobacco mosaic virus (TMV). The mineralization behavior was characterized in terms of the reduction and adsorption of precursor and nanocrystal formation processes. The BSMV surface-mediated reduction of Pd(2+) proceeded via first-order kinetics in both Pd(2+) and BSMV. The adsorption equilibrium relationship of PdCl3H2O- on the BSMV surface was described by a multistep Langmuir isotherm suggesting alternative adsorbate-adsorbent interactions when compared to those on TMV. It was deduced that the first local isotherm is governed by electrostatically driven adsorption, which is then followed by sorption driven by covalent affinity of metal precursor molecules for amino acid residues. Furthermore, the total adsorption capacity of palladium species on BSMV is more than double of that on TMV. Finally, study of the BSMV-Pd particles by combining USAXS and SAXS enabled the characterization of all length scales in the synthesized nanomaterials. Results confirm the presence of core-shell cylindrical particles with 1-2 nm grains. The nanorods were uniform and monodisperse, with controllable diameters and therefore, of similar quality to those synthesized with TMV. Overall, BSMV has been confirmed as a viable alternate biotemplate with unique biomineralization behavior. With these results, the biotemplate toolbox has been expanded for the synthesis of new materials and comparative study of biomineralization processes.

Mechanisms of quantitative disease resistance in plants.

Quantitative disease resistance (QDR) causes the reduction, but not absence, of disease, and is a major type of disease resistance for many crop species. QDR results in a continuous distribution of disease scores across a segregating population, and is typically due to many genes with small effects. It may also be a source of durable resistance. The past decade has seen significant progress in cloning genes underlying QDR. In this review, we focus on these recently cloned genes and identify new themes of QDR emerging from these studies.

Mechanistic study of the hydrothermal reduction of palladium on the Tobacco mosaic virus.

The fundamental mechanisms governing reduction and growth of palladium on the genetically engineered Tobacco mosaic virus in the absence of an external reducer have been elucidated via in situ X-ray absorption spectroscopy. In recent years, many virus-inorganic materials have been synthesized as a means to produce high quality nanomaterials. However, the underlying mechanisms involved in virus coating have not been sufficiently studied to allow for directed synthesis. We combined XAS, via XANES and EXAFS analysis, with TEM to confirm an autocatalytic reduction mechanism mediated by the TMV1Cys surface. This reduction interestingly proceeds via two first order regimes which result in two linear growth regimes as spherical palladium nanoparticles are formed. By combining this result with particle growth data, it was discovered that the first regime describes growth of palladium nanoparticles on the virion while the second regime describes a second layer of larger particles which grew sporadically on the first palladium nanoparticle layer. Subsequent aggregation of free solution based spherical particles and metallized nanorods characterize a third and final regime. At the end of the second reduction regime, the average particle diameter of particles tethered to the TMV1Cys surface are approximately 4.5 nm. The use of XAS to simultaneously monitor the kinetics of biotemplated reactions along with growth of metal nanoparticles will provide insight into the pertinent reduction and growth mechanisms so that nanorod properties can be controlled through their populating nanoparticles.

Bursal transcriptome of chickens protected by DNA vaccination versus those challenged with infectious bursal disease virus.

Infectious bursal disease virus (IBDV) infection destroys the bursa of Fabricius, causing immunosuppression and rendering chickens susceptible to secondary bacterial or viral infections. IBDV large-segment-protein-expressing DNA has been shown to confer complete protection of chickens from infectious bursal disease (IBD). The purpose of the present study was to compare DNA-vaccinated chickens and unvaccinated chickens upon IBDV challenge by transcriptomic analysis of bursa regarding innate immunity, inflammation, immune cell regulation, apoptosis and glucose transport. One-day-old specific-pathogen-free chickens were vaccinated intramuscularly three times at weekly intervals with IBDV large-segment-protein-expressing DNA. Chickens were challenged orally with 8.2 × 10(2) times the egg infective dose (EID)50 of IBDV strain variant E (VE) one week after the last vaccination. Bursae collected at 0.5, 1, 3, 5, 7, and 10 days post-challenge (dpc) were subjected to real-time RT-PCR quantification of bursal transcripts related to innate immunity, inflammation, immune cell regulation, apoptosis and glucose transport. The expression levels of granzyme K and CD8 in DNA-vaccinated chickens were significantly (p < 0.05) higher than those in unvaccinated chickens upon IBDV challenge at 0.5 or 1 dpc. The expression levels of other genes involved in innate immunity, inflammation, immune cell regulation, apoptosis and glucose transport were not upregulated or downregulated in DNA-vaccinated chickens during IBDV challenge. Bursal transcripts related to innate immunity and inflammation, including TLR3, MDA5, IFN-α, IFN-ß, IRF-1, IRF-10, IL-1ß, IL-6, IL-8, iNOS, granzyme A, granzyme K and IL-10, were upregulated or significantly (p < 0.05) upregulated at 3 dpc and later in unvaccinated chickens challenged with IBDV. The expression levels of genes related to immune cell regulation, apoptosis and glucose transport, including CD4, CD8, IL-2, IFN-γ, IL-12(p40), IL-18, GM-CSF, GATA-3, p53, glucose transporter-2 and glucose transporter-3, were upregulated or significantly (p < 0.05) upregulated at 3 dpc and later in unvaccinated chickens challenged with IBDV. Taken together, the results indicate that the bursal transcriptome involved in innate immunity, inflammation, immune cell regulation, apoptosis and glucose transport, except for granzyme K and CD8, was not differentially expressed in DNA-vaccinated chickens protected from IBDV challenge.

