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Dissecting Maize Productivity:Ideotypes Associated with Grain Yield under Drought Stress and Well-watered Conditions

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Journal of Integrative Plant Biology 2012年第12期54卷 1007-1020页

作者： jill e.cairns Ciro Sanchez Mateo Vargas Raziel Ordoez Jose Luis Araus Global Maize Program International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Bioinformatics and Statistics Unit International Maize and Wheat Improvement Center(CIMMYT)Mexico D.F.Mexico Unit of Plant Physiology Department of Plant BiologyUniversity of BarcelonaBarcelonaSpain

To increase maize （Zea mays L.） yields in drought-prone environments and offset predicted maize yield losses under future climates, the development of improved breeding pipelines using a multi-disciplinary approach is essential. elucidating key growth processes will provide opportunities to improve drought breeding progress through the identification of key phenotypic traits, ideotypes, and donors. In this study, we tested a large set of tropical and subtropical maize inbreds and single cross hybrids under reproductive stage drought stress and well-watered conditions. Patterns of biomass production, senescence, and plant water status were measured throughout the crop cycle. Under drought stress, early biomass production prior to anthesis was important for inbred yield, while delayed senescence was important for hybrid yield. Under well-watered conditions, the ability to maintain a high biomass throughout the growing cycle was crucial for inbred yield, while a stay-green pattern was important for hybrid yield. While new quantitative phenotyping tools such as spectral reflectance （Normalized Difference Vegetation Index, NDVI） allowed for the characterization of growth and senescence patterns as well as yield, qualitative measurements of canopy senescence were also found to be associated with grain yield.

关键词： Climate change drought stress ideotypes maize senescence spectral reflectance.

Redesigning crop varieties to win the race between climate change and food security

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Molecular Plant 2023年第10期16卷 1590-1611页

作者： Kevin V.Pixley jill e.cairns Santiago Lopez-Ridaura Chris O.Ojiewo Maryam Abba Dawud Inoussa Drabo Taye Mindaye Baloua Nebie Godfrey Asea Biswanath Das Happy Daudi Haile Desmae Benoit Joseph Batieno Ousmane Boukar Clare T.M.Mukankusi Stanley T.Nkalubo Sarah J.Hearne Kanwarpal S.Dhugga Harish Gandhi Sieglinde Snapp ernesto Adair Zepeda-Villarreal International Maize and Wheat Improvement Center(CIMMYT) TexcocoMexico International Maize and Wheat Improvement Center(CIMMYT) HarareZimbabwe International Maize and Wheat Improvement Center(CIMMYT) NairobiKenya Lake Chad Research Institute(LCRI) MaidiguriNigeria International Maize and Wheat Improvement Center(CIMMYT) DakarSenegal ethiopian Institute of Agricultural Research(eIAR) Addis AbabaEthiopia National Agricultural Research Organization(NARO) KampalaUganda Tanzania Agricultural Research Institute(TARI) NaliendeleTanzania Institut de l'environnement et de Recherches Agricoles(INeRA) OuagadougouBurkina Faso International Institute of Tropicl Agriculture(IITA) KanoNigeria Alliance of Bioversity International and CIAT KampalaUganda

Climate change poses daunting challenges to agricultural production and food *** temperatures,shifting weather patterns,and more frequent extreme events have already demonstrated their effects on local,regional,and global agricultural *** varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance,productivity,and profitability under climate-changed *** surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet,sorghum,maize,groundnut,cowpea,and common bean varieties,particularly in sub-Saharan *** then review the current progress and prospects for breeding three prioritized future-essential traits for each of these *** predict that most current breeding priorities will remain important,but that rates of genetic gain must increase to keep pace with climate challenges and consumer ***,the predicted future-essential traits include innovative breeding targets that must also be prioritized;for example,(1)optimized rhizosphere microbiome,with benefits for P,N,and water use efficiency,(2)optimized performance across or in specific cropping systems,(3)lower nighttime respiration,(4)improved stover quality,and(5)increased early *** further discuss cutting-edge tools and approaches to discover,validate,and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision,accuracy,and *** conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.

关键词： climate change food security crop breeding cropping systems expert survey sub-Saharan Africa

Metabolic and Phenotypic Responses of Greenhouse-Grown Maize Hybrids to experimentally Controlled Drought Stress

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Molecular Plant 2012年第2期5卷 401-417页

作者： Sandra Witt Luis Galicia Jan Lisec jill cairns Axel Tiessen Jose Luis Araus Natalia Palacios-Rojas Alisdair R. Fernie Max Planck Institute of Molecular Plant Physiology 14476 Potsdam-Golm Germany CIMMYT Apdo. Postal 6-641 06600 Mexico DF Mexico CIMMYT Int. PO Box MP 163 Mount Pleasant Harare Zimbabwe Departamento de Ingenieria CINVeSTAV Unidad Irapuato KM 9.8 Libramiento Norte CP 36821 Irapuato Guanajuato Mexico University of Barcelona Department of Vegetal Biology Faculty of Biology Av. Diagonal 645 08028 Barcelona Spain

