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Tahira Syed; Muhammad Askari; Zhigang Meng; Yanyan Li; Muhammad Abid; Yunxiao Wei; Sandui Guo; Chengzhen Liang; Rui Zhang. Correction: Syed, T., et al. Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers. Toxins 2020, 12, 522. Toxins 2021, 13, 200 .
AMA StyleTahira Syed, Muhammad Askari, Zhigang Meng, Yanyan Li, Muhammad Abid, Yunxiao Wei, Sandui Guo, Chengzhen Liang, Rui Zhang. Correction: Syed, T., et al. Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers. Toxins 2020, 12, 522. Toxins. 2021; 13 (3):200.
Chicago/Turabian StyleTahira Syed; Muhammad Askari; Zhigang Meng; Yanyan Li; Muhammad Abid; Yunxiao Wei; Sandui Guo; Chengzhen Liang; Rui Zhang. 2021. "Correction: Syed, T., et al. Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers. Toxins 2020, 12, 522." Toxins 13, no. 3: 200.
Continual reduction in sequencing cost is expanding the accessibility of genome sequencing data for routine clinical applications. However, the lack of methods to construct machine learning-based predictive models using these datasets has become a crucial bottleneck for the application of sequencing technology in clinics. Here we developed a new algorithm, eTumorMetastasis, which transforms tumor functional mutations into network-based profiles and identifies network operational gene signatures (NOG signatures). NOG signatures model the tipping point at which a tumor cell shifts from a state that doesn’t favor recurrence to one that does. We showed that NOG signatures derived from genomic mutations of tumor founding clones (i.e., the ‘most recent common ancestor’ of the cells within a tumor) significantly distinguished recurred and non-recurred breast tumors as well as outperformed the most popular genomic test (i.e., Oncotype DX breast cancer recurrence score). These results imply that mutations of the tumor founding clones are associated with tumor recurrence and can be used to predict clinical outcomes. As such, predictive tools could be used in clinics to guide treatment routes. Finally, the concepts underlying the eTumorMetastasis pave the way for the application of genome sequencing in predictions for other complex genetic diseases. ETumorMetastasis pseudocode and related data used in this study can be found in our Github directory (https://github.com/WangEdwinLab/eTumorMetastasis).
Jean-Sébastien Milanese; Chabane Tibiche; Naif Zaman; Jinfeng Zou; Pengyong Han; Zhigang Meng; Andre Nantel; Arnaud Droit; Edwin Wang. ETumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients. Genomics, Proteomics & Bioinformatics 2021, 1 .
AMA StyleJean-Sébastien Milanese, Chabane Tibiche, Naif Zaman, Jinfeng Zou, Pengyong Han, Zhigang Meng, Andre Nantel, Arnaud Droit, Edwin Wang. ETumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients. Genomics, Proteomics & Bioinformatics. 2021; ():1.
Chicago/Turabian StyleJean-Sébastien Milanese; Chabane Tibiche; Naif Zaman; Jinfeng Zou; Pengyong Han; Zhigang Meng; Andre Nantel; Arnaud Droit; Edwin Wang. 2021. "ETumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients." Genomics, Proteomics & Bioinformatics , no. : 1.
Allotetraploid cotton (Gossypium hirsutum and Gossypium barbadense) are cultivated worldwide for its white fiber. For centuries, conventional breeding approaches increase cotton yield at the cost of extensive erosion of natural genetic variability. Sea Island cotton (G. barbadense) is known for its superior fiber quality, but show poor adaptability as compared to Upland cotton. Here, in this study, we use ethylmethanesulfonate (EMS) as a mutagenic agent to induce genome-wide point mutations to improve the current germplasm resources of Sea Island cotton and develop diverse breeding lines with improved adaptability and excellent economic traits. We determined the optimal EMS experimental procedure suitable for construction of cotton mutant library. At M6 generation, mutant library comprised of lines with distinguished phenotypes of the plant architecture, leaf, flower, boll, and fiber. Genome-wide analysis of SNP distribution and density in yellow leaf mutant reflected the better quality of mutant library. Reduced photosynthetic efficiency and transmission electron microscopy of yellow leaf mutants revealed the effect of induced mutations at physiological and cellular level. Our mutant collection will serve as the valuable resource for basic research on cotton functional genomics, as well as cotton breeding.
Muhammad Ali Abid; Peilin Wang; Tao Zhu; Chengzhen Liang; Zhigang Meng; Waqas Malik; Sandui Guo; Rui Zhang. Construction of Gossypiumbarbadense Mutant Library Provides Genetic Resources for Cotton Germplasm Improvement. International Journal of Molecular Sciences 2020, 21, 6505 .
