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Construction of citrus gene coexpression networks from microarray data using random matrix theory

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Horticulture Research 2015年第1期2卷 193-200页

作者： Dongliang Du Nidhi Rawat Zhanao Deng fred g.gmitter Jr. Citrus Research and Education Center Institute of Food and Agricultural SciencesUniversity of FloridaLake AlfredFL 33850USA gulf Coast Research and Education Center Institute of Food and Agricultural SciencesUniversity of FloridaWimaumaFL 33598USA

After the sequencing of citrus genomes,gene function annotation is becoming a new *** coexpression analysis can be employed for function annotation using publicly available microarray data *** this study,230 sweet orange(Citrus sinensis)microarrays were used to construct seven coexpression networks,including one condition-independent and six condition-dependent(Citrus canker,Huanglongbing,leaves,flavedo,albedo,and flesh)*** total,these networks contain 37633 edges among 6256 nodes(genes),which accounts for 52.11%measurable genes of the citrus ***,these networks were partitioned into functional modules using the Markov Cluster *** enriched gene Ontology biological process terms and KEgg pathway terms were detected for 343 and 60 modules,***,independent verification of these networks was performed using another expression data of 371 *** study provides new targets for further functional analyses in citrus.

关键词： measurable orange partitioned

Marker Assisted Selection in Citrus Rootstock Breeding Based on a Major gene Locus ‘Tyr1’Controlling Citrus Nematode Resistance

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Agricultural Sciences in China 2010年第4期9卷 557-567页

作者： XIANg Xu DENg Zhan-ao CHEN Chun-xian fred g.gmitter Jr Kim Bowman Institute of Fruit Tree Research Guangdong Academy of Agricultural Sciences Guangzhou 510640 P.R.China gulf Coast Research and Education Center University of Florida Bradenton FL34203 USA Citrus Research and Education Center University of Florida Lake Alfred FL33850 USA US Horticultural Research Laboratory United States Department of Agriculture Ft. Pierce FL34945-3030 USA

Based on the former constructed ＇Tyrl＇ locus genetic map in family 9145, from LB6-2 [Clementine mandarin （C. reticulata） × Hamlin orange （C. sinensis）] × Swingle citrumelo （C. paradise × P. trifoliata）, 9 markers were chosen for application in evaluating their effectiveness in marker-assisted selection （MAS） for citrus rootstock breeding program from many F1 progeny of Poncirus trifoliata. As the mapping revealed that these markers were estimated within a range of 12.1 cM in the linkage group, and among them, SCO07 co-segregated with ＂Tyrl＇, and 7A4R as the closest to ＇Tyrl＇ with a distance of 1.5 cM, these markers were basically fitful to go MAS screening. The results of screening P. trifoliata F1 progeny indicated that all the markers were inherited in codominant fashion and most of them were heterozygous on PT （Pomery of P. trifoliata）., marker 4L17R/CfoI and 7A4（1407）/BfaI were proved to be consistently reliable for accurate scoring of genotypes and the revealed polymorphism was basically coincided with the citrus nematode resistant phenotype within tested populations. The polymorphic genotype with marker 4L17R/Cfol was found completely matched up with the phenotype of individuals that conferred high resistance to citrus nematode when the USDA hybrid rootstocks were screened. Utilization of these markers, especially the highly specific 4L17R/Cfol and 7A4（1407）/Bfal, should result in great benefit to world citrus industry for early selection in rootstock-breeding program.

关键词： citrus Poncirus trifoliata nematode resistance marker-assisted selection

genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing-tolerant Poncirus trifoliata and its hybrids

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Horticulture Research 2017年第1期4卷 77-84页

作者： Nidhi Rawat Brajendra Kumar Ute Albrecht Dongliang Du Ming Huang Qibin Yu Yi Zhang Yong-Ping Duan Kim D Bowman fred g.gmitter Jr Zhanao Deng University of Florida IFASGulf Coast Research and Education CenterWimaumaFLUSA Ocimum BioSolutions Ltd. Royal DemeurePlot no.12/2Sector-1HUDA Techno EnclaveMadhapurHyderabadIndia University of Florida IFASSouthwest Florida Research and Education CenterImmokaleeFLUSA University of Florida IFASCitrus Research and Education CenterLake AlfredFLUSA U.S.Department of Agriculture U.S.Horticultural Research LaboratoryAgricultural Research ServiceFort PierceFLUSA

