BackgroundTransposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.ResultsWe report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.ConclusionsOur study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

Sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce cardiovascular events in humans with type 2 diabetes (T2D); however, the underlying mechanism remains unclear. Activation of the NLR family, pyrin domain-containing 3 (NLRP3) inflammasome and subsequent interleukin (IL)-1β release induces atherosclerosis and heart failure. Here we show the effect of SGLT2 inhibitor empagliflozin on NLRP3 inflammasome activity. Patients with T2D and high cardiovascular risk receive SGLT2 inhibitor or sulfonylurea for 30 days, with NLRP3 inflammasome activation analyzed in macrophages. While the SGLT2 inhibitor's glucoselowering capacity is similar to sulfonylurea, it shows a greater reduction in IL-1β secretion compared to sulfonylurea accompanied by increased serum β-hydroxybutyrate (BHB) and decreased serum insulin. Ex vivo experiments with macrophages verify the inhibitory effects of high BHB and low insulin levels on NLRP3 inflammasome activation. In conclusion, SGLT2 inhibitor attenuates NLRP3 inflammasome activation, which might help to explain its cardioprotective effects.

Nonhost resistance, a resistance of plant species against all nonadapted pathogens, is considered the most durable and efficient immune system of plants but yet remains elusive. The underlying mechanism of nonhost resistance has been investigated at multiple levels of plant defense for several decades. In this review, we have comprehensively surveyed the latest literature on nonhost resistance in terms of preinvasion, metabolic defense, pattern-triggered immunity, effector-triggered immunity, defense signaling, and possible application in crop protection. Overall, we summarize the current understanding of nonhost resistance mechanisms. Pre- and postinvasion is not much deviated from the knowledge on host resistance, except for a few specific cases. Further insights on the roles of the pattern recognition receptor gene family, multiple interactions between effectors from nonadapted pathogen and plant factors, and plant secondary metabolites in host range determination could expand our knowledge on nonhost resistance and provide efficient tools for future crop protection using combinational biotechnology approaches. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

ObjectivesDried blood spot (DBS) technology is a microsampling alternative to traditional plasma or serum sampling for pharmaco- or toxicokinetic evaluation. DBS technology has been applied to diagnostic screening in drug discovery, nonclinical, and clinical settings. We have developed an improved elution protocol involving boiling of blood spots dried on Whatman filter paper.MethodsThe purpose of this study was to compare the quality, purity, and quantity of DNA isolated from frozen blood samples and DBSs. We optimized a method for extraction and estimation of DNA from blood spots dried on filter paper (3-mm FTA card). A single DBS containing 40 μL blood was used.ResultsDNA was efficiently extracted in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer by incubation at 37°C overnight. DNA was stable in DBSs that were stored at room temperature or frozen. The housekeeping genes GAPDH and beta-actin were used as positive standards for polymerase chain reaction (PCR) validation of general diagnostic screening.ConclusionOur simple and convenient DBS storage and extraction methods are suitable for diagnostic screening by using very small volumes of blood collected on filter paper, and can be used in biobanks for blood sample storage.

Plants possess hundreds of intracellular immune receptors encoding nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Autoactive NLRs, some cases a specific domain of NLR, induce plant cell death in the absence of pathogen infection. In this study, we identified a group of NLRs (ANLs; ancient and autonomous NLRs) carrying autoactive coiled-coil (CC A) domains in pepper (Capsicum annuum L.) by genome-wide transient expression analysis. The CC A-mediated cell death mimics hypersensitive cell death triggered by interaction between NLR and pathogen effectors. Sequence alignment and mutagenesis analyses revealed that the intact α1 helix of CC A is critical for both CC A-and ANL-mediated cell death. The cell death induced by CC A does not require NRG1/ADR1 or NRC type helper NLRs, suggesting ANLs may function as singleton NLRs. We also found that CC A localize in the plasma membrane as Arabidopsis singleton NLR ZAR1. Extended studies revealed that autoactive CC A s are well conserved in other Solanaceae plants as well as a monocot plant, rice. Further phylogenetic analyses revealed that ANLs are present in all tested seed plants (spermatophytes). Our studies not only uncover the autonomous NLR clade in plants but also provide powerful resources for dissecting the underlying molecular mechanism of NLR-mediated cell death in plant.

