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Plant mineral nutrient sensing and signaling

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Journal of Integrative Plant Biology 2014年第3期56卷 190-191页

作者： l.on v.kochian William J.lucas Robert W.Holley Center for Agriculture and Health USDA‐ARS Cornell University Department of Plant Biology College of Biological Sciences University of California

As terrestrial plants are sessile organisms and therefore must directly deal with an often complex and changing environment, they have had to develop complex and elegant strategies to survive and thrive in the face of environmental stress. This is particularly true for plant adaptation to the soil environment, where essential mineral nutrients often are found at sub- optimal levels and their concentrations can vary significantly, both spatially and temporally. Furthermore, plants also at times have to respond to excessively high and potentially toxic levels of essential nutrients, as well as toxic levels of non- essential metals and metalloids in the soil. Although plant mineral nutrition as a bona ~ide research discipline has a history of over 15o years, beginning with the pioneering work of Justus von liebieg and others in the mid-1800＇s, it is only very recently that researchers have begun to truly appreciate how sophisticated plants are with regards to the sensing of their mineral status and the maintaining of mineral homeostasis in the plant.

关键词： Plant mineral nutrient sensing and signaling root

The role of aluminum sensing and signaling in plant aluminum resistance

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Journal of Integrative Plant Biology 2014年第3期56卷 221-230页

作者： Jiping liu Miguel A.Piros l.on v.kochian USDA‐ARS Robert W.Holley Center for Agriculture and Health Tower Road Cornell University

As researchers have gained a better understanding in recent years into the physiological, molecular, and genetic basis of how plants deal with aluminum （AI） toxicity in acid soils prevalent in the tropics and sub-tropics, it has become clear that an important component of these responses is the triggering and regulation of cellular pathways and processes by AI. In this review of plant AI signaling, we begin by summarizing the understanding of physiological mechanisms of AI resistance, which first led researchers to realize that AI stress induces gene expression and modifies protein function during the activation of AI resistance responses. Subsequently, an overview of AI resistance genes and their function provides verification that AI induction of gene expression plays a major role in AI resistance in many plant species. More recent research into the mechanistic basis for Al-induced transcrip- tional activation of resistance genes has led to the identifica- tion of several transcription factors as well as cis-elements in the promoters of AI resistance genes that play a role in greater Al-induced gene expression as well as higher constitutive expression of resistance genes in some plant species. Finally, the post-transcriptional and translational regulation of AI resistance proteins is addressed, where recent research has shown that AI can both directly bind to and alter activity of certain organic acid transporters, and also influence AI resistance proteins indirectly, via protein phosphorylation.

关键词： AlMT aluminum resistance aluminum signaling aluminumtoxicity MATE

Identification of a novel pathway involving a GATA transcription factor in yeast and possibly in plant Zn uptake and homeostasis

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Journal of Integrative Plant Biology 2014年第3期56卷 271-280页

作者： Matthew J.Milner Nicole S.Pence Jiping liu l.on v.kochian Robert W.Holley Center for Agriculture and Health USDA‐ARS Cornell University Department of Plant Biology Cornell University

To gain a better understanding of the regulation of Zn homeostasis in plants and the degree of conservation of Zn homeostasis between plants and yeast, a cDNA library from the Zn/Cd hyperaccumulating plant species, Noccaea caerulescens, was screened for its ability to restore growth under Zn limiting conditions in the yeast mutant zaplA. ZAP1 is a transcription factor that activates the Zn dependent transcription of yeast genes involved in Zn uptake, including ZRT1, the yeast high affinity Zn transporter. From this screen two members of the E2F family of transcription factors were found to activate ZRT1 expression in a Zn independent manner. The activation of ZRTI by the plant E2F proteins involves E2F- mediated activation of a yeast GATA transcription factor which in turn activates ZRT1 expression. A ZRT1 promoter region necessary for activation by E2F and GATA proteins is upstream of two zinc responsive elements previously shown to bind ZAP1 in ZRT1. This activation may not involve direct binding of E2F to the ZRT1 promoter. The expression of E2F genes in yeast does not replace function of ZAP1; instead it appears to activate a novel GATA regulatory pathway involved in Zn uptake and homeostasis that is not Zn responsive.

关键词： E2F transcription factor GATA transcription factor ZRT1 Znhomeostasis

Developmental and genomic architecture of plant embryogenesis: from model plant to crops

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Plant Communications 2021年第1期2卷 1-12页

作者： Alma Armenta-Medina C.Stewart Gillmor Peng Gao Javier Mora-Macias l.on v.kochian Daoquan Xiang Raju Datla Global Institute for Food Security University of SaskatchewanSaskatoonSK S7N 4J8Canada laboratorio Nacional de Genòmica para la Biodiversidad(langebio) Unidad de Genòmica AvanzadaCentro de Investigaciòny Estudios Avanzados del IPN(CINVESTAV-IPN)IrapuatoGuanajuatoMéxico National Research Council Canada 110 Gymnasium PlaceSaskatoonSK S7N 0W9Canada

Embryonic development represents an important reproductive phase of sexually reproducing plant *** fusion of egg and sperm produces the plant zygote,a totipotent cell that,through cell division and cell identity specification in early embryogenesis,establishes the major cell lineages and tissues of the adult *** subsequent morphogenesis phase produces the full-sized embryo,while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination,ensuring continuation of the plant life *** this review on embryogenesis,we compare the model eudicot Arabidopsis thaliana with monocot crops,focusing on genome activation,paternal and maternal regulation of early zygote development,and key organizers of patterning,such as auxin and WOX transcription *** the early stages of embryo development are apparently conserved among plant species,embryo maturation programs have diversified between eudicots and *** diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation,and also assures seed germination in different environmental *** review describes the most important features of embryonic development in plants,and the scope and applications of genomics in plant embryo studies.

