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smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction

Molecular Plant 2022年第11期15卷 1664-1695页

作者： Yunbi Xu Xingping Zhang Huihui Li Hongjian Zheng Jianan Zhang michael s.olsen Rajeev K.Varshney Boddupalli M.Prasanna Qian Qian Institute of Crop sciences CIMMYT-ChinaChinese Academy of Agricultural SciencesBeijing 100081China CIMMYT-China Tropical Maize Research Center School of Food Science and EngineeringFoshan UniversityFoshanGuangdong 528231China Peking University Institute of Advanced Agricultural sciences WeifangShandong 261325China CIMMYT-China specialty Maize Research Center Shanghai Academy of Agricultural SciencesShanghai 201400China MolBreeding Biotechnology Co. Ltd.ShijiazhuangHebei 050035China National Nanfan Research Institute(sanya) Chinese Academy of Agricultural SciencesSanyaHainan 572024China CIMMYT(International Maize and Wheat Improvement Center) ICRAF CampusUnited Nations AvenueNairobiKenya state Agricultural Biotechnology Centre Centre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochAustralia

The first paradigm of plant breeding involves direct selection-based phenotypic observation,followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and,more recently,by incorporation of molecular marker ***,plant performance or phenotype(P)is determined by the combined effects of genotype(G),envirotype(E),and genotype by environment interaction(GEI).Phenotypes can be predicted more precisely by training a model using data collected from multiple sources,including spatiotemporal omics(genomics,phenomics,and enviromics across time and space).Integration of 3D information profiles(G-P-E),each with multidimensionality,provides predictive breeding with both tremendous opportunities and great ***,we first review innovative technologies for predictive *** then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy,particularly envirotypic data,which have largely been neglected in data collection and are nearly untouched in model *** propose a smart breeding scheme,integrated genomic-enviromic prediction(iGEP),as an extension of genomic prediction,using integrated multiomics information,big data technology,and artificial intelligence(mainly focused on machine and deep learning).We discuss how to implement iGEP,including spatiotemporal models,environmental indices,factorial and spatiotemporal structure of plant breeding data,and cross-species prediction.A strategy is then proposed for prediction-based crop redesign at both the macro(individual,population,and species)and micro(gene,metabolism,and network)***,we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding *** call for coordinated efforts in smart breeding through iGEP,institutional partnerships,and innovative technological support.

关键词： smart breeding genomic selection integrated genomic-enviromic selection spatiotemporal omics crop design machine and deep learning big data artificial intelligence

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Factors affecting genomic selection revealed by empirical evidence in maize

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The Crop Journal 2018年第4期6卷 341-352页

作者： Xiaogang Liu Hongwu Wang Hui Wang Zifeng Guo Xiaojie Xu Jiacheng Liu shanhong Wang Wen-Xue Li Cheng Zou Boddupalli M.Prasanna michael s.olsen Changling Huang Yunbi Xu Institute of Crop science National Key Facility of Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences International Maize and Wheat Improvement Center (CIMMYT) ICRAF campus International Maize and Wheat Improvement Center (CIMMYT)

Genomic selection(Gs) as a promising molecular breeding strategy has been widely implemented and evaluated for plant breeding, because it has remarkable superiority in enhancing genetic gain, reducing breeding time and expenditure, and accelerating the breeding process. In this study the factors affecting prediction accuracy(rMG) in Gs were evaluated systematically, using six agronomic traits(plant height, ear height, ear length, ear diameter,grain yield per plant and hundred-kernel weight) evaluated in one natural and two biparental populations. The factors examined included marker density, population size, heritability,statistical model, population relationships and the ratio of population size between the training and testing sets, the last being revealed by resampling individuals in different proportions from a population. Prediction accuracy continuously increased as marker density and population size increased and was positively correlated with heritability; rMGshowed a slight gain when the training set increased to three times as large as the testing set. Low predictive performance between unrelated populations could be attributed to different allele frequencies, and predictive ability and prediction accuracy could be improved by including more related lines in the training population. Among the seven statistical models examined, including ridge regression best linear unbiased prediction(RR-BLUP), genomic BLUP(GBLUP), Bayes A, Bayes B, Bayes C, Bayesian least absolute shrinkage and selection operator(Bayesian LAssO), and reproducing kernel Hilbert space(RKHs), the RKHs and additive-dominance model(Add + Dom model) showed credible ability for capturing non-additive effects, particularly for complex traits with low heritability. Empirical evidence generated in this study for Gs-relevant factors will help plant breeders to develop Gs-assisted breeding strategies for more efficient development of varieties.

