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Nucleotide-binding domain leucine-rich repeat (NLR) immune receptors are important components of plant and metazoan innate immunity that can function as individual units or as pairs or networks. Upon activation, NLRs form multiprotein complexes termed resistosomes or inflammasomes. Although metazoan paired NLRs, such as NAIP/NLRC4, form hetero-complexes upon activation, the molecular mechanisms underpinning activation of plant paired NLRs, especially whether they associate in resistosome hetero-complexes, is unknown. In asterid plant species, the NLR required for cell death (NRC) immune receptor network is composed of multiple resistance protein sensors and downstream helpers that confer immunity against diverse plant pathogens. Here, we show that pathogen effector-activation of the NLR proteins Rx (confers virus resistance), and Bs2 (confers bacterial resistance) leads to oligomerization of their helper NLR, NRC2. Activated Rx does not oligomerize or enter into a stable complex with the NRC2 oligomer and remains cytoplasmic. In contrast, activated NRC2 oligomers accumulate in membrane-associated puncta. We propose an activation-and-release model for NLRs in the NRC immune receptor network. This points to a distinct activation model compared with mammalian paired NLRs. more...

Parasites counteract host immunity by suppressing helper NLR proteins that function as central nodes in immune receptor networks. Understanding the mechanisms of immunosuppression can lead to strategies for bioengineering disease resistance. Here, we show that a cyst nematode virulence effector binds and inhibits oligomerization of the helper NLR protein NRC2 by physically preventing intramolecular rearrangements required for activation. A single amino acid polymorphism at the binding interface between NRC2 and the inhibitor is sufficient for this helper NLR to evade immune suppression, thereby restoring the activity of multiple disease resistance genes. This points to a novel strategy for resurrecting disease resistance in crop genomes.One sentence summaryA helper NLR is mutated to evade inhibition by a parasite effector. more...

Nanoparticles of Zn0.85Al0.15Te and Pb0.98Na0.02Te were used as the starting materials to prepare p-type Pb0.833Na0.017(Zn0.85Al0.15)0.15Te-Te composite. The resulting powder was densified, sintered at 380 °C for 24 h in an evacuated and encapsulated ampoule and its thermoelectric transport property was characterized between 300 K and 600 K. At 300 K, the electrical resistivity of Pb0.833Na0.017(Zn0.85Al0.15)0.15Te-Te composite is 4.2 mΩ-cm; exhibits nonmetal-like behavior from 300 K to 375 K and degenerate behavior beyond 375 K. The temperature dependence of the electrical conductivity shows deviation from the normal power law (1/Tδ, δ ≈ 1.84–2.27 for lead chalcogenides), suggesting a sharp drop in mobility in 425 K–600 K which is ascribed to defects, grain boundaries, and potential energy fluctuation due to atomic disorders. The maximum thermopower of Pb0.833Na0.017(Zn0.85Al0.15)0.15Te-Te is 400 μVK-1 at 600 K. Assuming acoustic phonon scattering is the dominant mechanism, we calculate the reduced Fermi energy and Lorenz numbers and compare them with other materials. As-calculated Lorenz numbers is used to estimate the lattice thermal conductivity, which is 11% lower than the total thermal conductivity at 300 K. The lattice thermal conductivity varies as κL ~ T-0.46 proving the presence of grain boundary scattering, dislocations, and alloy scattering. The maximum power factor (P.F.) of 17.7 μWcm-1K-2 is observed at 400 K. Finally, the Pb0.833Na0.017(Zn0.85Al0.15)0.15Te-Te composite exhibits a dimensionless figure-of-merit (zT) of 1.08 at 600 K, demonstrating the material from the current study can compete with many high performing PbTe-based materials. more...