关键词： embryogenesis embryo patterning zygote genome activation transcription factors genomics transcriptomics

Semantic Segmentation of lumbar vertebrae Using Meijering U-Net(MU-Net)on Spine Magnetic Resonance Images

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 733-757页

作者： lakshmi S v v Shiloah Elizabeth Darmanayagam Sunil Retmin Raj Cyril Department of Computer Science and Engineering College of Engineering GuindyAnna UniversityChennai600025India Department of Information Technology Madras Institute of TechnologyAnna UniversityChrompetChennai600044India

lower back pain is one of the most common medical problems in the world and it is experienced by a huge percentage of people *** to its ability to produce a detailed view of the soft tissues,including the spinal cord,nerves,intervertebral discs,and vertebrae,Magnetic Resonance Imaging is thought to be the most effective method for imaging the *** semantic segmentation of vertebrae plays a major role in the diagnostic process of lumbar *** is difficult to semantically partition the vertebrae in Magnetic Resonance Images from the surrounding variety of tissues,including muscles,ligaments,and intervertebral discs.U-Net is a powerful deep-learning architecture to handle the challenges of medical image analysis tasks and achieves high segmentation *** work proposes a modified U-Net architecture namely MU-Net,consisting of the Meijering convolutional layer that incorporates the Meijering filter to perform the semantic segmentation of lumbar vertebrae l1 to l5 and sacral vertebra ***-colour mask images were generated and used as ground truth for training the *** work has been carried out on 1312 images expanded from T1-weighted mid-sagittal MRI images of 515 patients in the lumbar Spine MRI Dataset publicly available from Mendeley *** proposed MU-Net model for the semantic segmentation of the lumbar vertebrae gives better performance with 98.79%of pixel accuracy(PA),98.66%of dice similarity coefficient(DSC),97.36%of Jaccard coefficient,and 92.55%mean Intersection over Union(mean IoU)metrics using the mentioned dataset.

关键词： Computer aided diagnosis(CAD) magnetic resonance imaging(MRI) semantic segmentation lumbar vertebrae deep learning U-Net model

Constitutive basis of root system architecture:uncovering a promising trait for breeding nutrient-and drought-resilient crops

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aBIOTECH 2023年第4期4卷 315-331页

作者： Zhigang liu Tongfei Qin Michaella Atienza Yang Zhao Hanh Nguyen Huajin Sheng Toluwase Olukayode Hao Song Karim Panjvani Jurandir Magalhaes William J.lucas l.on v.kochian Global Institute for Food Security University of SaskatchewanSaskatoonSK S7N 4L8Canada Department of Computer Science University of SaskatchewanSaskatoonSK S7N 5C9Canada Embrapa Maize and Sorghum Brazilian Agricultural Research CorporationSete LagoasMG 35701-970Brazil Department of Plant Biology College of Biological SciencesUniversity of CaliforniaDavisCA 95616USA

Root system architecture(RSA)plays a pivotal role in efficient uptake of essential nutrients,such as phosphorous(P),nitrogen(N),and water In soils with heterogeneous nutrient distribution,root plasticity can optimize acquisition and plant ***,we present evidence that a constitutive RSA can confer benefits for sorghum grown under both sufficient and limiting growth *** studies,using P efficient SC103 and inefficient BTx635 sorghum cultivars,identified significant differences in root traits,with SC103 developing a larger root system with more and longer lateral roots,and enhanced shoot biomass,under both nutrient sufficient and deficient *** addition to this constitutive attribute,under P deficiency,both cultivars exhibited an initial increase in lateral root development;however,SC103 still maintained the larger root *** N deficiency and drought stress inhibited both root and shoot growth,for both sorghum cultivars,SC103 again maintained the better *** findings reveal that SC103,a P efficient sorghum cultivar,also exhibited enhanced growth performance under N deficiency and *** results provide evidence that this constitutive nature of RSA can provide an avenue for breeding nutrient-and drought-resilient crops.