AMA StyleMuhammad Ali Abid, Peilin Wang, Tao Zhu, Chengzhen Liang, Zhigang Meng, Waqas Malik, Sandui Guo, Rui Zhang. Construction of Gossypiumbarbadense Mutant Library Provides Genetic Resources for Cotton Germplasm Improvement. International Journal of Molecular Sciences. 2020; 21 (18):6505.
Chicago/Turabian StyleMuhammad Ali Abid; Peilin Wang; Tao Zhu; Chengzhen Liang; Zhigang Meng; Waqas Malik; Sandui Guo; Rui Zhang. 2020. "Construction of Gossypiumbarbadense Mutant Library Provides Genetic Resources for Cotton Germplasm Improvement." International Journal of Molecular Sciences 21, no. 18: 6505.
Bacillus thuringiensis (Bt) is a gram negative soil bacterium. This bacterium secretes various proteins during different growth phases with an insecticidal potential against many economically important crop pests. One of the important families of Bt proteins is vegetative insecticidal proteins (Vip), which are secreted into the growth medium during vegetative growth. There are three subfamilies of Vip proteins. Vip1 and Vip2 heterodimer toxins have an insecticidal activity against many Coleopteran and Hemipteran pests. Vip3, the most extensively studied family of Vip toxins, is effective against Lepidopteron. Vip proteins do not share homology in sequence and binding sites with Cry proteins, but share similarities at some points in their mechanism of action. Vip3 proteins are expressed as pyramids alongside Cry proteins in crops like maize and cotton, so as to control resistant pests and delay the evolution of resistance. Biotechnological- and in silico-based analyses are promising for the generation of mutant Vip proteins with an enhanced insecticidal activity and broader spectrum of target insects.
Tahira Syed; Muhammad Askari; Zhigang Meng; Yanyan Li; Muhammad Abid; Yunxiao Wei; Sandui Guo; Chengzhen Liang; Rui Zhang. Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers. Toxins 2020, 12, 522 .
AMA StyleTahira Syed, Muhammad Askari, Zhigang Meng, Yanyan Li, Muhammad Abid, Yunxiao Wei, Sandui Guo, Chengzhen Liang, Rui Zhang. Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers. Toxins. 2020; 12 (8):522.
Chicago/Turabian StyleTahira Syed; Muhammad Askari; Zhigang Meng; Yanyan Li; Muhammad Abid; Yunxiao Wei; Sandui Guo; Chengzhen Liang; Rui Zhang. 2020. "Current Insights on Vegetative Insecticidal Proteins (Vip) as Next Generation Pest Killers." Toxins 12, no. 8: 522.
Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na+/H+ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of Gossypium barbadense in comparison with Gossypium hirsutum. In G. barbadense, 25 NHX genes were identified on the basis of the Na+_H+ exchanger domain. All except one of the G. barbadense NHX transporters have an Amiloride motif that is a known inhibitor of Na+ ions in plants. A phylogenetic analysis inferred three classes of GbNHX genes—viz., Vac (GbNHX1, 2 and 4), Endo (GbNHX6), and PM (GbNHX7). A high number of the stress-related cis-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of GbNHX genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of G. barbadense NHX transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In G. barbadense, the expression was higher in the stem, while in G. hirsutum the leaf and root showed a high expression. Moreover, our results revealed that NHX2 homologues in both species have a high expression under salinity stress at higher time intervals, followed by NHX7. The protein-protein prediction study revealed that GbNHX7 is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na+ transport for the further functional study of Gossypium NHX genes.
Umar Akram; Yuhan Song; Chengzhen Liang; Muhammad Ali Abid; Muhammad Askari; Aye Aye Myat; Mubashir Abbas; Waqas Malik; Zulfiqar Ali; Sandui Guo; Rui Zhang; Zhigang Meng. Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum. Genes 2020, 11, 803 .
AMA StyleUmar Akram, Yuhan Song, Chengzhen Liang, Muhammad Ali Abid, Muhammad Askari, Aye Aye Myat, Mubashir Abbas, Waqas Malik, Zulfiqar Ali, Sandui Guo, Rui Zhang, Zhigang Meng. Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum. Genes. 2020; 11 (7):803.
Chicago/Turabian StyleUmar Akram; Yuhan Song; Chengzhen Liang; Muhammad Ali Abid; Muhammad Askari; Aye Aye Myat; Mubashir Abbas; Waqas Malik; Zulfiqar Ali; Sandui Guo; Rui Zhang; Zhigang Meng. 2020. "Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum." Genes 11, no. 7: 803.