关键词： Marker density Population size Population relationship Zea mays

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Emerging structures and dynamic mechanisms ofγ-secretase for Alzheimer’s disease

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Neural Regeneration Research 2025年第1期20卷 174-180页

作者： Yinglong Miao michael s.Wolfe Computational Medicine Program and Department of Pharmacology University of North Carolina–Chapel HillChapel HillNCUSA Department of Medicinal Chemistry University of KansasLawrenceKSUSA

γ-secretase,called“the proteasome of the membrane,”is a membrane-embedded protease complex that cleaves 150+peptide substrates with central roles in biology and medicine,including amyloid precursor protein and the Notch family of cell-surface *** inγ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer’s disease.γ-secretase has thus served as a critical drug target for treating familial Alzheimer’s disease and the more common late-onset Alzheimer’s disease as ***,critical gaps remain in understanding the mechanisms of processive proteolysis of substrates,the effects of familial Alzheimer’s disease mutations,and allosteric modulation of substrate cleavage byγ-*** this review,we focus on recent studies of structural dynamic mechanisms ofγ-*** mechanisms,including the“Fit-stay-Trim,”“sliding-Unwinding,”and“Tilting-Unwinding,”have been proposed for substrate proteolysis of amyloid precursor protein byγ-secretase based on all-atom molecular dynamics *** an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-boundγ-secretase,molecular dynamics simulations on a resolved model of Notch1-boundγ-secretase that was reconstructed using the amyloid precursor protein-boundγ-secretase as a template successfully capturedγ-secretase activation for proper cleavages of both wildtype and mutant Notch,being consistent with biochemical experimental *** approach could be potentially applied to decipher the processing mechanisms of various substrates byγ-*** addition,controversy over the effects of familial Alzheimer’s disease mutations,particularly the issue of whether they stabilize or destabilizeγ-secretase-substrate complexes,is ***,an outlook is provided for future studies ofγ-secretase,including pathways of substrate binding and product release,effects of modulators on familial Alzheimer’s disease mutations

关键词： Alzheimer’s disease amyloid precursor protein cryo-EM structures drug design intramembrane proteolysis molecular dynamics Notch

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Determining the IgG concentrations in bovine colostrum and calf sera with a novel enzymatic assay

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Journal of Animal science and Biotechnology 2019年第1期10卷 239-247页

作者： M.Drikic C.Windeyer s.olsen Y.Fu L.Doepel J.De Buck Department Production Animal Health Faculty of Veterinary MedicineUniversity of Calgary

Background: Immune protection in newborn calves relies on a combination of the timing,volume and quality of colostrum consumed by the calf after *** quality colostrum with inadequate immunoglobulin concentration contributes to failed transfer of passive immunity in calves,leading to higher calf morbidity and ***,estimating colostrum quality and ensuring the transfer of passive immunity on farm is of critical ***,there are no on-farm tools that directly measure immunoglobulin content in colostrum or *** aim of this study was to apply a novel molecular assay,split trehalase immunoglobulin G assay(sTIGA),to directly estimate immunoglobulin content in dairy and beef colostrum and calf sera,and to examine its potential to be developed as on-farm *** sTIGA is based on a split version of trehalase TreA,an enzyme that converts trehalose into glucose,enabling the use of a common glucometer for signal *** a first study,60 dairy and64 beef colostrum and 83 dairy and 84 beef calf sera samples were tested with sTIGA,and the resulting glucose production was measured and compared with radial immunodiffusion,the standard method for measuring immunoglobulin ***: Pearson correlation coefficients between the methods were determined and the sensitivity,specificity,and accuracy of the test were calculated for different colostrum quality and failed transfer of passive immunity cut-off *** correlations of the sTIGA measured by colorimetric enzymatic reaction compared to radial immunodiffusion for dairy and beef colostrum were 0.72 and 0.73,respectively,whereas the correlations for dairy and beef sera were 0.9 and 0.85,***,sTIGA was tested in a blinded study with fresh colostrum and serum samples where the correlation coefficient was 0.93 and 0.94,***,the performance of sTIGA followed by glucometer readings resulted in correlations with radial immunodiffusion of 0.7 and

关键词： Cattle Colostrum Immunoglobulins Passive immunity Radial immunodiffusion split trehalase

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What′s new with the XYZ mesons?

