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11. Evolution and function of receptor-like kinases in arbuscular mycorrhizal symbiosis

Author

Chiu, Chai Hao and Paszkowski, Uta

Subjects
arbuscular mycorrhiza, kinases, plants, receptors, root development, symbiosis
Abstract

Evolution of the nutritional mutualism between plants and arbuscular mycorrhizal (AM) fungi was crucial to evolution of life, as it enabled the conquest of the green lineage and its ecosystem on land. Today, apart from AM fungi, plants co-exist with a plethora of micro-organisms, and exactly how the plant immune system balances the need for defence against detrimental micro-organisms and beneficial ones such as AM fungi remains enigmatic. This work characterised plant plasma membrane receptors that perceive microbial carbohydrate patterns, and how they bring about cellular and developmental changes. To understand the origins of the Lysin-motif (LysM) receptor-like kinases (RLKs) and Symbiosis Receptor Kinase (SYMRK), comprehensive phylogenomic analyses of these receptors in more than a hundred plant genomes revealed their deep origins in green algae. I then defined the major clades of LysM-RLKs, their correlation with plant symbiotic capabilities, how the pseudokinases have diversified and refined, and how the ancestral LysM-RLK gave rise to the repertoire in extant land plants. Independent events involving domain fusions of LysM with kinase domains in the plant kingdom and beyond demonstrate how modularity of protein domains enable genetic innovations in the tree of life. A clearly defined receptor phylogeny also enabled systematic genetic dissection of the RLKs. Functions of four different receptor clades were carefully analysed in rice using single and double mutants. Careful assessment of AM colonisation in these mutants reveal chitin and lipochito-oligosaccharides as redundant signals, perceived by an equally redundant set of RLKs, as well as a symbiosis-specific receptor that represents a second checkpoint of symbiotic scrutiny - confirming insights from phylogenomic analyses. Perception of AM fungi also result in plants producing more lateral roots, a response observed for decades. Here, molecular mechanisms of this developmental response are elucidated, where general perception of chitin-derived molecules through LysM receptors and SYMRK activate lateral organ production. This response is also conserved in non-AM hosts, revealing the existence of an ancestral signalling function of these RLKs in shaping plant development - which may have been recruited in the evolution of nitrogen fixing root-nodules. Transgenic lines containing tagged-RLKs were also characterised, paving the way for future biochemical experiments to understand how the receptor complexes activate downstream signalling components for their biological functions.

Published
2022
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18. Robust Identification of Gene-Environment Interactions under High-Dimensional Accelerated Failure Time Models

Author

Zhang, Qingzhao, Chai, Hao, and Ma, Shuangge

Subjects
Statistics - Methodology, Statistics - Applications
Abstract

For complex diseases, beyond the main effects of genetic (G) and environmental (E) factors, gene-environment (G-E) interactions also play an important role. Many of the existing G-E interaction methods conduct marginal analysis, which may not appropriately describe disease biology. Joint analysis methods have been developed, with most of the existing loss functions constructed based on likelihood. In practice, data contamination is not uncommon. Development of robust methods for interaction analysis that can accommodate data contamination is very limited. In this study, we consider censored survival data and adopt an accelerated failure time (AFT) model. An exponential squared loss is adopted to achieve robustness. A sparse group penalization approach, which respects the "main effects, interactions" hierarchy, is adopted for estimation and identification. Consistency properties are rigorously established. Simulation shows that the proposed method outperforms direct competitors. In data analysis, the proposed method makes biologically sensible findings.

Published
2020

31. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2

Author

Xin-Ran Li, Jongho Sun, Doris Albinsky, Darius Zarrabian, Raphaella Hull, Tak Lee, Edwin Jarratt-Barnham, Chai Hao Chiu, Amy Jacobsen, Eleni Soumpourou, Alessio Albanese, Wouter Kohlen, Leonie H. Luginbuehl, Bruno Guillotin, Tom Lawrensen, Hui Lin, Jeremy Murray, Emma Wallington, Wendy Harwood, Jeongmin Choi, Uta Paszkowski, and Giles E. D. Oldroyd

Subjects
Science
Abstract

Lipochitooligosaccharide (LCO) perception by legumes is required to establish symbiotic relationships with nitrogen fixing bacteria. Here the authors show that nutrient starvation can activate LCO perception in cereals to promote symbiotic association with arbuscular mycorrhizal fungi.