Plant genetic transformation systems have facilitated insights into molecular plant biology and revolutionized commercial agriculture. Unfortunately, agrobacterium-mediated transformation was still the main method although its subsequent regeneration process from tissue culture in cotton remained arduous even after 30 years of technological advances. At the same time, a number of transformation methods based on pollen grains have been developed, such as electroporation, biolistic bombardment, ultra-sonication, and Agrobacterium incubation in plant pollens. But these pollen-based techniques have not been widely adopted. In this chapter, we have presented a protocol of pollen-based transformation technology in cotton, “pollen magnetofection,” to directly produce transgenic seeds without tissue culturing. In this system, magnetic nanoparticles loaded with pure plasmid DNA carrying functional genes were delivered into pollens via pollen apertures in the presence of a magnetic field. Afterward, these magnetofected pollens were used for pollination, to produce transformed seeds. Pollen magnetofection is a genotype-independent transformation system; in addition, exogenous DNA was successfully integrated into the genome and stably expressed in the successive generations. We emphasize that pollen magnetofection is a most efficient platform for genetic transformation of cotton and other crops with high-throughput and efficient potential infield operation.
Rui Zhang; Zhigang Meng; Muhammad Ali Abid; Xiang Zhao. Novel Pollen Magnetofection System for Transformation of Cotton Plant with Magnetic Nanoparticles as Gene Carriers. Advanced Structural Safety Studies 2018, 47 -54.
AMA StyleRui Zhang, Zhigang Meng, Muhammad Ali Abid, Xiang Zhao. Novel Pollen Magnetofection System for Transformation of Cotton Plant with Magnetic Nanoparticles as Gene Carriers. Advanced Structural Safety Studies. 2018; ():47-54.
Chicago/Turabian StyleRui Zhang; Zhigang Meng; Muhammad Ali Abid; Xiang Zhao. 2018. "Novel Pollen Magnetofection System for Transformation of Cotton Plant with Magnetic Nanoparticles as Gene Carriers." Advanced Structural Safety Studies , no. : 47-54.
Genetic modification plays a vital role in breeding new crops with excellent traits. Almost all the current genetic modification methods require regeneration from tissue culture, involving complicated, long and laborious processes. In particular, many crop species such as cotton are difficult to regenerate. Here, we report a novel transformation platform technology, pollen magnetofection, to directly produce transgenic seeds without regeneration. In this system, exogenous DNA loaded with magnetic nanoparticles was delivered into pollen in the presence of a magnetic field. Through pollination with magnetofected pollen, transgenic plants were successfully generated from transformed seeds. Exogenous DNA was successfully integrated into the genome, effectively expressed and stably inherited in the offspring. Our system is culture-free and genotype independent. In addition, it is simple, fast and capable of multi-gene transformation. We envision that pollen magnetofection can transform almost all crops, greatly facilitating breeding processes of new varieties of transgenic crops.
Xiang Zhao; Zhigang Meng; Yan Wang; Wenjie CHEN; Changjiao Sun; Bo Cui; Jinhui Cui; Manli Yu; Zhanghua Zeng; Sandui Guo; Dan Luo; Jerry Q. Cheng; Rui Zhang; Haixin Cui. Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers. Nature Plants 2017, 3, 956 -964.
AMA StyleXiang Zhao, Zhigang Meng, Yan Wang, Wenjie CHEN, Changjiao Sun, Bo Cui, Jinhui Cui, Manli Yu, Zhanghua Zeng, Sandui Guo, Dan Luo, Jerry Q. Cheng, Rui Zhang, Haixin Cui. Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers. Nature Plants. 2017; 3 (12):956-964.
Chicago/Turabian StyleXiang Zhao; Zhigang Meng; Yan Wang; Wenjie CHEN; Changjiao Sun; Bo Cui; Jinhui Cui; Manli Yu; Zhanghua Zeng; Sandui Guo; Dan Luo; Jerry Q. Cheng; Rui Zhang; Haixin Cui. 2017. "Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers." Nature Plants 3, no. 12: 956-964.
The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse. We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results with acceptable efficiency compared with currently available tools. GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization. The online version of this article (10.1186/s12859-017-1930-3) contains supplementary material, which is available to authorized users.
Tao Zhu; Chengzhen Liang; Zhigang Meng; Sandui Guo; Rui Zhang. GFF3sort: a novel tool to sort GFF3 files for tabix indexing. BMC Bioinformatics 2017, 18, 482 .
AMA StyleTao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang. GFF3sort: a novel tool to sort GFF3 files for tabix indexing. BMC Bioinformatics. 2017; 18 (1):482.