Adaptation to abiotic stresses like drought is an important acquirement of agriculturally relevant crops like maize. Development of enhanced drought tolerance in crops grown in climatic zones where drought is a very dominant stress factor therefore plays an essential role in plant breeding. Previous studies demonstrated that corn yield potential and enhanced stress tolerance are associated traits. In this study, we analyzed six different maize hybrids for their ability to deal with drought stress in a greenhouse experiment. We were able to combine data from morphophysiological parameters measured under well-watered conditions and under water restriction with metabolic data from different organs. These different organs possessed distinct metabolite compositions, with the leaf blade displaying the most considerable metabolome changes following water deficiency. Whilst we could show a general increase in metabolite levels under drought stress, including changes in amino acids, sugars, sugar alcohols, and intermediates of the TCA cycle, these changes were not differential between maize hybrids that had previously been designated based on field trial data as either drought-tolerant or susceptible. The fact that data described here resulted from a greenhouse experiment with rather different growth conditions compared to natural ones in the field may explain why tolerance groups could not be confirmed in this study. We were, however, able to highlight several metabolites that displayed conserved responses to drought as well as metabolites whose levels correlated well with certain physiological traits.

关键词： carbon metabolism metabolomics water relations.

Relationship between single and bulk mechanical properties for zeolite ZSM5 spray-dried particles

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Particuology 2014年第3期12卷 130-138页

作者： M.Marigo D.L.cairns J.Bowen A.Ingram e.H.Stitt Johnson Matthey Technology Centre P.O.Box 1Belasis AvenueBillinghamCleveland TS23 1LBUnited Kingdom Centre for Formulation engineering Chemical EngineeringSchool of EngineeringThe University of BirminghamB15 2TTUnited Kingdom

In this work typical mechanical properties for a catalyst support material, ZSM5 （a spray-dried granular zeolite）, have been measured in order to relate the bulk behaviour of the powder material to the single particle mechanical properties. Particle shape and size distribution of the powders, determined by laser diffraction and scanning electron microscopy （SeM）, confirmed the spherical shape of the spray-dried particles. The excellent flowability of the material was assessed by typical methods such as the Hausner ratio and the Cart index, This was confirmed by bulk measurements of the particle-particle internal friction parameter and flow function using a Schulze shear cell, which also illustrated the low compressibility of the material. Single particle compression was used to characterize single particle mechanical properties such as reduced elastic modulus and strength from Hertz contact mechanics theory. Comparison with surface properties obtained from nanoindentation suggests heterogeneity, the surface being harder than the core. In order to evaluate the relationship between single particle mechanical properties and bulk compression behaviour, uniaxial confined compression was carried out. It was determined that the Adams model was suitable for describing the bulk compression and furthermore that the Adams model parameter, apparent strength of single particles, was in good agreement with the single particle strength determined from single particle compression test.

关键词： Zeolite particle Flowability Powder flow function effective angle of internal friction Schulze shear cell Nanoindentation Single particle compression Bulk compression

Contemporary and Historic Population Structure of Abies spectabilis at Treeline in Barun Valley,eastern Nepal Himalaya

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Journal of Mountain Science 2015年第3期12卷 558-570页

作者： Parveen Kumar CHHeTRI David M.cairns Department of Geography Texas A&M UniversityCollege Station

Treeline ecotone dynamics of Abies spectabilis （D. Don） Mirb. in the Barun valley, Makalu Barun National Park, eastern Nepal Himalaya were studied by establishing seven plots （20 m x variable length） from the foresfline to the tree species limit： three plots on the south- and north-facing slopes each （S1-S3, N1-N3）, and one plot on the east- facing slope （e） in the relatively undisturbed forests. A dendroecological method was used to study treeline advance rate and recruitment pattern. In all the plots, most trees established in the early 20th century, and establishment in the second half of the 20th century was confined to the foresfline area. Treeline position has not advanced substantially in the Barun valley, with 0nly 22 m average elevational shift in the last 13o years, and with average current shifting rate of 14 cm/yr. Moreover, no significant relationship was found between tree age and elevation on the south-, north-, and east-facing slopes. The number of seedlings and saplings in near the treeline area was negligible compared to that near the foresfline area. Therefore, A. spectabilis treeline response to the temperature change was slow, despite the increasing temperature trend in the region. Beside the temperature change, factors such as high inter-annual variability in temperature, dense shrub cover, and local topography also play an important role in treeline advance and controlling recruitment pattern above the treeline.