Published
2022
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32. miR-505-5p alleviates acute rejection of liver transplantation by inhibiting Myd88 and inducing M2 polarizationof Kupffer cells

Author

Chai Hao, Lei Zilun, Liu Yanyao, Gong Junhua, Cao Zhenrui, Huang Zuotian, Yang Hang, and Wu Zhongjun

Subjects
immune tolerance, liver transplantation, macrophages, miR-505-5p, Myd88, Biochemistry, QD415-436, Genetics, QH426-470
Abstract

The occurrence of acute rejection after liver transplantation seriously impairs the prognosis of patients. miRNA is involved in many physiological and pathological processes of the body, but the mechanism of miRNA action in liver transplantation is not completely clear. In this study, we discuss the role of miR-505-5p in acute rejection after liver transplantation and its putative regulating mechanism. We construct an allogeneic rat liver transplantation model, observe the morphological and pathological changes in liver tissue, detect the expression levels of Myd88, miR-505-5p, IL-10 and TNF-α, and confirm that Myd88 is one of the direct targets of miR-505. The effects of miR-505-5p on the Myd88/TRAF6/NF-κB and MAPK pathways are detected both in vitro and in vivo, and the standard markers of Kupffer cell M1/M2 polarization are also detected. The results of qRT-PCR experiments show that miR-505-5p has a downward trend in rats with acute rejection. Western blot analysis reveals that over-expression of miR-505-5p induces the reduction of NF-κB and MAPK pathways both in vitro and in vivo. The role of miR-505-5p in alleviating acute rejection after transplantation may be accomplished by inducing M2-type polarization of Kupffer cells. In conclusion, we find that miR-505-5p alleviates acute rejection of liver transplantation by inducing M2 polarization of macrophages via the Myd88/TRAF6 axis, which suggests a potential strategy based on miRNAs in the follow-up treatment of liver transplantation.

Published
2022
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36. Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness.

Author

Zhao, Zhengxiang, Pei, Shuang, Song, Yuying, Yang, Tiantian, Gao, Yuan, Chai, Hao, Luan, Feishi, Zhu, Zicheng, and Wang, Xuezheng

Subjects
LOCUS (Genetics), GENETIC regulation, GERMPLASM, CHROMOSOMES, WATERMELONS, FLUORESCENCE
Abstract

Rind thickness (RT) is an important agronomic trait in watermelon [Citrullus lanatus (Thunb.) Mansf.] and affects watermelon storability. However, genetic studies on this trait, as well as gene regulation studies, are scarce and of limited production significance. We constructed a temporary F2 generation using the highly differentiated thick-rind watermelon 'XiaoXiGua-4' and the thin-rind watermelon 'DuanMan' as parents and localized the Cla97C02G044120 gene, which controls the thickness of watermelon rind, to the intervals of chromosome 2, CL2-32303995 and CL2-32316840, through 2 years of genetic analysis. No exonic mutations were found in this gene, but two promoter mutations resulted in changes in the promoter progenitor. Fluorescence quantitative PCR analysis revealed highly significant differences in expression at 1 d and 28 d, and the expression was significantly lower in thick-skinned watermelon varieties. Marker-assisted selection (MAS) for this trait was performed using the Caps marker CL2-32303995 and the InDel marker CL2-32316840, which not only verified the stability of the localization interval but also distinguished thick rind from thin rind. These results can be used for germplasm resource screening and have strong breeding significance. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2

Author

Li, Xin-Ran, Sun, Jongho, Albinsky, Doris, Zarrabian, Darius, Hull, Raphaella, Lee, Tak, Jarratt-Barnham, Edwin, Chiu, Chai Hao, Jacobsen, Amy, Soumpourou, Eleni, Albanese, Alessio, Kohlen, Wouter, Luginbuehl, Leonie H., Guillotin, Bruno, Lawrensen, Tom, Lin, Hui, Murray, Jeremy, Wallington, Emma, Harwood, Wendy, Choi, Jeongmin, Paszkowski, Uta, and Oldroyd, Giles E. D.