Chicago/Turabian StyleTao Zhu; Chengzhen Liang; Zhigang Meng; Sandui Guo; Rui Zhang. 2017. "GFF3sort: a novel tool to sort GFF3 files for tabix indexing." BMC Bioinformatics 18, no. 1: 482.
SummaryDesigning specific primers for multiple sites across the whole genome is still challenging, especially in species with complex genomes. Here we present PrimerServer, a high-throughput primer design and specificity-checking platform with both web and command-line interfaces. This platform efficiently integrates site selection, primer design, specificity checking and data presentation. In our case study, PrimerServer achieved high accuracy and a fast running speed for a large number of sites, suggesting its potential for molecular biology applications such as molecular breeding or medical testing.Availability and ImplementationSource code for PrimerServer is available at https://github.com/billzt/PrimerServer. A demo server is freely accessible at https://primerserver.org, with all major browsers [email protected] or [email protected]
Tao Zhu; Chengzhen Liang; Zhigang Meng; Yanyan Li; Yayu Wu; Sandui Guo; Rui Zhang. PrimerServer: a high-throughput primer design and specificity-checking platform. 2017, 181941 .
AMA StyleTao Zhu, Chengzhen Liang, Zhigang Meng, Yanyan Li, Yayu Wu, Sandui Guo, Rui Zhang. PrimerServer: a high-throughput primer design and specificity-checking platform. . 2017; ():181941.
Chicago/Turabian StyleTao Zhu; Chengzhen Liang; Zhigang Meng; Yanyan Li; Yayu Wu; Sandui Guo; Rui Zhang. 2017. "PrimerServer: a high-throughput primer design and specificity-checking platform." , no. : 181941.
Background:The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexed by tabix, a novel strategy that is more convenient than the original conversion process. However, current tools available for GFF3 file sorting have some limitations and their sorting results would lead to erroneous rendering in JBrowse.Results:We developed GFF3sort, a script to sort GFF3 files for tabix indexing. Specifically designed for JBrowse rendering, GFF3sort can properly deal with the order of features that have the same chromosome and start position, either by remembering their original orders or by conducting parent-child topology sorting. Based on our test datasets from seven species, GFF3sort produced accurate sorting results with acceptable efficiency compared with currently available tools.Conclusions:GFF3sort is a novel tool to sort GFF3 files for tabix indexing. We anticipate that GFF3sort will be useful to help with genome annotation data processing and visualization.
Tao Zhu; Chengzhen Liang; Zhigang Meng; Sandui Guo; Rui Zhang. GFF3sort: a novel tool to sort GFF3 files for tabix indexing. 2017, 145938 .
AMA StyleTao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang. GFF3sort: a novel tool to sort GFF3 files for tabix indexing. . 2017; ():145938.
Chicago/Turabian StyleTao Zhu; Chengzhen Liang; Zhigang Meng; Sandui Guo; Rui Zhang. 2017. "GFF3sort: a novel tool to sort GFF3 files for tabix indexing." , no. : 145938.
Cotton (Gossypium spp.) is the single most important spinning fiber that has economic significance worldwide. Cotton is one of the most value-added crops and an excellent model system for the analysis of polyploidization and cell development. Thus, the Cotton Genome Consortium has made rapid and significant progress in whole genome sequencing studies in the last decade. Developments in cotton genome sequencing and assembly provide powerful tools for dissecting the genetic and molecular bases of agronomically important traits and establishing regulatory networks on these processes, which leads to molecular breeding. Here, we briefly review these advances, emphasizing their implications in the genetic improvement of cotton with a particular focus on fiber quality and yield. Moreover, major progresses in chloroplast and mitochondrial genomes have also been summarized.
Rong Yan; Chengzhen Liang; Zhigang Meng; Waqas Malik; Tao Zhu; Xuefeng Zong; Sandui Guo; Rui Zhang. Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.). 3 Biotech 2016, 6, 217 .
AMA StyleRong Yan, Chengzhen Liang, Zhigang Meng, Waqas Malik, Tao Zhu, Xuefeng Zong, Sandui Guo, Rui Zhang. Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.). 3 Biotech. 2016; 6 (2):217.
Chicago/Turabian StyleRong Yan; Chengzhen Liang; Zhigang Meng; Waqas Malik; Tao Zhu; Xuefeng Zong; Sandui Guo; Rui Zhang. 2016. "Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.)." 3 Biotech 6, no. 2: 217.
