A calmodulin-gated calcium channel links pathogen patterns to plant immunity.

Pathogen-associated molecular patterns (PAMPs) activate innate immunity in both animals and plants. Although calcium has long been recognized as an essential signal for PAMP-triggered immunity in plants, the mechanism of PAMP-induced calcium signalling remains unknown1,2. Here we report that calcium nutrient status is critical for calcium-dependent PAMP-triggered immunity in plants. When calcium supply is sufficient, two genes that encode cyclic nucleotide-gated channel (CNGC) proteins, CNGC2 and CNGC4, are essential for PAMP-induced calcium signalling in Arabidopsis3-7. In a reconstitution system, we find that the CNGC2 and CNGC4 proteins together-but neither alone-assemble into a functional calcium channel that is blocked by calmodulin in the resting state. Upon pathogen attack, the channel is phosphorylated and activated by the effector kinase BOTRYTIS-INDUCED KINASE1 (BIK1) of the pattern-recognition receptor complex, and this triggers an increase in the concentration of cytosolic calcium8-10. The CNGC-mediated calcium entry thus provides a critical link between the pattern-recognition receptor complex and calcium-dependent immunity programs in the PAMP-triggered immunity signalling pathway in plants.

Unintended consequences: Disrupting microbial communities of Nilaparvata lugens with non-target pesticides.

Insects are frequently exposed to a range of insecticides that can alter the structure of the commensal microbiome. However, the effects of exposure to non-target pesticides (including non-target insecticides and fungicides) on insect pest microbiomes are still unclear. In the present study, we exposed Nilaparvata lugens to three target insecticides (nitenpyram, pymetrozine, and avermectin), a non-target insecticide (chlorantraniliprole), and two fungicides (propiconazole and tebuconazole), and observed changes in the microbiome's structure and function. Our results showed that both non-target insecticide and fungicides can disrupt the microbiome's structure. Specifically, symbiotic bacteria of N. lugens were more sensitive to non-target insecticide compared to target insecticide, while the symbiotic fungi were more sensitive to fungicides. We also found that the microbiome in the field strain was more stable under pesticides exposure than the laboratory strain (a susceptible strain), and core microbial species g_Pseudomonas, s_Acinetobacter soli, g_Lactobacillus, s_Metarhizium minus, and s_Penicillium citrinum were significantly affected by specifically pesticides. Furthermore, the functions of symbiotic bacteria in nutrient synthesis were predicted to be significantly reduced by non-target insecticide. Our findings contribute to a better understanding of the impact of non-target pesticides on insect microbial communities and highlight the need for scientific and rational use of pesticides.

Coronatine promotes maize water uptake by directly binding to the aquaporin ZmPIP2;5 and enhancing its activity.

Water uptake is crucial for crop growth and development and drought stress tolerance. The water channel aquaporins (AQP) play important roles in plant water uptake. Here, we discovered that a jasmonic acid analog, coronatine (COR), enhanced maize (Zea mays) root water uptake capacity under artificial water deficiency conditions. COR treatment induced the expression of the AQP gene Plasma membrane intrinsic protein 2;5 (ZmPIP2;5). In vivo and in vitro experiments indicated that COR also directly acts on ZmPIP2;5 to improve water uptake in maize and Xenopus oocytes. The leaf water potential and hydraulic conductivity of roots growing under hyperosmotic conditions were higher in ZmPIP2;5-overexpression lines and lower in the zmpip2;5 knockout mutant, compared to wild-type plants. Based on a comparison between ZmPIP2;5 and other PIP2s, we predicted that COR may bind to the functional site in loop E of ZmPIP2;5. We confirmed this prediction by surface plasmon resonance technology and a microscale thermophoresis assay, and showed that deleting the binding motif greatly reduced COR binding. We identified the N241 residue as the COR-specific binding site, which may activate the channel of the AQP tetramer and increase water transport activity, which may facilitate water uptake under hyperosmotic stress.

Dynamics of Microbial Communities across the Life Stages of Nilaparvata lugens (Stål).