Published
2022
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43. Identifying Gene-Environment Interactions with A Least Relative Error Approach

Author

Zang, Yangguang, Zhao, Yinjun, Zhang, Qingzhao, Chai, Hao, Zhang, Sanguo, and Ma, Shuangge

Subjects
Statistics - Methodology
Abstract

For complex diseases, the interactions between genetic and environmental risk factors can have important implications beyond the main effects. Many of the existing interaction analyses conduct marginal analysis and cannot accommodate the joint effects of multiple main effects and interactions. In this study, we conduct joint analysis which can simultaneously accommodate a large number of effects. Significantly different from the existing studies, we adopt loss functions based on relative errors, which offer a useful alternative to the "classic" methods such as the least squares and least absolute deviation. Further to accommodate censoring in the response variable, we adopt a weighted approach. Penalization is used for identification and regularized estimation. Computationally, we develop an effective algorithm which combines the majorize-minimization and coordinate descent. Simulation shows that the proposed approach has satisfactory performance. We also analyze lung cancer prognosis data with gene expression measurements., Comment: 16 pages

Published
2016

48. A Robust Approach for Identifying Gene-Environment Interactions for Prognosis

Author

Chai, Hao, Zhang, Qingzhao, Jiang, Yu, Wang, Guohua, Zhang, Sanguo, and Ma, Shuangge

Subjects
Statistics - Applications
Abstract

For many complex diseases, prognosis is of essential importance. It has been shown that, beyond the main effects of genetic (G) and environmental (E) risk factors, the gene-environment (G$\times$E) interactions also play a critical role. In practice, the prognosis outcome data can be contaminated, and most of the existing methods are not robust to data contamination. In the literature, it has been shown that even a single contaminated observation can lead to severely biased model estimation. In this study, we describe prognosis using an accelerated failure time (AFT) model. An exponential squared loss is proposed to accommodate possible data contamination. A penalization approach is adopted for regularized estimation and marker selection. The proposed method is realized using an effective coordinate descent (CD) and minorization maximization (MM) algorithm. Simulation shows that without contamination, the proposed method has performance comparable to or better than the unrobust alternative. With contamination, it outperforms the unrobust alternative and, under certain scenarios, can be superior to the robust method based on quantile regression. The proposed method is applied to the analysis of TCGA (The Cancer Genome Atlas) lung cancer data. It identifies interactions different from those using the alternatives. The identified marker have important implications and satisfactory stability., Comment: 27 pages, 1 figure

Published
2015

49. Micromechanical study of loess permeability and seepage erosion based on microstructure functional basic unit and seepage simulation in pore domain.

Author

Wang, Weiping, Li, Xi-An, Dong, Haoyang, Chai, Hao, and Yang, Wenfu

Abstract

The vast majority of geological disasters in loess-covered areas are caused by seepage erosion in loess. Therefore, this study focuses on the microscopic mechanism of loess seepage erosion and constructs a loess microstructure model based on particle "core + coat". On this basis, the scanning electron microscope (SEM) photos are imported into COMSOL to simulate the micro-scale seepage in the pore domain. Through the actual permeability test, combined with the micro-quantitative information obtained by Image-Pro-Plus and Arcgis, the micro-factors affecting loess permeability are quantitatively analyzed by grey relational analysis. The results show that the dry density affects the porosity of loess and ultimately determines the permeability of loess. Different pore types and proportions lead to different seepage erosion of loess. The erosion process mainly occurs at the junction of pores. The sudden increase of velocity, pressure drop, and maximum shear rate at the throat indicate that this area is the main action area of loess seepage erosion. The research results of this study provide an important theoretical basis for the research and prevention of geological disasters and engineering diseases related to seepage deformation and failure in loess area. [ABSTRACT FROM AUTHOR]

Published
2024
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