The photosystem II oxygen-evolving complex protein PsbP interacts with the coat protein of Alfalfa mosaic virus and inhibits virus replication.

Alfalfa mosaic virus (AMV) coat protein (CP) is essential for many steps in virus replication from early infection to encapsidation. However, the identity and functional relevance of cellular factors that interact with CP remain unknown. In an unbiased yeast two-hybrid screen for CP-interacting Arabidopsis proteins, we identified several novel protein interactions that could potentially modulate AMV replication. In this report, we focus on one of the novel CP-binding partners, the Arabidopsis PsbP protein, which is a nuclear-encoded component of the oxygen-evolving complex of photosystem II. We validated the protein interaction in vitro with pull-down assays, in planta with bimolecular fluorescence complementation assays, and during virus infection by co-immunoprecipitations. CP interacted with the chloroplast-targeted PsbP in the cytosol and mutations that prevented the dimerization of CP abolished this interaction. Importantly, PsbP overexpression markedly reduced virus accumulation in infected leaves. Taken together, our findings demonstrate that AMV CP dimers interact with the chloroplast protein PsbP, suggesting a potential sequestration strategy that may preempt the generation of any PsbP-mediated antiviral state.

Phosphorylation of alfalfa mosaic virus movement protein in vivo.

The 32-kDa movement protein, P3, of alfalfa mosaic virus (AMV) is essential for cell-to-cell spread of the virus in plants. P3 shares many properties with other virus movement proteins (MPs); however, it is not known if P3 is posttranslationally modified by phosphorylation, which is important for the function of other MPs. When expressed in Nicotiana tabacum, P3 accumulated primarily in the cell walls of older leaves or in the cytosol of younger leaves. When expressed in Pischia pastoris, P3 accumulated primarily in a soluble form. Metabolic labeling indicated that a portion of P3 was phosphorylated in both tobacco and yeast, suggesting that phosphorylation regulates the function of this protein as it does for other virus MPs.

Arabidopsis thaliana is an asymptomatic host of Alfalfa mosaic virus.

The susceptibility of Arabidopsis thaliana ecotypes to infection by Alfalfa mosaic virus (AMV) was evaluated. Thirty-nine ecotypes supported both local and systemic infection, 26 ecotypes supported only local infection, and three ecotypes could not be infected. No obvious symptoms characteristic of virus infection developed on the susceptible ecotypes under standard conditions of culture. Parameters of AMV infection were characterized in ecotype Col-0, which supported systemic infection and accumulated higher levels of AMV than the symptomatic host Nicotiana tabacum. The formation of infectious AMV particles in infected Col-0 was confirmed by infectivity assays on a hypersensitive host and by electron microscopy of purified virions. Replication and transcription of AMV was confirmed by de novo synthesis of AMV subgenomic RNA in Col-0 protoplasts transfected with AMV RNA or plasmids harboring AMV cDNAs.

The importance of alfalfa mosaic virus coat protein dimers in the initiation of replication.

Deletion and substitution mutations affecting the oligomerization of alfalfa mosaic virus (AMV) coat protein (CP) were studied in protoplasts to determine their effect on genome activation, an early step in AMV replication. The CP mutants that formed dimers, CPDeltaC9 and CPC-A(R)F, were highly active in initiating replication with 63-84% of wild-type (wt) CP activity. However, all mutants that did not form dimers, CPDeltaC18, CPDeltaC19, CPC-WFP, and CPC-W, were much less active with 19-33% of wt CP activity. The accumulation and solubility of mutant CPs expressed from a virus-based vector in Nicotiana benthamiana were similar to that of wt CP. Analysis of CP-RNA interactions indicated that CP dimers and CP monomers interacted very differently with AMV RNA 3' ends. These results suggest that CP dimers are more efficient for replication than CP monomers because of differences in RNA binding rather than differences in expression and accumulation of the mutant CPs in infected cells.

Regulatory effect of cytokine production in asthma patients by SOOJI CHIM (Koryo Hand Acupuncture Therapy).

Acupuncture has become quite familiar to many Koreans not only for pain, but also for many other health problems, both in acute and chronic conditions. Actually, acupuncture is a therapeutic technique that is part of a larger system of traditional oriental medicine. There are several styles of acupuncture. We investigated the regulatory effects of cytokine production in peripheral blood of asthma patients (AP) by SOOJI CHIM (Koryo Hand Acupuncture Therapy, KHT). Clinical signs of asthma disappeared markedly by KHT. The mean interleukin (IL)-2 and IL-6 plasma levels were lower in the AP group than in the normal group, whereas the mean interferon (IFN)-gamma, IL-4, and tumor necrosis factor (TNF)-alpha levels were higher in the AP group. Plasma IFN-gamma and IL-2 levels derived from T helper (Th)1 cells and IL-4 levels derived from Th2 cells were elevated in the AP group by KHT. Especially, plasma IL-6 levels derived from Th2 cells were elevated significantly in the AP group by KHT. Reduced plasma levels of TNF-alpha were observed in the AP group by KHT. Plasma IgE levels were also measured but there were no significant differences from each other. During the KHT, there were no other adverse effects. These results indicate that KHT has a good asthma treatment effect, and that its action may be due to the regulation of cytokine production.