Understanding the composition of microorganismal communities hosted by insect pests is an important prerequisite for revealing their functions and developing new pest control strategies. Although studies of the structure of the microbiome of Nilaparvata lugens have been published, little is known about the dynamic changes in this microbiome across different developmental stages, and an understanding of the core microbiota is still lacking. In this study, we investigated the dynamic changes in bacteria and fungi in different developmental stages of N. lugens using high-throughput sequencing technology. We observed that the microbial diversity in eggs and mated adults was higher than that in nymphs and unmated adults. We also observed a notable strong correlation between fungal and bacterial α-diversity, which suggests that fungi and bacteria are closely linked and may perform functions collaboratively during the whole developmental period. Arsenophonus and Hirsutella were the predominant bacterial and fungal taxa, respectively. Bacteria were more conserved than fungi during the transmission of the microbiota between developmental stages. Compared with that in the nymph and unmated adult stages of N. lugens, the correlation between bacterial and fungal communities in the mated adult and egg stages was stronger. Moreover, the core microbiota across all developmental stages in N. lugens was identified, and there were more bacterial genera than fungal genera; notably, the core microbiota of eggs, nymphs, and mated and unmated adults showed distinctive functional enrichment. These findings highlight the potential value of further exploring microbial functions during different developmental stages and developing new pest management strategies.

MR-YOLO: An Improved YOLOv5 Network for Detecting Magnetic Ring Surface Defects.

Magnetic rings are widely used in automotive, home appliances, and consumer electronics. Due to the materials used, processing techniques, and other factors, there will be top cracks, internal cracks, adhesion, and other defects on individual magnetic rings during the manufacturing process. To find such defects, the most sophisticated YOLOv5 target identification algorithm is frequently utilized. However, it has problems such as high computation, sluggish detection, and a large model size. This work suggests an enhanced lightweight YOLOv5 (MR-YOLO) approach for the identification of magnetic ring surface defects to address these issues. To decrease the floating-point operation (FLOP) in the feature channel fusion process and enhance the performance of feature expression, the YOLOv5 neck network was added to the Mobilenetv3 module. To improve the robustness of the algorithm, a Mosaic data enhancement technique was applied. Moreover, in order to increase the network's interest in minor defects, the SE attention module is inserted into the backbone network to replace the SPPF module with substantially more calculations. Finally, to further increase the new network's accuracy and training speed, we substituted the original CIoU-Ioss for SIoU-Loss. According to the test, the FLOP and Params of the modified network model decreased by 59.4% and 47.9%, respectively; the reasoning speed increased by 16.6%, the model's size decreased by 48.1%, and the mAP only lost by 0.3%. The effectiveness and superiority of this method are proved by an analysis and comparison of examples.

Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats.

Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.

Danger-Associated Peptides Close Stomata by OST1-Independent Activation of Anion Channels in Guard Cells.

The plant elicitor peptides (Peps), a family of damage/danger-associated molecular patterns (DAMPs), are perceived by two receptors, PEPR1 and PEPR2, and contribute to plant defense against pathogen attack and abiotic stress. Here, we show that the Peps-PEPR signaling pathway functions in stomatal immunity by activating guard cell anion channels in Arabidopsis thaliana The mutant plants lacking both PEPR1 and PEPR2 (pepr1 pepr2) displayed enhanced bacterial growth after being sprayed with Pseudomonas syringae pv tomato (Pst) DC3000, but not after pathogen infiltration into leaves, implicating PEPR function in stomatal immunity. Indeed, synthetic Arabidopsis Peps (AtPeps) effectively induced stomatal closure in wild-type but not pepr1 pepr2 mutant leaves, suggesting that the AtPeps-PEPR signaling pathway triggers stomatal closure. Consistent with this finding, patch-clamp recording revealed AtPep1-induced activation of anion channels in the guard cells of wild-type but not pepr1 pepr2 mutant plants. We further identified two guard cell-expressed anion channels, SLOW ANION CHANNEL1 (SLAC1) and its homolog SLAH3, as functionally overlapping components responsible for AtPep1-induced stomatal closure. The slac1 slah3 double mutant, but not slac1 or slah3 single mutants, failed to respond to AtPep1 in stomatal closure assays. Interestingly, disruption of OPEN STOMATA1 (OST1), an essential gene for abscisic acid-triggered stomatal closure, did not affect the AtPep1-induced anion channel activity and stomatal response. Together, these results illustrate a DAMP-triggered signaling pathway that, unlike the flagellin22-FLAGELLIN-SENSITIVE2 pathway, triggers stomata immunity through an OST1-independent mechanism.

A chloride efflux transporter, BIG RICE GRAIN 1, is involved in mediating grain size and salt tolerance in rice.