A series of Pb1-y(Zn0.85Al0.15)yTe-Te nanocomposites (y = 0, 0.04, 0.06, 0.08, and 0.11) was fabricated by hydrothermal synthesis of PbTe and Zn0.85Al0.15Te nanoparticles separately, followed by intimate mixing, pressing, and sintering in evacuated-and-encapsulated Pyrex ampoules at 380 °C for 12 h. Thermoelectric properties were characterized from 120-600 K. With increasing Zn content, the peak thermopower shifts to higher temperatures, Hall carrier concentration increases, and the lattice thermal conductivity decreases. As compared to the pristine PbTe, thermoelectric properties of Pb1-y(Zn0.85Al0.15)yTe-Te nanocomposites have improved considerably. The y = 0.11 sample exhibits the highest zT ~1 comparable to the state-of-the-art p-type PbTe-based materials. The enhanced zT is ascribed to reduced thermal conductivity, elevated electrical conductivity and thermopower. This unique new method of material synthesis and doping is very promising to obtain high-performance thermoelectric materials in addition to tuning their nanostructures. more...

Nicotiana benthamiana has emerged as a complementary experimental system to Arabidopsis thaliana. It enables fast-forward in vivo analyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of nucleotide-binding leucine-rich repeat (NLR) plant immune receptors has greatly advanced following the discovery of the Arabidopsis HOPZ-ACTIVATED RESISTANCE1 (ZAR1) resistosome. Here, we describe a vector system of 72 plasmids that enables functional studies of the ZAR1 resistosome in N. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs (CC-NLRs) for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as the N. benthamiana ortholog of Arabidopsis ZAR1. Effector-activated and autoactive NbZAR1 triggers the cell death response in N. benthamiana and this activity is dependent on a functional N-terminal α1 helix. C-terminally tagged NbZAR1 remains functional in N. benthamiana, thus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source pZA plasmid collection forms an additional experimental system to Arabidopsis for in planta resistosome studies. more...

Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/. more...

Together with pathogenic microbes and herbivorous insects, parasitic plants are emerging as aggressive threats on agriculture worldwide. Among them, Cuscuta (dodder), a stem holoparasite, extracts nutrients and water from host plants through phloem feeding. Dodder is parasitic on a very wide variety of plants, including a number of important agricultural and horticultural crops such as alfalfa, clover, tomatoes, and potatoes. Dodder infestations cause major economic concerns, including crop yield reduction and cost increase of crop harvesting. Understanding resistance mechanisms against dodder can provide potential solutions to effectively control dodder infestations. more...

NLR immune receptors form one of the most diverse protein families in flowering plants (angiosperms). NLRs have massively expanded through birth-and-death evolution and typically exhibit hallmarks of rapid evolution even at the intraspecific level. Here, we reconstructed the evolutionary history of ZAR1, an atypically conserved NLR that traces its origin to early angiosperm lineages ~220 to 150 million years ago (Jurassic period). We used iterative sequence similarity searches coupled with phylogenetic analyses to determine the degree to which ZAR1 orthologs and paralogs occur in plants. We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colacasia esculenta, the magnoliid Cinnamomum micranthum and the majority of eudicots, notably the early diverging eudicot species Aquilegia coerulea. Analyses of the ortholog sequences revealed highly conserved features of ZAR1, including regions for pathogen effector recognition, intramolecular interactions and cell death activation. This also uncovered a new conserved surface on the underside of the activated ZAR1 resistosome wheel. Throughout its evolution, ZAR1 also acquired novel features. Nine ZAR1 orthologs from cassava and cotton carry an integrated thioredoxin-like domain at their C-termini. ZAR1 also duplicated into two paralog families ZAR1-SUB and ZAR1-CIN. ZAR1-SUB, which emerged in the eudicots, is a large class of sequence diverse ZAR1 paralogs that lack several of the conserved motifs of ZAR1. A second family, ZAR1-CIN, comprises an expansion of 11 paralogs unique to a ~500 kb locus in the C. micranthum genome and located about 48 Mb from ZAR1. We conclude that ZAR1 stands out among angiosperm NLRs for having an ancient origin and having experienced relatively limited gene duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 did also give rise to non-canonical NLR proteins with integrated domains and degenerated molecular features. more...