Huanglongbing(HLB)is the most destructive bacterial disease of citrus *** most citrus varieties are susceptible to HLB,Poncirus trifoliata,a close relative of Citrus,and some of its hybrids with Citrus are tolerant to *** specific HLB tolerance genes have been identified in *** but recent studies have shown that constitutive disease resistance(CDR)genes were expressed at much higher levels in HLB-tolerant Poncirus hybrids and the expression of CDR genes was modulated by Candidatus Liberibacter asiaticus(CLas),the pathogen of *** current study was undertaken to mine and characterize the CDR gene family in Citrus and Poncirus and to understand its association with HLB tolerance in *** identified 17 CDR genes in two citrus genomes,deduced their structures,and investigated their phylogenetic *** revealed that the expansion of the CDR family in Citrus seems to be due to segmental and tandem duplication *** genome resequencing and transcriptome sequencing,we identified eight CDR genes in the Poncirus genome(PtCDR1-PtCDR8).The number of SNPs was the highest in PtCDR2 and the lowest in *** of the deletion and insertion events were observed in the UTR regions of Citrus and Poncirus CDR ***2 and PtCDR8 were in abundance in the leaf transcriptomes of two HLB-tolerant Poncirus genotypes and were also upregulated in HLB-tolerant,Poncirus hybrids as revealed by real-time PCR *** two CDR genes seem to be good candidate genes for future studies of their role in citrus-CLas interactions.

关键词： Poncirus citrus Citrus

Pristine point of zero charge (p.p.z.c.) and zeta potentials of boehmite’s nanolayer and nanofiber surfaces

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International Journal of Smart and Nano Materials 2016年第1期7卷 1-21页

作者： Leonid A.Kaledin fred Tepper Tatiana g.Kaledin Department of Chemistry Argonide Corporation291 Power CourtSanfordFL 32771USA

The pristine point of zero charge(p.p.z.c)and zeta potential as a function of pH of boehmite oxide/hydroxide(α-Al_(2)O_(3)·H_(2)O)have been determined for three filter *** active component in the first two filter media is boehmite nanofibers,only 2 nm in diameter and about 300 nm *** nanofibers create high zeta potential(ζtrue≥46 mV)in aqueous solutions in the pH range of 3–*** *** were determined to be 11.60±0.15 for nanofibers grafted onto microglass fibers and 11.40±0.15 for agglomerated *** the third filter media,a boehmite nanolayer in the form of monocrystalline oxide/hydroxide with a thickness of approximately 1.2 nm is electroadhesively deposited onto siliceous support material with large surface area of about 50 m^(2)/g,therefore forming a highly electropositive composite of boehmite nanolayer on the second highly electronegative ***’s oxide-hydroxide nanolayer surface creates high zeta potential(ζtrue≥50 mV)in aqueous solutions in the pH range of 3–*** *** was determined to be 11.38±*** reported values are within accuracy,but they are much higher than the values reported in the literature.X-ray powder diffraction data were supplemented by microscopy,infrared spectroscopy in order to characterize fully synthetic boehmite surfaces.

关键词： Boehmite’s nanolayer pristine point of zero charge(p.p.z.c) zeta potential isoelectric point(i.e.p.)

Long-range attractive forces extending from the alumina’s nanolayer surface in aqueous solutions

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International Journal of Smart and Nano Materials 2015年第3期6卷 171-194页

作者： Leonid A.Kaledin fred Tepper Tatiana g.Kaledin Argonide Corporation Nanomaterial&Filtration Technologies291 Power CourtSanfordFL 32771USA

Aluminum oxide-hydroxide nanolayer with a thickness of approximately 1.2 nm is electroadhesively deposited onto silicious support material with large surface area of about 50 m2/g,forming a highly electropositive composite of boehmite nanolayer in the form of monocrystalline oxide/hydroxide(α-Al2O3·H2O)on the second electronegative *** composite can be viewed as a sphere with a rough surface and charge density of approximately 0.08 C/*** creates a significant electric field with negligible screening(ka1)in the region close to the surface of the *** field attracts nano-and micron-sized particles from as far as 200μm in a few seconds,many orders of magnitude greater than conventional Derjaguin–Landau–Verwey–Overbeek(DLVO)theory,which predicts only nanometer-scale effects arising from the presence of the *** strong electric field on the surface is then able to retain small particles such as viruses,atomically thin sheets of graphene oxide,RNA,DNA,proteins,dyes as well as heavy metals such as cobalt,arsenic,and ***’s nanolayer surface can be further functionalized by adding other submicron or nano-sized particles to target a specific *** example is shown where alumina nanolayer is coated with nano-sized iron monohydrate to yield an arsenic sorbent that shows high sorption capacity.