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Chinese Physics C 2008年第6期32卷 455-462页

作者： s.L.olsen Institute of High Energy Physics Chinese Academy of Sciences

I review some of the recent experimental results on the so-called XYZ mesons.

关键词： charmonium multiquark mesons quark-gluon hybrids

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Acute and chronic excitotoxicity in ischemic stroke and late-onset Alzheimer's disease

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Neural Regeneration Research 2025年第7期20卷 1981-1988页

作者： shan Ping Yu Emily Choi michael QJiang Ling Wei Department of Anesthesiology Emory University School of MedicineAtlantaGAUSA Center for Visual and Neurocognitive Rehabilitation Atlanta Veterans Affairs Medical CenterDecaturGAUSA

stroke and Alzheimer's disease are common neurological disorders and often occur in the same *** comorbidity of the two neurological disorders represents a grave health threat to older *** review presents a brief background of the development of novel concepts and their clinical *** activity of glutamatergic N-methyl-D-aspartate receptors and N-methyl-D-aspartate receptor-mediated Ca^(2+)influx is critical for neuronal *** ischemic insult induces prompt and excessive glutamate release and drastic increases of intracellular Ca^(2+)mainly via N-methyl-D-aspartate receptors,particularly of those at the extrasynaptic *** Ca^(2+)-evoked neuronal cell death in the ischemic core is dominated by necrosis within a few hours and days known as acute ***,mild but sustained Ca^(2+)increases under neurodegenerative conditions such as in the distant penumbra of the ischemic brain and early stages of Alzheimer's disease are not immediately toxic,but gradually set off deteriorating Ca^(2+)-dependent signals and neuronal cell loss mostly because of activation of programmed cell death *** on the Ca^(2+)hypothesis of Alzheimer's disease and recent advances,this Ca^(2+)-activated“silent”degenerative excitotoxicity evolves from years to decades and is recognized as a unique slow and chronic *** N-methyl-D-aspartate receptor subunit GluN3A,primarily at the extrasynaptic site,serves as a gatekeeper for the N-methyl-D-aspartate receptor activity and is neuroprotective against both acute and chronic *** stroke and Alzheimer's disease,therefore,share an N-methyl-D-aspartate receptor-and Ca^(2+)-mediated mechanism,although with much different time *** is thus proposed that early interventions to control Ca^(2+)homeostasis at the preclinical stage are pivotal for individuals who are susceptible to sporadic late-onset Alzheimer's disease and Alzheimer's disease-related

关键词： Ca^(2+)hypothesis cognitive deficits hyperactivity late-onset Alzheimer's disease neurodegeneration N-methyl-D-aspartate receptors N-methyl-D-aspartate receptor subunits pathogenesis preventive treatment

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Deepening Collaboration China and Africa need to further align development strategies to realise the immense potential of economic cooperation

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ChinAfrica 2025年第1期17卷 24-26页

作者： EHIZUELEN michael MITCHELL OMORUYI Centre for Nigerian studies Institute of African StudiesZhejiang Normal University

Humming factories,bustling ports,and shuttling merchants highlight the vibrancy of China-Africa economic and trade *** the years,this partnership has grown significantly,optimising trade structures and fostering mutual *** deepening collaboration is evident in China’s role as Africa’s largest bilateral trading partner for 15 consecutive *** the first seven months of 2024,trade between China and African countries reached$167 billion,reflecting a 5.5-percent increase compared to the same period in *** to the International Monetary Fund,approximately 20 percent of Africa’s exports now go to China,while 16 percent of its imports originate there.