Background: The mosquito Aedes aegypti is a major vector for transmission of viruses causing dengue fever, yellow fever, Zika, and chikungunya infection. Functional analysis of mosquito genes and individual viral genes can be a powerful approach to study vector–virus interactions but is often hampered by a lack of suitable promoters to drive exogenous viral gene expression in mosquito cells in vitro and in vivo. Object: To search for potential promoter candidates that can be used to express foreign genes and particularly viral proteins in a mosquito model system. Materials and Methods: we characterized the ability of the promoters of three Ae. aegypti antimicrobial peptide (AMP) genes to drive the expression of marker proteins (luciferase, GFP, the NS3 protein of two flaviviruses, and rabies virus glycoprotein) in mosquito cells and adult female mosquitoes, and in other insect cells as well. Results: The promoters of the defensin A4 and cecropin B1 genes produced robust expression of luciferase and GFP in the Ae. aegypti cell line CCL125, Aedes albopictus cell line C6/36, Drosophila melanogaster cell line S2, and Spodoptera frugiperda cell line Sf21. These AMP gene promoters also had the ability to drive NS3 and GFP expression in adult tissues of Ae. aegypti, Ae. albopictus, and Culex tritaeniorhynchus in vivo, which may suggest evolutionary conservation of AMP gene promoter activity across mosquito lineages. Conclusions: These promoters could provide a valuable tool for ectopically expressing viral genes and studying their interactions with the mosquito vectors. more...

Motivation MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants. A systematic approach to determine novel miRNAs without reference sequences is thus necessary. Results In this study, an effective method was developed to identify miRNAs from non-model plants based only on NGS datasets. The miRNA prediction model was trained with several duplex structure-related features of mature miRNAs and their passenger strands using a support vector machine algorithm. The accuracy of the independent test reached 96.61% and 93.04% for dicots (Arabidopsis) and monocots (rice), respectively. Furthermore, true small RNA sequencing data from orchids was tested in this study. Twenty-one predicted orchid miRNAs were selected and experimentally validated. Significantly, 18 of them were confirmed in the qRT-PCR experiment. This novel approach was also compiled as a user-friendly program called microRPM (miRNA Prediction Model). Availability and implementation This resource is freely available at http://microRPM.itps.ncku.edu.tw. Supplementary information Supplementary data are available at Bioinformatics online. more...

Summary Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are the two most prevalent viruses infecting orchids and causing economic losses worldwide. Mixed infection of CymMV and ORSV could induce intensified symptoms as early at 10 days post‐inoculation in inoculated Phalaenopsis amabilis, where CymMV pathogenesis was unilaterally enhanced by ORSV. To reveal the antiviral RNA silencing activity in orchids, we characterized the viral small‐interfering RNAs (vsiRNAs) from CymMV and ORSV singly or synergistically infecting P. amabilis. We also temporally classified the inoculated leaf‐tip tissues and noninoculated adjacent tissues as late and early stages of infection, respectively. Regardless of early or late stage with single or double infection, CymMV and ORSV vsiRNAs were predominant in 21‐ and 22‐nt sizes, with excess positive polarity and under‐represented 5ʹ‐guanine. While CymMV vsiRNAs mainly derived from RNA‐dependent RNA polymerase‐coding regions, ORSV vsiRNAs encompassed the coat protein gene and 3ʹ‐untranslated region, with a specific hotspot residing in the 3ʹ‐terminal pseudoknot. With double infection, CymMV vsiRNAs increased more than 5‐fold in number with increasing virus titres. Most vsiRNA features remained unchanged with double inoculation, but additional ORSV vsiRNA hotspot peaks were prominent. The potential vsiRNA‐mediated regulation of the novel targets in double‐infected tissues thereby provides a different view of CymMV and ORSV synergism. Hence, temporally profiled vsiRNAs from taxonomically distinct CymMV and ORSV illustrate active antiviral RNA silencing in their natural host, Phalaenopsis, during both early and late stages of infection. Our findings provide insights into offence–defence interactions among CymMV, ORSV and orchids. more...

Taxonomically distinct Cymbidium mosaic potexvirus (CymMV) and Odontoglossum ringspot tobamovirus (ORSV) are two of the most prevalent viruses worldwide; when co-infecting orchids, they cause synergistic symptoms. Because of the huge economic loss in quality and quantity in the orchid industry with virus-infected orchids, virus-resistant orchids are urgently needed. To date, no transgenic resistant lines against these two viruses have been reported. In this study, we generated transgenic Nicotiana benthamiana expressing various constructs of partial CymMV and ORSV genomes. Several transgenic lines grew normally and remained symptomless after mixed inoculation with CymMV and ORSV. The replication of CymMV and ORSV was approximately 70–90% lower in protoplasts of transgenic lines than wild-type (WT) plants. Of note, we detected extremely low or no viral RNA or capsid protein of CymMV and ORSV in systemic leaves of transgenic lines after co-infection. Grafting experiments further revealed that CymMV and ORSV trafficked extremely inefficiently from co-infected WT stocks to transgenic scions, presumably due to RNA-mediated interference. This study reports the first successful creation of dual resistant transgenic lines against CymMV and ORSV. Our studies shed light on the commercial development of transgenic orchid production to combat the global viral threat. more...