Grain size is determined by the size and number of cells in the grain. The regulation of grain size is crucial for improving crop yield; however, the genes and molecular mechanisms that control grain size remain elusive. Here, we report that a member of the detoxification efflux carrier /Multidrug and Toxic Compound Extrusion (DTX/MATE) family transporters, BIG RICE GRAIN 1 (BIRG1), negatively influences grain size in rice (Oryza sativa L.). BIRG1 is highly expressed in reproductive organs and roots. In birg1 grain, the outer parenchyma layer cells of spikelet hulls are larger than in wild-type (WT) grains, but the cell number is unaltered. When expressed in Xenopus laevis oocytes, BIRG1 exhibits chloride efflux activity. Consistent with this role of BIRG1, the birg1 mutant shows reduced tolerance to salt stress at a toxic chloride level. Moreover, grains from birg1 plants contain a higher level of chloride than those of WT plants when grown under normal paddy field conditions, and the roots of birg1 accumulate more chloride than those of WT under saline conditions. Collectively, the data suggest that BIRG1 in rice functions as a chloride efflux transporter that is involved in mediating grain size and salt tolerance by controlling chloride homeostasis.

Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons.

Unloading sugar from sink phloem by transporters is complex and much remains to be understood about this phenomenon in the watermelon fruit. Here, we report a novel vacuolar sugar transporter (ClVST1) identified through map-based cloning and association study, whose expression in fruit phloem is associated with accumulation of sucrose (Suc) in watermelon fruit. ClVST197 knockout lines show decreased sugar content and total biomass, whereas overexpression of ClVST197 increases Suc content. Population genomic and subcellular localization analyses strongly suggest a single-base change at the coding region of ClVST197 as a major molecular event during watermelon domestication, which results in the truncation of 45 amino acids and shifts the localization of ClVST197 to plasma membranes in sweet watermelons. Molecular, biochemical and phenotypic analyses indicate that ClVST197 is a novel sugar transporter for Suc and glucose efflux and unloading. Functional characterization of ClVST1 provides a novel strategy to increase sugar sink potency during watermelon domestication.

The interaction of CaM7 and CNGC14 regulates root hair growth in Arabidopsis.

Oscillations in cytosolic free calcium determine the polarity of tip-growing root hairs. The Ca2+ channel cyclic nucleotide gated channel 14 (CNGC14) contributes to the dynamic changes in Ca2+ concentration gradient at the root hair tip. However, the mechanisms that regulate CNGC14 are unknown. In this study, we detected a direct interaction between calmodulin 7 (CaM7) and CNGC14 through yeast two-hybrid and bimolecular fluorescence complementation assays. We demonstrated that the third EF-hand domain of CaM7 specifically interacts with the cytosolic C-terminal domain of CNGC14. A two-electrode voltage clamp assay showed that CaM7 completely inhibits CNGC14-mediated Ca2+ influx, suggesting that CaM7 negatively regulates CNGC14-mediated calcium signaling. Furthermore, CaM7 overexpressing lines phenocopy the short root hair phenotype of a cngc14 mutant and this phenotype is insensitive to changes in external Ca2+ concentrations. We, thus, identified CaM7-CNGC14 as a novel interacting module that regulates polar growth in root hairs by controlling the tip-focused Ca2+ signal.

The influence of temperature on the toxicity of insecticides to Nilaparvata lugens (Stål).

The toxicity of insecticides is associated with a variety of factors including temperature, and global warming is bound to lead to the outbreak of pests; therefore, it is important to study the influence of temperature on insecticide toxicity and pest control. In this study, the influence of temperature on the toxicity of insecticides to Nilaparvata lugens (BPH) was determined. The results showed that the sensitivity of BPH to cycloxaprid (LC50 = 42.5-0.388 mg/L), nitenpyram (LC50 = 3.49-0.187 mg/L), triflumezopyrim (LC50 = 0.354-0.0533 mg/L) and chlorpyrifos (LC50 = 36.3-7.41 mg/L) increased significantly when the temperature changed from 18 °C to 36 °C. BPH sensitivity to etofenprox (LC50 = 9.04-54.2 mg/L) was also affected by temperature. Additionally, the feeding amount and the activities of three detoxification enzymes [cytochrome P450 (P450), glutathione S-transferase (GST) and carboxylesterase (CarE)] of BPH at different temperatures were also measured. The feeding amounts were positively correlated with temperature increases while the activities of P450 and GST were significantly inhibited. The correlation analysis showed that changes in P450 activity (but not GST activity) were closely related to the sensitivity of BPH to cycloxaprid, nitenpyram, chlorpyrifos, and etofenprox according to the variation in temperatures. This study provides a theoretical basis for the rational use of chemical pesticides under the global warming trend and provides a reference for the integrated management of BPH in the field.