The bZIP transcription factor (TF) act as an important regulator for the abscisic acid (ABA) mediated abiotic stresses signaling pathways in plants. Here, we reported the cloning and characterization of GhABF2, encoding for typical cotton bZIP TF. Overexpression of GhABF2 significantly improved drought and salt stress tolerance both in Arabidopsis and cotton. However, silencing of GhABF2 made transgenic cotton sensitive to PEG osmotic and salt stress. Expression of GhABF2 was induced by drought and ABA treatments but repressed by high salinity. Transcriptome analysis indicated that GhABF2 increases drought and salt tolerance by regulating genes related to ABA, drought and salt response. The proline contents, activity of superoxide dismutase (SOD) and catalase (CAT) were also significantly increased in GhABF2-overexpression cottons in comparison to wild type after drought and salt treatment. Further, an increase in fiber yield under drought and saline-alkali wetland exhibited the important role of GhABF2 in enhancing the drought and salt tolerance in transgenic lines. In conclusion, manipulation of GhABF2 by biotechnological tools could be a sustainable strategy to deploy drought and salt tolerance in cotton.
Chengzhen Liang; Zhaohong Meng; Zhigang Meng; Waqas Malik; Rong Yan; Khin Myat Lwin; Fazhuang Lin; Yuan Wang; Guoqing Sun; Tao Zhu; Jianying Li; Shuangxia Jin; Sandui Guo; Rui Zhang. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.). Scientific Reports 2016, 6, 35040 .
AMA StyleChengzhen Liang, Zhaohong Meng, Zhigang Meng, Waqas Malik, Rong Yan, Khin Myat Lwin, Fazhuang Lin, Yuan Wang, Guoqing Sun, Tao Zhu, Jianying Li, Shuangxia Jin, Sandui Guo, Rui Zhang. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.). Scientific Reports. 2016; 6 (1):35040.
Chicago/Turabian StyleChengzhen Liang; Zhaohong Meng; Zhigang Meng; Waqas Malik; Rong Yan; Khin Myat Lwin; Fazhuang Lin; Yuan Wang; Guoqing Sun; Tao Zhu; Jianying Li; Shuangxia Jin; Sandui Guo; Rui Zhang. 2016. "GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.)." Scientific Reports 6, no. 1: 35040.
Guoqing Sun; Dongling Zhang; Rui Zhang; Yuan Wang; Zhigang Meng; Tao Zhu; Chenzhen Liang; Sandui Guo. Bt protein expression in the transgenic insect-resistant cotton in China. Science Bulletin 2016, 61, 1555 -1557.
AMA StyleGuoqing Sun, Dongling Zhang, Rui Zhang, Yuan Wang, Zhigang Meng, Tao Zhu, Chenzhen Liang, Sandui Guo. Bt protein expression in the transgenic insect-resistant cotton in China. Science Bulletin. 2016; 61 (20):1555-1557.
Chicago/Turabian StyleGuoqing Sun; Dongling Zhang; Rui Zhang; Yuan Wang; Zhigang Meng; Tao Zhu; Chenzhen Liang; Sandui Guo. 2016. "Bt protein expression in the transgenic insect-resistant cotton in China." Science Bulletin 61, no. 20: 1555-1557.
The components of the target of rapamycin (TOR) signaling pathway have been well characterized in heterotrophic organisms from yeast to humans. However, because of rapamycin insensitivity, embryonic lethality in tor null mutants and a lack of reliable ways of detecting TOR protein kinase in higher plants, the key players upstream and downstream of TOR remain largely unknown in plants. Using engineered rapamycin‐sensitive Binding Protein 12‐2 (BP12‐2) plants, the present study showed that combined treatment with rapamycin and active‐site TOR inhibitors (asTORis) results in synergistic inhibition of TOR activity and plant growth in Arabidopsis. Based on this system, we revealed that TOR signaling plays a crucial role in modulating the transition from heterotrophic to photoautotrophic growth in Arabidopsis. Ribosomal protein S6 kinase 2 (S6K2) was identified as a direct downstream target of TOR, and the growth of TOR‐suppressed plants could be rescued by up‐regulating S6K2. Systems, genetic, and biochemical analyses revealed that Brassinosteriod Insensitive 2 (BIN2) acts as a novel downstream effector of S6K2, and the phosphorylation of BIN2 depends on TOR‐S6K2 signaling in Arabidopsis. By combining pharmacological with genetic and biochemical approaches, we determined that the TOR‐S6K2‐BIN2 signaling pathway plays important roles in regulating the photoautotrophic growth of Arabidopsis.
Fangjie Xiong; Rui Zhang; Zhigang Meng; Kexuan Deng; Yumei Que; Fengping Zhuo; Li Feng; Sundui Guo; Raju Datla; Maozhi Ren. Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis. New Phytologist 2016, 213, 233 -249.