Operationally-simple and reusable Pd-catalyzed mono and double Mizoroki–Heck reactions of aryl halides and dialkyl vinylphosphonates using iPr2NH as a base in aqueous medium under air were developed. For aryl iodides, the reaction could be conducted at 80 °C under a low catalyst loading (0.1–1 mol%). When aryl bromides were applied, however, a greater amount of catalyst (5 mol%) and a longer reaction time at 120 °C were required. Simply changing dialkyl vinylphosphonates as the limiting reagent led to the formation of 2,2-diaryl vinylphosphonates in good to high yields. After reaction, the residual aqueous solution could be reused for both mono and double Mizoroki–Heck reactions, making the reactions greener and reducing wastage of precious metals and use of harmful organic solvents as the reaction medium. more...

A series of Ag2Te1−x Se x /Ag nanocomposites with x = 0, 0.01, and 0.02 is fabricated using aqueous solution method at room temperature followed by sintering in an evacuated-and-encapsulated ampoule. The resulting materials are characterized by power x-ray diffraction, field-emission scanning electron microscopy, high resolution tunneling electron microscopy and thermoelectric property measurements. Slight doping of Se for Te results in higher resistivity and absolute thermopower as compared to nondoped Ag2Te/Ag nanocomposites. As a result, the power factor is significantly enhanced around structural transition temperature as well as in the temperature interval of 550 K and 650 K. A maximum power factor of 13.7 μW/cm-K2 is attained for x = 0.01 at 425 K. more...

Background Diabetics has become a serious public health burden in China. Multiple complications appear with the progression of diabetics pose a serious threat to the quality of human life and health. We can prevent the progression of prediabetics to diabetics and delay the progression to diabetics by early identification of diabetics and prediabetics and timely intervention, which have positive significance for improving public health. Objective Using machine learning techniques, we establish the noninvasive diabetics risk prediction model based on tongue features fusion and predict the risk of prediabetics and diabetics. Methods Applying the type TFDA-1 Tongue Diagnosis Instrument, we collect tongue images, extract tongue features including color and texture features using TDAS, and extract the advanced tongue features with ResNet-50, achieve the fusion of the two features with GA_XGBT, finally establish the noninvasive diabetics risk prediction model and evaluate the performance of testing effectiveness. Results Cross-validation suggests the best performance of GA_XGBT model with fusion features, whose average CA is 0.821, the average AUROC is 0.924, the average AUPRC is 0.856, the average Precision is 0.834, the average Recall is 0.822, the average F1-score is 0.813. Test set suggests the best testing performance of GA_XGBT model, whose average CA is 0.81, the average AUROC is 0.918, the average AUPRC is 0.839, the average Precision is 0.821, the average Recall is 0.81, the average F1-score is 0.796. When we test prediabetics with GA_XGBT model, we find that the AUROC is 0.914, the Precision is 0.69, the Recall is 0.952, the F1-score is 0.8. When we test diabetics with GA_XGBT model, we find that the AUROC is 0.984, the Precision is 0.929, the Recall is 0.951, the F1-score is 0.94. Conclusions Based on tongue features, the study uses classical machine learning algorithm and deep learning algorithm to maximum the respective advantages. We combine the prior knowledge and potential features together, establish the noninvasive diabetics risk prediction model with features fusion algorithm, and detect prediabetics and diabetics noninvasively. Our study presents a feasible method for establishing the association between diabetics and the tongue image information and prove that tongue image information is a potential marker which facilitates effective early diagnosis of prediabetics and diabetics. more...