The pepper Pvr4 protein encoding coiled-coil (CC) nucleotide-binding (NB) leucine-rich repeat (LRR) (NLR) confer hypersensitive response (HR) to potyviruses, including Pepper mottle virus (PepMoV), by recognizing the viral avirulence protein NIb. To figure out the Pvr4-mediated HR mechanism, we analyzed signaling component genes and structure-function relationships of Pvr4, using chimeras and deletion mutants in Nicotiana benthamiana. Molecular chaperone components including HSP90, SGT1, and RAR1 were required, while plant hormones and mitogen-activated protein kinase signaling components had little effect on Pvr4-NIb-mediated HR cell death. Domain swap analyses indicated that the LRR domain of Pvr4 determines recognition of PepMoV-NIb. Our deletion analysis further revealed that the CC domain or CC-NBARC domain alone can trigger autoactive cell death in N. benthamiana. However, the fragments having only an LRR domain could suppress CC-NBARC domain-induced cell death in trans. Further, C-terminal truncation analysis of Pvr4 revealed that a minimum three of five LRR exons showing high similarity was essential for Pvr4 function. The LRR domain may maintain Pvr4 in an inactive state in the absence of NIb. These results provide further insight into the structure and function of NLR protein signaling in plants.

Determining the exact positional relationship between mandibular third molar (M3) and inferior alveolar nerve (IAN) is important for surgical extractions. Panoramic radiography is the most common dental imaging test. The purposes of this study were to develop an artificial intelligence (AI) model to determine two positional relationships (true contact and bucco-lingual position) between M3 and IAN when they were overlapped in panoramic radiographs and compare its performance with that of oral and maxillofacial surgery (OMFS) specialists. A total of 571 panoramic images of M3 from 394 patients was used for this study. Among the images, 202 were classified as true contact, 246 as intimate, 61 as IAN buccal position, and 62 as IAN lingual position. A deep convolutional neural network model with ResNet-50 architecture was trained for each task. We randomly split the dataset into 75% for training and validation and 25% for testing. Model performance was superior in bucco-lingual position determination (accuracy 0.76, precision 0.83, recall 0.67, and F1 score 0.73) to true contact position determination (accuracy 0.63, precision 0.62, recall 0.63, and F1 score 0.61). AI exhibited much higher accuracy in both position determinations compared to OMFS specialists. In determining true contact position, OMFS specialists demonstrated an accuracy of 52.68% to 69.64%, while the AI showed an accuracy of 72.32%. In determining bucco-lingual position, OMFS specialists showed an accuracy of 32.26% to 48.39%, and the AI showed an accuracy of 80.65%. Moreover, Cohen’s kappa exhibited a substantial level of agreement for the AI (0.61) and poor agreements for OMFS specialists in bucco-lingual position determination. Determining the position relationship between M3 and IAN is possible using AI, especially in bucco-lingual positioning. The model could be used to support clinicians in the decision-making process for M3 treatment.

Potassium is the most abundant cation and a myriad of transporters regulate K+ homeostasis in plant. Potassium plays a role as a major osmolyte to regulate stomatal movements that control water utility of land plants. Here we report the characterization of two inward rectifying shaker-like potassium channels, OsKAT2 and OsKAT3, expressed in guard cell of rice plants. While OsKAT2 showed typical potassium channel activity, like that of Arabidopsis KAT1, OsKAT3 did not despite high sequence similarity between the two channel proteins. Interestingly, the two potassium channels physically interacted with each other and such interaction negatively regulated the OsKAT2 channel activity in CHO cell system. Furthermore, deletion of the C-terminal domain recovered the channel activity of OsKAT3, suggesting that the C-terminal region was regulatory domain that inhibited channel activity. Two homologous channels with antagonistic interaction has not been previously reported and presents new information for potassium channel regulation in plants, especially in stomatal regulation.