AMA StyleFangjie Xiong, Rui Zhang, Zhigang Meng, Kexuan Deng, Yumei Que, Fengping Zhuo, Li Feng, Sundui Guo, Raju Datla, Maozhi Ren. Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis. New Phytologist. 2016; 213 (1):233-249.
Chicago/Turabian StyleFangjie Xiong; Rui Zhang; Zhigang Meng; Kexuan Deng; Yumei Que; Fengping Zhuo; Li Feng; Sundui Guo; Raju Datla; Maozhi Ren. 2016. "Brassinosteriod Insensitive 2 (BIN2) acts as a downstream effector of the Target of Rapamycin (TOR) signaling pathway to regulate photoautotrophic growth in Arabidopsis." New Phytologist 213, no. 1: 233-249.
The development of genetically modified crops requires new promoters and regulatory regions to achieve high gene expression and/or tissue-specific expression patterns in plants. To obtain promoter sequences of plants with new properties, we analyzed the expression traits of the cotton (Gossypium hirsutum) translation elongation factor 1A gene family. The results showed that the GhEF1A8 gene is highly expressed in different organs of cotton plants, and showed much higher transcript levels in stems and leaves. Its promoter (GhEF1A1.7) and the 5′ untranslated region (5′ UTR), comprising a regulatory region named PGhEF1A8, were isolated from cotton and studied in stably transformed tobacco plants. The regulatory region sequences were fused to the β-glucuronidase (GUS) reporter gene to characterize its expression pattern in tobacco. Histochemical and fluorometric GUS activity assays demonstrated that PGhEF1A8 could direct GUS gene expression in all tissues and organs in transgenic tobacco, including leaves, stems, flowers, and roots. The level of GUS activity in the leaves and stems was significantly higher than in cauliflower mosaic virus (CaMV) 35S promoter::GUS plants, but as same as CaMV 35S promoter::GUS plants in flower and root tissues. GUS expression levels decreased 2–10-fold when the 5′ UTR was absent from PGhEF1A8. Deletion analysis of the PGhEF1A8 sequence showed that the region −647 to −323 might possess negative elements that repress transgene expression in tobacco plants. The results suggested that the GhEF1A8 regulation region may represent a practical choice to direct high-level constitutive expression of transgenes and could be a valuable new tool in plant genetic engineering.
Bao Sun; Guo-Qing Sun; Zhigang Meng; Rui Zhang; San-Dui Guo. A novel constitutive promoter and its downstream 5′ UTR derived from cotton (Gossypium spp.) drive high-level gene expression in stem and leaf tissues. Journal of Integrative Agriculture 2016, 15, 755 -762.
AMA StyleBao Sun, Guo-Qing Sun, Zhigang Meng, Rui Zhang, San-Dui Guo. A novel constitutive promoter and its downstream 5′ UTR derived from cotton (Gossypium spp.) drive high-level gene expression in stem and leaf tissues. Journal of Integrative Agriculture. 2016; 15 (4):755-762.
Chicago/Turabian StyleBao Sun; Guo-Qing Sun; Zhigang Meng; Rui Zhang; San-Dui Guo. 2016. "A novel constitutive promoter and its downstream 5′ UTR derived from cotton (Gossypium spp.) drive high-level gene expression in stem and leaf tissues." Journal of Integrative Agriculture 15, no. 4: 755-762.
Arginase is the only enzyme capable of producing urea in plants. This enzyme also contributes to many important biological functions during plant growth and development, such as seed development, root development and plant nitrogen using. The unique rice arginase gene OsARG is known to affect nitrogen use efficiency and is also associated with higher yields in rice. In this study, we transformed OsARG into upland cotton R18 by Agrobacterium-mediated genetic transformation and analyzed the function of OsARG in transgenic cotton. Two independent OsARG expression transgenic cotton lines, ARG-26 and ARG-38, were obtained via transformation. Southern blot analysis indicated that two copies and one copy of the OsARG gene were integrated into the ARG-26 and ARG-38 genomes, respectively. Enzyme activity and RNA transcription analysis revealed that the OsARG gene is highly expressed in cotton. The nitric oxide content and the morphology of ARG-26 and ARG-38 seedlings were both affected by expression of the OsARG gene. Field experiments indicated that the polyamine and nitrogen content increased by more than two-fold in the T3 generation plants of the transgenic cotton lines ARG-26-2, ARG-26-7, ARG-38-8, and ARG-38-11, as compared with the control plants. After harvesting cotton fibers grown in field conditions, we analyzed the quality of fiber and found that the fiber length was increased in the transgenic lines. The average cotton fiber length for all of the transgenic cotton lines was two millimeters longer than the fibers of the control plants; the average cotton fiber lengths were 31.94 mm, 32.00 mm, 32.68 mm and 32.84 mm in the ARG-26ARG-26-2, ARG-26-7, ARG-38-8 and ARG-38-11 lines, respectively, but the average fiber length of the control plants was 29.36mm. Our results indicate that the OsARG gene could potentially be used to improve cotton fiber length traits.