Nanostructured Zn1−xAlxTe (0≤x≤0.15) samples have been fabricated using hydrothermal synthesis and evacuating-and-encapsulating sintering. Thermoelectric properties are measured at 300–600 K. The thermopower of all the samples is positive, indicating that the predominant carriers are holes over the entire temperature range. The hole concentration increases with increasing Al3+ content. Based on the charge neutrality, the hole concentration is expected to decrease upon Al doping. However, the x-ray absorption spectroscopy indicates the electrons transfer from Zn 4s to Te 5d states upon Al doping, which might explain that the increase of hole concentration upon partial Al3+ substitution of Zn2+. Using Slack's model for estimating the lattice thermal conductivity, the Gruneisen parameter at 300 K is found to increase with Al doping content. The highest power factor (1.52 µW m−1 K−2) and highest dimensionless figure of merit (0.075) are attained at 575 K for Zn0.85Al0.15Te, representing an improvement of about 508% and 851% with respect to the nondoped ZnTe at the same temperature. These results suggest that aluminum is an effective doping element for improving the thermoelectric properties of ZnTe. more...

Objective. In this study, machine learning was utilized to classify and predict pulse wave of hypertensive group and healthy group and assess the risk of hypertension by observing the dynamic change of the pulse wave and provide an objective reference for clinical application of pulse diagnosis in traditional Chinese medicine (TCM). Method. The basic information from 450 hypertensive cases and 479 healthy cases was collected by self-developed H20 questionnaires and pulse wave information was acquired by self-developed pulse diagnostic instrument (PDA-1). H20 questionnaires and pulse wave information were used as input variables to obtain different machine learning classification models of hypertension. This method was aimed at analyzing the influence of pulse wave on the accuracy and stability of machine learning model, as well as the feature contribution of hypertension model after removing noise by K-means. Result. Compared with the classification results before removing noise, the accuracy and the area under the curve (AUC) had been improved. The accuracy rates of AdaBoost, Gradient Boosting, and Random Forest (RF) were 86.41%, 86.41%, and 85.33%, respectively. AUC were 0.86, 0.86, and 0.85, respectively. The maximum accuracy of SVM increased from 79.57% to 83.15%, and the AUC stability increased from 0.79 to 0.83. In addition, the features of importance on traditional statistics and machine learning were consistent. After removing noise, the features with large changes were h1/t1, w1/t, t, w2, h2, t1, and t5 in AdaBoost and Gradient Boosting (top10). The common variables for machine learning and traditional statistics were h1/t1, h5, t, Ad, BMI, and t2. Conclusion. Pulse wave-based diagnostic method of hypertension has significant value in reference. In view of the feasibility of digital-pulse-wave diagnosis and dynamically evaluating hypertension, it provides the research direction and foundation for Chinese medicine in the dynamic evaluation of modern disease diagnosis and curative effect. more...

A rapid scene indexing method is proposed to improve retrieval performance for students accessing instructional videos. This indexing method is applied to anchor suitable indices to the instructional video so that students can obtain several small lesson units to gain learning mastery. The method also regulates online course progress. These anchored points not only provide students with fast access to specific material but also can link to certain quizzes or problems to show the interactive e-learning content that course developers deposited in the learning management system, which enhances the learning process. This allows students to click on the anchored point to repeat their lesson, or work through the quizzes or problems until they reach formative assessment. Hence, their learning can be guided by the formative assessment results. In order to quickly find the scene to index, some specific description of it was needed. Actually, most of the instructional videos were recorded by teachers, and were part of their PowerPoint presentations. Based on the features of the PowerPoint slides in the instructional videos, such as the title or page number, the specified scene can be found. Since we used specific scene descriptions, it was easy to employ the rapid scene detection method using an image filter and Sobel mask. Finally, we applied an experimental design to check the precision of the scene detection and evaluate user satisfaction. The results showed that rapid scene indexing can definitely assist learners in their online learning; that is, it gives them better learning mastery and provides regulation for the online learning environment. more...

Treatment of difluorobenzyldiphenylphosphine with the Ir(III) dimer [(dfppy)2Ir(mu-Cl)]2 gives (N,N)-trans-[Ir(dfppy)2(dfbdpH)Cl], followed by skeletal isomerization to form its (N,N)-cis analogue, and then the fully cyclometalated complex [Ir(dfppy)2(dfbdp)]; the last complex and its derivative are suitable for fabrication of true-blue phosphorescent OLEDs. more...