Characterization of nitenpyram resistance in Nilaparvata lugens (Stål).

Nitenpyram is very effective in controlling Nilaparvata lugens (brown planthopper, BPH), and its resistance has been reported in field populations; however, the resistance mechanism remains unclear. In the present study, cross-resistance and resistance mechanisms in nitenpyram-resistant BPH were investigated. A resistant strain (NR) with a high resistance level (164.18-fold) to nitenpyram was evolved through successive selection for 42 generations from a laboratory susceptible strain (NS). The bioassay results showed that the NR exhibited cross-resistance to imidacloprid (37.46-fold), thiamethoxam (71.66-fold), clothianidin (149.17-fold), dinotefuran (98.13-fold), sulfoxaflor (47.24-fold), cycloxaprid (9.33-fold), etofenprox (10.51-fold) and isoprocarb (9.97-fold) but not to triflumezopyrim, chlorpyrifos and buprofezin. The NR showed a 3.21-fold increase in cytochrome P450 monooxygenase (P450) activity compared to that in the NS, while resistance was also synergized (4.03-fold) with the inhibitor piperonyl butoxide (PBO), suggesting a role of P450. Furthermore, the mRNA expression levels of cytochrome P450 (CYP) genes by quantitative real-time PCR results indicated that twelve P450 genes were significantly overexpressed in the NR strain, especially CYP6ER1 (203.22-fold). RNA interference (RNAi) suppression of CYP6ER1 through injection of dsCYP6ER1 led to significant susceptibility in the NR strain. The current study expands our understanding of the nitenpyram resistance mechanism in N. lugens, provides an important reference for integrated pest management (IPM), and enriches the theoretical system of insect toxicology.

SbHKT1;4, a member of the high-affinity potassium transporter gene family from Sorghum bicolor, functions to maintain optimal Na⁺ /K⁺ balance under Na⁺ stress.

In halophytic plants, the high-affinity potassium transporter HKT gene family can selectively uptake K⁺ in the presence of toxic concentrations of Na⁺. This has so far not been well examined in glycophytic crops. Here, we report the characterization of SbHKT1;4, a member of the HKT gene family from Sorghum bicolor. Upon Na⁺ stress, SbHKT1;4 expression was more strongly upregulated in salt-tolerant sorghum accession, correlating with a better balanced Na⁺ /K⁺ ratio and enhanced plant growth. Heterogeneous expression analyses in mutants of Saccharomyces cerevisiae and Arabidopsis thaliana indicated that overexpressing SbHKT1;4 resulted in hypersensitivity to Na⁺ stress, and such hypersensitivity could be alleviated with the supply of elevated levels of K⁺, implicating that SbHKT1;4 may mediate K⁺ uptake in the presence of excessive Na⁺. Further electrophysiological evidence demonstrated that SbHKT1;4 could transport Na⁺ and K⁺ when expressed in Xenopus laevis oocytes. The relevance of the finding that SbHKT1;4 functions to maintain optimal Na⁺ /K⁺ balance under Na⁺ stress to the breeding of salt-tolerant glycophytic crops is discussed.

Green synthesis of reduced graphene oxide/chitosan/gold nanoparticles composites and their catalytic activity for reduction of 4-nitrophenol.