Zhigang Meng; Zhaohong Meng; Rui Zhang; Chengzhen Liang; Jianmin Wan; Yanling Wang; Honghong Zhai; Sandui Guo. Expression of the Rice Arginase Gene OsARG in Cotton Influences the Morphology and Nitrogen Transition of Seedlings. PLOS ONE 2015, 10, e0141530 -e0141530.
AMA StyleZhigang Meng, Zhaohong Meng, Rui Zhang, Chengzhen Liang, Jianmin Wan, Yanling Wang, Honghong Zhai, Sandui Guo. Expression of the Rice Arginase Gene OsARG in Cotton Influences the Morphology and Nitrogen Transition of Seedlings. PLOS ONE. 2015; 10 (11):e0141530-e0141530.
Chicago/Turabian StyleZhigang Meng; Zhaohong Meng; Rui Zhang; Chengzhen Liang; Jianmin Wan; Yanling Wang; Honghong Zhai; Sandui Guo. 2015. "Expression of the Rice Arginase Gene OsARG in Cotton Influences the Morphology and Nitrogen Transition of Seedlings." PLOS ONE 10, no. 11: e0141530-e0141530.
Modified magnetic nanoparticles are used as non-viral gene carriers in biological applications. To achieve successful gene delivery, it is critical that nanoparticles effectually assemble with nucleic acids. However, relatively little work has been conducted on the assemble mechanisms between nanoparticles and DNA, and its effects on transfection efficiency. Using biophysical and biochemical characterization, along with Atomic force microscopy (AFM) and Transmission electron microscopy (TEM), we investigate the morphologies, assembling structures and gene delivering abilities of the PEI modified magnetic nanoparticles (MNPs) gene delivery system. In this gene delivery system, MNP/DNA complexes are formed via binding of DNA onto the surface of MNPs. MNPs are favorable to not only increase DNA concentration but also prevent DNA degradation. Magnetofection experiments showed that MNPs has low cytotoxicity and introduces highly stable transfection in mammalian somatic cells. In addition, different binding ratios between MNPs and DNA result in various morphologies of MNP/DNA complexes and have an influence on transfection efficiency. Dose–response profile indicated that transfection efficiency positively correlate with MNP/DNA ratio. Furthermore, intracellular tracking demonstrate that MNPs move though the cell membranes, deliver and release exogenous DNA into the nucleus.
Xiang Zhao; Haixin Cui; Wenjie Chen; Yan Wang; Bo Cui; Changjiao Sun; Zhigang Meng; Guoqiang Liu. Morphology, Structure and Function Characterization of PEI Modified Magnetic Nanoparticles Gene Delivery System. PLoS ONE 2014, 9, e98919 .
AMA StyleXiang Zhao, Haixin Cui, Wenjie Chen, Yan Wang, Bo Cui, Changjiao Sun, Zhigang Meng, Guoqiang Liu. Morphology, Structure and Function Characterization of PEI Modified Magnetic Nanoparticles Gene Delivery System. PLoS ONE. 2014; 9 (6):e98919.
Chicago/Turabian StyleXiang Zhao; Haixin Cui; Wenjie Chen; Yan Wang; Bo Cui; Changjiao Sun; Zhigang Meng; Guoqiang Liu. 2014. "Morphology, Structure and Function Characterization of PEI Modified Magnetic Nanoparticles Gene Delivery System." PLoS ONE 9, no. 6: e98919.