关键词： trading deepening Africa

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scalable Ir-Doped NiFe<sub>2sub>O<sub>4sub>/TiO<sub>2sub> Heterojunction Anode for Decentralized saline Wastewater Treatment and H<sub>2sub> Production

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NANO-MICRO LETTERs 2025年第1期17卷 1-18页

作者： Hong, sukhwa Kim, Jiseon Park, Jaebeom Im, sunmi Hoffmann, michael R. Cho, Kangwoo Pohang Univ sci & Technol POsTECH Div Environm Sci & Engn Pohang 790784 South Korea CALTECH Linde Labs Pasadena CA 91125 USA Yonsei Univ Int Campus Inst Convergence Res & Educ Adv Technol I CREATE Incheon 21983 South Korea

Wastewater electrolysis cells (WECs) for decentralized wastewater treatment/reuse coupled with H-2 production can reduce the carbon footprint associated with transportation of water, waste, and energy carrier. This study reports Ir-doped NiFe2O4 (NFI, similar to 5 at% Ir) spinel layer with TiO2 overlayer (NFI/TiO2), as a scalable heterojunction anode for direct electrolysis of wastewater with circumneutral pH in a single-compartment cell. In dilute (0.1 M) NaCl solutions, the NFI/TiO2 marks superior activity and selectivity for chlorine evolution reaction, outperforming the benchmark IrO2. Robust operation in near-neutral pH was confirmed. Electroanalyses including operando X-ray absorption spectroscopy unveiled crucial roles of TiO2 which serves both as the primary site for Cl- chemisorption and a protective layer for NFI as an ohmic contact. Galvanostatic electrolysis of NH4+-laden synthetic wastewater demonstrated that NFI/TiO2 not only achieves quasi-stoichiometric NH4+-to-N-2 conversion, but also enhances H-2 generation efficiency with minimal competing reactions such as reduction of dissolved oxygen and reactive chlorine. The scaled-up WEC with NFI/TiO2 was demonstrated for electrolysis of toilet wastewater.

关键词： Wastewater electrolysis cell Ir-doped NiFe2O4 Reactive chlorine species Decentralized H-2 production On-site wastewater treatment

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Revisiting cerebral endothelial cells in Alzheimer’s disease

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Neural Regeneration Research 2025年第10期20卷 2911-2912页

作者： Amira s.Hanafy Department of Neurosurgery University Hospital BonnBonnGermany

Alzheimer’s disease(AD)is the most common neurodegenerative disorder characterized by slow and progressive decline of cognitive and memory *** only approximately 5%of the cases,AD is familial,as often predisposed by genetic mutations(Hoogmartens et al.,2021),while sporadic AD accounts for approximately 95%of the *** amyloid cascade hypothesis is one of the fundamental hypotheses put out to explain AD pathogenesis as dysregulated homeostasis of amyloid-β(Aβ)peptides that leads to the accumulation of Aβplaques in the parenchyma,an anatomical hallmark of AD.

关键词： Alzheimer Aβ cerebral

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A systematic review of progenitor survival and maturation in Parkinsonian models

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Neural Regeneration Research 2025年第11期20卷 3172-3178页

作者： Giulia Comini Eilís Dowd Pharmacology&Therapeutics and Galway Neuroscience Center University of GalwayGalwayIreland

stem cell-based brain repair is a promising emergent therapy for Parkinson's disease based on years of foundational research using human fetal donors as a cell *** current therapeutic options for patients,this approach has the potential to provide longterm stem cell–derived reconstruction and restoration of the dopaminergic input to denervated regions of the brain allowing for restoration of certain functions to *** ultimate clinical success of stem cell–derived brain repair will depend on both the safety and efficacy of the approach and the latter is dependent on the ability of the transplanted cells to survive and differentiate into functional dopaminergic neurons in the Parkinsonian *** the pre-clinical literature suggests that there is considerable variability in survival and differentiation between studies,the aim of this systematic review was to assess these parameters in human stem cell-derived dopaminergic progenitor transplant studies in animal models of Parkinson's disease.A defined systematic search of the PubMed database was completed to identify relevant studies published up to March *** screening,76 articles were included in the analysis from which 178 separate transplant studies were *** these,graft survival could be assessed in 52 studies and differentiation in 129 ***,we found that graft survival ranged froms transplanted,with a median of 51%of transplanted cells surviving in the brain;while dopaminergic differentiation of the cells ranged from 0% to 46% of cells transplanted with a median of 3%.This systematic review suggests that there is considerable scope for improvement in the differentiation of stem cell-derived dopaminergic progenitors to maximize the therapeutic potential of this approach for patients.

关键词： cell replacement therapy differentiation embryonic stem cells graft induced pluripotent stem cells Parkinson's disease survival transplant

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