关键词： Constitutive root system architecture Abiotic stress Nutrient efficiency Drought resilience Plant breeding

Autism spectrum disorder:difficulties in diagnosis and microRNA biomarkers

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Neural Regeneration Research 2025年第10期20卷 2776-2786页

作者： Bridget Martinez Philip v.Peplow Department of Pharmacology University of Nevada-RenoRenoNVUSA Department of Medicine University of Nevada-RenoRenoNVUSA Department of Anatomy University of OtagoDunedinNew Zealand

We performed a PubMed search for microRNAs in autism spectrum disorder that could serve as diagnostic biomarkers in patients and selected 17 articles published from January 2008 to December 2023,of which 4 studies were performed with whole blood,4 with blood plasma,5 with blood serum,1 with serum neural cell adhesion molecule l1-captured extracellular vesicles,1 with blood cells,and 2 with peripheral blood mononuclear *** of the studies involved children and the study cohorts were largely *** of the studies had performed microRNA sequencing or quantitative polymerase chain reaction assays to measure microRNA *** five studies had used real-time polymerase chain reaction assay to validate microRNA expression in autism spectrum disorder subjects compared to *** microRNAs that were validated in these studies may be considered as potential candidate biomarkers for autism spectrum disorder and include miR-500a-5p,-197-5p,-424-5p,-664a-3p,-365a-3p,-619-5p,-664a-3p,-3135a,-328-3p,and-500a-5p in blood plasma and miR-151a-3p,-181b-5p,-320a,-328,-433,-489,-572,-663a,-101-3p,-106b-5p,-19b-3p,-195-5p,and-130a-3p in blood serum of children,and miR-15b-5p and-6126 in whole blood of *** important limitations were identified in the studies reviewed,and need to be taken into account in future *** studies are warranted with children and adults having different levels of autism spectrum disorder severity and consideration should be given to using animal models of autism spectrum disorder to investigate the effects of suppressing or overexpressing specific microRNAs as a novel therapy.

关键词： autism spectrum disorder biomarker blood cells blood plasma blood serum diagnosis microRNA peripheral blood mononuclear cells serum neural cell adhesion molecule l1-captured extracellular vesicles whole blood

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic variants Regulating Root Architecture Traits

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Plant Phenomics 2023年第4期5卷 728-745页

作者： Rahul Chandnani Tongfei Qin Heng Ye Haifei Hu Karim Panjvani Mutsutomo Tokizawa Javier Mora Macias Alma Armenta Medina Karine C.Bernardino Pierre-luc Pradier Pankaj Banik Ashlyn Mooney Jurandir v.Magalhaes Henry T.Nguyen l.on v.kochian Global Institute for Food Security University of SaskatchewanSaskatoonSKCanada NRGene Canada 110 Research Dr Suite 101SaskatoonSKCanada Division of Plant Sciences and Technology University of MissouriColumbiaM065211USA School of Biological Sciences The University of Western AustraliaCrawleyWA 6009Australia Rice Research Institute Guangdong Academy of Agricultural Sciences&Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural Affairs&Guangdong Key Laboratory of New Technology in Rice Breeding&Guangdong Rice Engineering LaboratoryGuangdongChina Embrapa Maize and Sorghum Sete LagoasBrazil

Nutrient-efficient root system architecture(RSA)is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition *** variants shaping soybean RSA is key in improving nutrient and water ***,we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in *** also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers,which can be erroneously quantified as root *** platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 mill.on single-nucleotide *** was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips(95%correlation),when the background was cleaned of nonroot materials compared to root images without the background corrected(79%).Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root ***-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth,total root length and surface area,and root system volume and surface area of thicker roots(DOF1-like zinc finger transcription factor,protein of unknown function,and C2H2 zinc finger protein).We also identified a putative negative regulator(gibberellin 20 oxidase 3)of the total number of lateral roots.

关键词： Python Root submerged

Evolving technologies for growing,imaging and analyzing 3D root system architecture of crop plants

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Journal of Integrative Plant Biology 2016年第3期58卷 230-241页

作者： Miguel A.Pieros Brandon G.larson Jon E.Shaff David J.Schneider Alexandre Xavier Falcao lixing Yuan Randy T.Clark Eric J.Craft Tyler W.Davis Pierre-luc Pradier Nathanael M.Shaw Ithipong Assaranurak Susan R.Mc Couch Craig Sturrock Malcolm Bennett l.on v.kochian USDA-ARS Robert Holley Center for Agriculture and Health538 Tower RoadIthacaNY 14580USA Department of Information Systems Institute of ComputingUniversity of CampinasAv.Albert Einstein1251CEP 13083-852CampinasSPBrazil Department of Plant Nutrition China Agricultural UniversityBeijing 100193China Department of Plant Breeding and Genetics Cornell UniversityIthacaNY 14853USA Centre for Plant Integrative Biology School of BiosciencesUniversity of NottinghamSutton BoningtonLE12 5RDUK College of Science King Saud UniversityRiyadh 11451Kingdom of Saudi Arabia

A plant＇s ability to maintain or improve its yield under limiting conditions,such as nutrient de ficiency or drought,can be strongly in fluenced by root system architecture（RSA）,the three-dimensional distribution of the different root types in the soil. The ability to image,track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system,while allowing for aeration,solution replenishment and the imposition of nutrient treatments,as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modi fications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity（detection of fine roots and other root details）,higher ef ficiency,and a broad array of growing conditions for plants that more closely mimic those found under field conditions.

关键词： Abiotic stress digital root phenotyping mineral nutrition root system architecture