In flowering plants, male gametophytes are generated in anthers from microsporocytes. However, more evidence is needed to reveal the genetic mechanisms which regulate the differentiation and interaction of these highly specialized cells in anthers. Here we report the characterization of a series of male-sterile cotton (Gossypium hirsutum) mutants, including mutants with normal fertility, semi-sterility and complete sterility. These mutants are forms of transgenic cotton containing RNAi vectors with partial cDNA fragments of GhSERK1. The GhSERK1 gene encodes a putative leucine-rich repeat receptor protein kinase (LRR-RLK), and generally has 11 domains. In previous research, we found plants containing GhSERK1 produce an abundance of male reproductive tissue. In this paper, three RNAi constructs were designed separately to analyze its function in anther. After the three RNAi vectors were transformed into the cotton, transgenic plants with the specialized fragment exhibited normal fertility or the pollen energy decreased slightly, as ones with the homologous fragments exhibited various degrees of male sterility with different expression levels of GhSERK1 mRNA. In conclusion, for the transgenic plants with conserved fragments, lower expression levels of GhSERK1 mRNA were in transgenic plants, and a higher degree of male sterility was observed. Taking together, these findings demonstrate the GhSERK1 gene has a role in the development of anthers, especially in the formation of pollen grains. Also, we infer there must be another homolog of GhSERK1 in cotton, and both of GhSERK1 and its homolog function redundantly as important control points in controlling anther pollen production.
Ya-Li Shi; San-Dui Guo; Rui Zhang; Zhigang Meng; Mao-Zhi Ren. The role of Somatic embryogenesis receptor-like kinase 1 in controlling pollen production of the Gossypium anther. Molecular Biology Reports 2013, 41, 411 -422.
AMA StyleYa-Li Shi, San-Dui Guo, Rui Zhang, Zhigang Meng, Mao-Zhi Ren. The role of Somatic embryogenesis receptor-like kinase 1 in controlling pollen production of the Gossypium anther. Molecular Biology Reports. 2013; 41 (1):411-422.
Chicago/Turabian StyleYa-Li Shi; San-Dui Guo; Rui Zhang; Zhigang Meng; Mao-Zhi Ren. 2013. "The role of Somatic embryogenesis receptor-like kinase 1 in controlling pollen production of the Gossypium anther." Molecular Biology Reports 41, no. 1: 411-422.
FKBP12 encodes a prolyl isomerase and highly conserved in eukaryotic species. In yeasts and animals, FKBP12 can interact with rapamycin and FK506 to form rapamycin-FKBP12 and FK506-FKBP12 complex, respectively. In higher plants, FKBP12 protein lost its function to bind rapamycin and FK506. Early studies showed that yeast and human FKBP12 protein can restore the rapamycin sensitivity in Arabidopsis, but the used concentration is 100–1000 folds higher than that in yeast and animals. High concentration of drugs would increase the cost and cause the potential secondary effects on plant growth and development. Here we further discovered that BP12 plants generated in our previous study are hypersensitive to rapamycin at the concentration as low as that is effective in yeast and animals. It is surprising to observe that WT and BP12 plants are not sensitive to FK506 in normal growth condition. These findings advance the current understanding of rapamycin-TOR signaling in plants.
Rui Zhang; Zhigang Meng; Tao Zhou; Yong Deng; Li Feng; Yuan Wang; Guoqing Sun; Sandui Guo; Maozhi Ren. ScFKBP12 bridges rapamycin and AtTOR inArabidopsis. Plant Signaling & Behavior 2013, 8, e26115 .
AMA StyleRui Zhang, Zhigang Meng, Tao Zhou, Yong Deng, Li Feng, Yuan Wang, Guoqing Sun, Sandui Guo, Maozhi Ren. ScFKBP12 bridges rapamycin and AtTOR inArabidopsis. Plant Signaling & Behavior. 2013; 8 (11):e26115.
Chicago/Turabian StyleRui Zhang; Zhigang Meng; Tao Zhou; Yong Deng; Li Feng; Yuan Wang; Guoqing Sun; Sandui Guo; Maozhi Ren. 2013. "ScFKBP12 bridges rapamycin and AtTOR inArabidopsis." Plant Signaling & Behavior 8, no. 11: e26115.
Ya-Li Shi; Rui Zhang; Xiao-Ping Wu; Zhigang Meng; San-Dui Guo. Cloning and Characterization of a Somatic Embryogenesis Receptor-Like Kinase Gene in Cotton (Gossypium hirsutum). Journal of Integrative Agriculture 2012, 11, 898 -909.
AMA StyleYa-Li Shi, Rui Zhang, Xiao-Ping Wu, Zhigang Meng, San-Dui Guo. Cloning and Characterization of a Somatic Embryogenesis Receptor-Like Kinase Gene in Cotton (Gossypium hirsutum). Journal of Integrative Agriculture. 2012; 11 (6):898-909.
Chicago/Turabian StyleYa-Li Shi; Rui Zhang; Xiao-Ping Wu; Zhigang Meng; San-Dui Guo. 2012. "Cloning and Characterization of a Somatic Embryogenesis Receptor-Like Kinase Gene in Cotton (Gossypium hirsutum)." Journal of Integrative Agriculture 11, no. 6: 898-909.