关键词： Climate change Treeline ecotone Treeline advance Recruitment pattern

primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

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Journal of Genetics and Genomics 2023年第2期50卷 108-121页

作者： Amy e.elias Thomas A.Nuñez Bianca Kun jill A.Kreiling Roche WilmingtonMA 01887USA. Department of Molecular Biology Cell Biology and BiochemistryBrown UniversityProvidenceRI02903USA Public Health Genetics University of PittsburghPittsburghPA 15260USA

Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between cell types within ***,our understanding of regulatory RNAs,such as microRNAs(miRNAs),is limited through both single-cell and single-nucleus techniques due to the short length of miRNAs in the cytoplasm and the incomplete reference of longer primary miRNA(pri-miRNA)transcripts in the *** build a custom reference to align and count pri-miRNA sequences in singlenucleus *** young and aged subventricular zone(SVZ)nuclei,we show differential expression of pri-miRNAs targeting genes involved in neural stem cells(NSC)differentiation in the aged ***,using wild-type and 5XFAD mouse model cortex nuclei,to validate the use of primiReference,we find cell-type-specific expression of pri-miRNAs known to be involved in Alzheimer’s disease(AD).pri-miRNAs likely contribute to NSC dysregulation with age and AD *** is paramount in capturing a global profile of gene expression and regulation in single-nucleus data and can provide key insights into cell-type-specific expression of pri-miRNAs,paving the way for future studies of regulation and pathway *** looking at pri-miRNA abundance and transcriptional differences,regulation of gene expression by miRNAs in disease and aging can be further explored.

关键词： Primary-microRNA Aging Subventricular zone Alzheimer’s disease Single-nucleus RNA-Seq microRNA Transcriptomics

Cases on human performance improvement technologies

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Cases on human performance improvement technologies

Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL

作者： jill e. Stefaniak.

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 535-550页

作者： David earl Hostallero Lixuan Wei Liewei Wang Junmei cairns Amin emad Department of electrical and Computer engineering McGill UniversityMontrealQC H3A 0E9Canada Mila–Quebec Artificial Intelligence Institute MontrealQC H2S 3H1Canada Department of Molecular Pharmacology and experimental Therapeutics Mayo ClinicRochesterMN 55905USA The Rosalind and Morris Goodman Cancer Institute McGill UniversityMontrealQC H3A 1A3Canada

Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized ***,we developed a deep learning framework called TINDL,completely trained on preclinical cancer cell lines(CCLs),to predict the response of cancer patients to different *** utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient ***,by making the deep learning black box interpretable,this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model,enabling identification of biomarkers of drug *** data from two large databases of CCLs and cancer tumors,we showed that this model can distinguish between sensitive and resistant tumors for 10(out of 14)drugs,outperforming various other machine learning *** addition,our small interfering RNA(siRNA)knockdown experiments on 10 genes identified by this model for one of the drugs(tamoxifen)confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells,and seven of these genes in T47D ***,genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling *** summary,this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in *** code can be accessed at https://***/ddhostallero/tindl.

关键词： Drug response Deep learning explainable AI Cancer Gene knockdown experiment

Prospects for the continued development of environmentally-realistic toxicity test susing microorganisms

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Journal of environmental Sciences 1993年第3期5卷 253-268页

作者： John cairns,Jr. Paul V.McCormick Scott e.Belanger Department of Biology and University Center for environmental and Hazardous Materials Studies Virginia Polytechnic Institute and State UniversityBlacksburgVirginia 24061-0415U.S.A. Department of Biology Elizabethtown CollegeElizabethtownPennsylvania-17022-2298U.S.A.and Senior Research AssociateUniversity Center for Environmental and Hazardous Materials StudiesVirginia Polytechnic Institute and State UniversityBlacksburgVirginia-24061-0415U.S.A. Stream ecosystem Research Section Environmental Safety DepartmentThe Procter and Gamble CompanyCincinnatiOhio-45217U.S.A.

The focus of environmental regulations has changed significantly since the introduction of the bioassay as a standard means of assessing environmental *** in this change is an increasing emphasis on protecting the integrity of natural ecosystems,which incorporate community-and system-level properties as well as organismal and population ***,support for the use of multispecies testing has widened to include not only ecologists in academia but environmental scientists in the regulatory and industrial sector as *** reason for this trend is clear:the additional environmental realism gained from tests utilizing communities of organisms allows for greater insight into the potential hazard of chemicals and other forms of human activity to natural ecosystems that cannot be obtained from single species tests *** of the problems cited for multispecies testing early in their evolution as a hazard assessment tool have been refuted or *** particular,the use of natural microbial communities minimizes several shortcomings typically associated with multispecies toxicity *** discussion includes the utility of microcosm and mesocosm tests using aquatic microbial communities as hazard assessment tools in conjunction with accumulating information on their performance in toxicity testing *** increasing body of experimental evidence supports an expansion in the use of these tests for a variety of regulatory and research purposes.A shift in research focus is needed,however,to answer remaining questions and further refine standard protocols for these valuable ecotoxicological tools.

关键词： environmentally-realistic toxicity tests microorganisms.