Iron(Fe)is an essential micronutrient for all organisms.Fe availability in the soil is usually much lower than that required for plant growth,and Fe deficiencies seriously restrict crop growth and yield.Calcium(Ca2+)i...Iron(Fe)is an essential micronutrient for all organisms.Fe availability in the soil is usually much lower than that required for plant growth,and Fe deficiencies seriously restrict crop growth and yield.Calcium(Ca2+)is a second messenger in all eukaryotes;however,it remains largely unknown how Ca2+regulates Fe deficiency.In this study,mutations in CPK21 and CPK23,which are two highly homologous calcium-dependent protein kinases,conferredimpaired growth and rootdevelopment under Fe-deficient conditions,whereas constitutively active CPK21 and CPK23 enhanced plant tolerance to Fe-deficient conditions.Furthermore,we found that CPK21 and CPK23 interacted with and phosphorylated the Fe transporter IRONREGULATED TRANSPORTER1(IRT1)at the Ser149 residue.Biochemical analyses and complementation of Fe transport in yeast and plants indicated that IRT1 Ser149 is critical for IRT1 transport activity.Taken together,these findings suggest that the CPK21/23-IRT1 signaling pathway is critical for Fe homeostasis in plants and provides targets for improving Fe-deficient environments and breeding crops resistant to Fe-deficient conditions.展开更多
The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe res...The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding ^13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.展开更多
Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chr...Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.展开更多
Developing secure software systems is a major challenge in the software industry due to errors or weaknesses that bring vulnerabilities to the software system.To address this challenge,researchers often use the source...Developing secure software systems is a major challenge in the software industry due to errors or weaknesses that bring vulnerabilities to the software system.To address this challenge,researchers often use the source code features of vulnerabilities to improve vulnerability detection.Notwithstanding the success achieved by these techniques,the existing studies mainly focus on the conceptual description without an accurate definition of vulnerability features.In this study,we introduce a novel and efficient Memory-Related Vulnerability Detection Approach using Vulnerability Features (MRVDAVF).Our framework uses three distinct strategies to improve vulnerability detection.In the first stage,we introduce an improved Control Flow Graph (CFG) and Pointer-related Control Flow Graph (PCFG) to describe the features of some common vulnerabilities,including memory leak,doublefree,and use-after-free.Afterward,two algorithms,namely Vulnerability Judging algorithm based on Vulnerability Feature (VJVF) and Feature Judging (FJ) algorithm,are employed to detect memory-related vulnerabilities.Finally,the proposed model is validated using three test cases obtained from Juliet Test Suite.The experimental results show that the proposed approach is feasible and effective.展开更多
基金supported by the National Natural Science Foundation of China(32222008,32100215,31900236)Northwest A&F University(Z111021604)+1 种基金the open funds of China Postdoctoral Science Foundation(2018M643740)Natural Science Basic Research Plan in Shaanxi Province of China(2019JQ-150).
文摘Iron(Fe)is an essential micronutrient for all organisms.Fe availability in the soil is usually much lower than that required for plant growth,and Fe deficiencies seriously restrict crop growth and yield.Calcium(Ca2+)is a second messenger in all eukaryotes;however,it remains largely unknown how Ca2+regulates Fe deficiency.In this study,mutations in CPK21 and CPK23,which are two highly homologous calcium-dependent protein kinases,conferredimpaired growth and rootdevelopment under Fe-deficient conditions,whereas constitutively active CPK21 and CPK23 enhanced plant tolerance to Fe-deficient conditions.Furthermore,we found that CPK21 and CPK23 interacted with and phosphorylated the Fe transporter IRONREGULATED TRANSPORTER1(IRT1)at the Ser149 residue.Biochemical analyses and complementation of Fe transport in yeast and plants indicated that IRT1 Ser149 is critical for IRT1 transport activity.Taken together,these findings suggest that the CPK21/23-IRT1 signaling pathway is critical for Fe homeostasis in plants and provides targets for improving Fe-deficient environments and breeding crops resistant to Fe-deficient conditions.
基金This work was supported by National Natural Science Foundation of China (31200615, 31600238), Postgraduate Research and Innovation Project of Hunan Province (CX2014B302), National Key Laboratory Cultivation Base Construction Project (15KFXM09), the National Science-Technology Support Plan Projects of China (2012BAI29B04), The talent introduction Science Foundation of Hunan Agricultural University (13YJ09), and the Natural Science Foundation of Hunan Province (2016JJ4040).
文摘The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding ^13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.
基金financially supported by Hunan Provincial Natural Science Foundation of China(grant 2017JJ1017)National Key R&D Program of China(grant 2017YFD0501403)+1 种基金National Natural Science Foundation of China(grant 31400275)Hunan Provincial Natural Science Foundation of China(2018JJ2172).
文摘Gelsemium elegans(G.elegans)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae family.Here,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were generated.After filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage depth.The de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 Mb.The vast majority(99.2%)of the G.elegans assembled sequence was anchored onto 8 pseudo-chromosomes.The genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the assembly.Genome annotation revealed that 43.16%of the G.elegans genome is composed of repetitive elements and 23.9%is composed of long terminal repeat elements.We predicted 26,768 protein-coding genes,of which 84.56%were functionally annotated.The genomic sequences of G.elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.
基金funded by the National Natural Science Foundation of China(Nos.U1836116 and 61872167)the Project of Jiangsu Provincial Six Talent Peaks(No.XYDXXJS-016)the Graduate Research Innovation Project of Jiangsu Province(No.KYCX171807)。
文摘Developing secure software systems is a major challenge in the software industry due to errors or weaknesses that bring vulnerabilities to the software system.To address this challenge,researchers often use the source code features of vulnerabilities to improve vulnerability detection.Notwithstanding the success achieved by these techniques,the existing studies mainly focus on the conceptual description without an accurate definition of vulnerability features.In this study,we introduce a novel and efficient Memory-Related Vulnerability Detection Approach using Vulnerability Features (MRVDAVF).Our framework uses three distinct strategies to improve vulnerability detection.In the first stage,we introduce an improved Control Flow Graph (CFG) and Pointer-related Control Flow Graph (PCFG) to describe the features of some common vulnerabilities,including memory leak,doublefree,and use-after-free.Afterward,two algorithms,namely Vulnerability Judging algorithm based on Vulnerability Feature (VJVF) and Feature Judging (FJ) algorithm,are employed to detect memory-related vulnerabilities.Finally,the proposed model is validated using three test cases obtained from Juliet Test Suite.The experimental results show that the proposed approach is feasible and effective.