Gold nanoparticles (AuNPs) have attracted extensive attention in the past few years due to their unique properties and great potential application in catalysis. However, the application of AuNPs remains a significant challenge due to the lack of high efficiency and stability caused by aggregation. Immobilization of AuNPs on appropriate support shows promising results in avoiding aggregation and improving catalytic activity. In this work, reduced graphene oxide/chitosan/gold nanoparticles (rGO/CHS/AuNPs) composites were prepared using chitosan with different molecular weights (MW) as a reducing agent and stabilizer, and characterized by FT-IR, XRD, XPS, SEM, FESEM, EDS, TEM, HRTEM, and TGA. The preparation conditions of rGO/CHS/AuNPs composites, including chitosan MW, CHS/GO mass ratio, reaction temperature and time, and HAuCl4 concentration were investigated in detail. The results indicated that reduction activity of chitosan for GO increased with the decrease of chitosan MW. The C/O ratio of rGO reduced by low molecular weight chitosan (LMWC) with viscosity-average molecular weight (Mv) of 21 kDa was 6.34. Small spherical AuNPs were uniformly immobilized on the rGO surface. The particle size of AuNPs increased from 9.29 to 13.03 nm as chitosan MW decreased from 465 to 21 kDa. The rGO/CHS/AuNPs showed good catalytic activity for the reduction of 4-NP in the presence of NaBH4. The catalytic activity of rGO/CHS/AuNPs was closely related to chitosan MW. rGO/CHS/AuNPs synthesized by LMWC with Mv of 21 kDa showed the highest kinetic rate constant of 0.2067 min-1. The results of this experimental study could be useful in the development of effective catalysts for the reduction of aromatic nitro compounds.

The insecticidal activity and mechanism of tebuconazole on Nilaparvata lugens (Stål).

BACKGROUND: Previous studies have shown that fungicides have insecticidal activity that can potentially be used as an insecticide resistance management strategy in the brown planthopper Nilaparvata lugens (Stål). However, the mechanism that induces mortality of N. lugens remains elusive. RESULTS: In the present study, the insecticidal activities of 14 fungicides against N. lugens were determined, of which tebuconazole had the highest insecticidal activity compared with the other fungicides. Furthermore, tebuconazole significantly inhibited the expression of the chitin synthase gene NlCHS1; the chitinase genes NlCht1, NlCht5, NlCht7, NlCht9, and NlCht10; and the ß-N-acetylhexosaminidase genes NlHex3, NlHex4, NlHex5 and NlHex6; it significantly suppressed the expression of ecdysteroid biosynthetic genes as well, including SDR, CYP307A2, CYP307B1, CYP306A2, CYP302A1, CYP315A1 and CYP314A1 of N. lugens. Additionally, tebuconazole affected the diversity, structure, composition, and function of the symbiotic fungi of N. lugens, as well as the relative abundance of saprophytes and pathogens, suggesting that tebuconazole reshapes the diversity and function of symbiotic fungi of N. lugens. CONCLUSION: Our findings illustrate the insecticidal mechanism of tebuconazole, possibly by inhibiting normal molting or disrupting microbial homeostasis in N. lugens, and provide an important rationale for developing novel insect management strategies to delay escalating insecticide resistance. © 2023 Society of Chemical Industry.

Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens.

Microbiome-mediated insecticide resistance is an emerging phenomenon found in insect pests. However, microbiome composition can vary by host genotype and environmental factors, but how these variations may be associated with insecticide resistance phenotype remains unclear. In this study, we compared different field and laboratory strains of the brown planthopper Nilaparvata lugens in their microbiome composition, transcriptome, and insecticide resistance profiles to identify possible patterns of correlation. Our analysis reveals that the abundances of core bacterial symbionts are significantly correlated with the expression of several host detoxifying genes (especially NlCYP6ER1, a key gene previously shown involved in insecticides resistance). The expression levels of these detoxifying genes correlated with N. lugens insecticide susceptibility. Furthermore, we have identified several environmental abiotic factors, including temperature, precipitation, latitude, and longitude, as potential predictors of symbiont abundances associated with expression of key detoxifying genes, and correlated with insecticide susceptibility levels of N. lugens. These findings provide new insights into how microbiome-environment-host interactions may influence insecticide susceptibility, which will be helpful in guiding targeted microbial-based strategies for insecticide resistance management in the field.

Odorant binding protein 3 is associated with nitenpyram and sulfoxaflor resistance in Nilaparvata lugens.

Odorant binding protein (OBP) can interact with small-molecule compounds insecticides and thereby modulate variation in insecticide susceptibility in insects. However, the regulatory mechanism of OBP-mediated insecticide resistance in Nilaparvata lugens, a destructive rice pest in Asia, remains unclear. Here, we explored the role of NlOBP3 in the resistance of N. lugens to nitenpyram and sulfoxaflor. The results showed that NlOBP3 was overexpressed in association with nitenpyram and sulfoxaflor resistance, and NlOBP3 silencing significantly increased the mortality of N. lugens to nitenpyram and sulfoxaflor, suggesting that NlOBP3 may be associated with nitenpyram and sulfoxaflor resistance in N. lugens. OBP localization revealed that NlOBP3 was highly expressed in all nymph stages and was enriched in the antennae, legs, body wall, and fat body. RT-qPCR analyses showed that the mRNA levels of NlOBP3 were significantly affected by nitenpyram and sulfoxaflor. Additionally, molecular docking predicted that there were multiple binding sites that may played key roles in the binding of NlOBP3 with nitenpyram and sulfoxaflor. The current study identifies a previously undescribed mechanism of insecticide resistance in N. lugens, showing that NlOBP3 is likely to be involved in the evolution of nitenpyram and sulfoxaflor resistance in N. lugens.

miRNAs targeting CYP6ER1 and CarE1 are involved in nitenpyram resistance in Nilaparvata lugens.

The evolution of nitenpyram resistance has been confirmed to be related to overexpression of two key metabolic enzyme genes, CYP6ER1 and CarE1, in Nilaparvata lugens, a highly destructive rice pest that causes substantial economic losses and has developed insecticide resistance. As microRNAs (miRNAs) are important post-transcriptional regulators of gene expression, whether they are involved in nitenpyram resistance is poorly understood in N. lugens. In this study, knockdown of key genes in the miRNA biogenesis pathway (Dicer1, Drosha, and Argonaute1) changed CYP6ER1 and CarE1 abundance, which confirmed the importance of miRNAs in nitenpyram resistance. Furthermore, global screening of miRNAs associated with nitenpyram resistance in N. lugens was performed, and a total of 42 known and 178 novel miRNAs were identified; of these, 57 were differentially expressed between the susceptible and resistant strains, and two (novel_85 and novel_191) were predicted to target CYP6ER1 and CarE1, respectively. Luciferase reporter assays demonstrated that novel_85 and novel_191 bind to the CYP6ER1 and CarE1 coding regions, respectively, and downregulate their expression. Moreover, modulating novel_85 and novel_191 expression by injection of miRNA inhibitors and mimics significantly altered N. lugens nitenpyram susceptibility. This is the first study to systematically screen and identify miRNAs associated with N. lugens nitenpyram resistance, and provides important information that can be used to develop new miRNA-based targets in insecticide resistance management.

Lilikoi V2.0: a deep learning-enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data.

BACKGROUND: previously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, it is important to update Lilikoi software. RESULTS: here we report the next version of Lilikoi as a significant upgrade. The new Lilikoi v2.0 R package has implemented a deep learning method for classification, in addition to popular machine learning methods. It also has several new modules, including the most significant addition of prognosis prediction, implemented by Cox-proportional hazards model and the deep learning-based Cox-nnet model. Additionally, Lilikoi v2.0 supports data preprocessing, exploratory analysis, pathway visualization, and metabolite pathway regression. CONCULSION: Lilikoi v2.0 is a modern, comprehensive package to enable metabolomics analysis in R programming environment.

Carboxylesterase genes in nitenpyram-resistant brown planthoppers, Nilaparvata lugens.

Carboxylesterases (CarEs) represent one of the major detoxification enzyme families involved in insecticide resistance. However, the function of specific CarE genes in insecticide resistance is still unclear in the insect Nilaparvata lugens (Stål), a notorious rice crop pest in Asia. In this study, a total of 29 putative CarE genes in N. lugens were identified, and they were divided into seven clades; further, the ß-esterase clade was significantly expanded. Tissue-specific expression analysis found that 17 CarE genes were abundantly distributed in the midgut and fat body, while 12 CarE genes were highly expressed in the head. The expression of most CarE genes was significantly induced in response to the challenge of nitenpyram, triflumezopyrim, chlorpyrifos, isoprocarb and etofenprox. Among these, the expression levels of NlCarE2, NlCarE4, NlCarE9, NlCarE17 and NlCarE24 were increased by each insecticide. Real-time quantitative polymerase chain reaction and RNA interference assays revealed the NlCarE1 gene to be a candidate gene mainly involved in nitenpyram resistance, while simultaneously silencing NlCarE1 and NlCarE19 produced a stronger effect than silencing either one individually, suggesting a cooperative relationship in resistance formation. These findings lay the foundation for further clarification of insecticide resistance mediated by CarE in N. lugens.