关键词： alumina nanolayer electric double layer electrostatic adsorption

Long-range attractive forces extending from alumina nanofiber surface

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International Journal of Smart and Nano Materials 2014年第3期5卷 133-151页

作者： Leonid A.Kaledin fred Tepper Tatiana g.Kaledin Argonide Corporation 291 Power CourtSanfordFL 32771USA

Aluminum oxide-hydroxide nanofibers,2 nm in diameter and approximately 250 nm long,are electroadhesively grafted onto glass microfibers,therefore forming a macroscopic assembly of alumina nanofibers on the second solid in highly organized *** assembly can be viewed as a straight cylinder with rough surface and charge density of approximately 0.08 C/m^(2).This creates a significant electric field with negligible screening(ka≪1)in the region close to the surface of the *** field attracts nano-and micron-size particles from as far as 0.3 mm in less than a few seconds,many orders of magnitude greater than the conventional Derjaguin–Landau–Verwey–Overbeek theory that predicts only nanometer-scale effects arising from the presence of the *** strong electric field on the surface is then able to retain particles such as micron-size powdered activated carbon as well as much smaller particles such as fumed silica nanoparticles of 10–15 nm in diameter,viruses,atomically thick sheets of graphene oxide,latex spheres,RNA,DNA,proteins,and dyes.

关键词： alumina nanofibers electric double layer electrostatic adsorption

Developmental rate： A unifying mechanism for sympatric divergence in postglacial fishes？

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Current Zoology 2012年第1期58卷 21-34页

作者： Mcphee, Megan V. Noakes, David L. g. ALLendorf, fred W. Fisheries Division University of Alaska Fairbanks Juneau Alaska 99801 USA Department of Fisheries and Wildlife and Oregon Hatchery Research Center Oregon State University Corvallis Oregon 97331-3803 USA Division of Biological Sciences University of Montana Missoula MT 59812 USA

Morphologically divergent ecotypes arise in fish populations on postglacial time scales, and resource polymorphisms are often invoked to explain their origin. However, genetic recombination can constrain the ability of divergent selection to pro- duce reproductive isolation in sympatry. Recombination breaks up favorable combinations of traits （＂adaptive suites＂） if indivi- dual traits are affected by different loci. Recombination also breaks up any association between traits under divergent selection and traits contributing to reproductive isolation. Thus, ecological speciation in the absence of preexisting barriers to gene flow is more likely when pleiotropy minimizes the number of loci involved. Here, we revisit research conducted by Carl Hubbs in the early 1900s on the effects of developmental rate on morphological traits in fishes. Hubbs＇ work provides a mechanism to explain how sympatric divergence by trophic polymorphism can occur despite the challenges of recombination. We consider the implica- tions of Hubbs＇ observations for ecological speciation with gene flow in fishes, as well as rapid evolution in captive fish popula- tions [Current Zoology 58 （1）： 21-34, 2012].

关键词： Pleiotropy Resource polymorphism Selection-recombination antagonism

Modeling neuropsychiatric disorders using human induced pluripotent stem cells

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Protein & Cell 2020年第1期11卷 45-59页

作者： Meiyan Wang Lei Zhang fred H.gage Laboratory of genetics The Salk Institute for Biological Studies10010 N.Torrey Pines RdLa JollaCA 92037USA Neurobiology Section Division of Biological SciencesUniversity of California San DiegoLa JollaCA 92093USA

Neuropsychiatric disorders are complex disorders characterized by heterogeneous genetic variations,variable symptoms,and widespread changes in anatomical *** the context of neuropsychiatric disorders,limited access to relevant tissue types presents challenges for understanding disease etiology and developing effective *** pluripotent stem cells(iPSCs)reprogrammed from patient somatic cells offer an opportunity to recapitulate disease development in relevant cell types,and they provide novel approaches for understanding disease mechanisms and for development of effective *** we review recent progress and challenges in differentiation paradigms for generating disease-relevant cells and recent studies of neuropsychiatric disorders using human pluripotent stem cell(hPSC)models where cellular phenotypes linked to disease have been *** use of iPSC-based disease models holds great promise for understanding disease mechanisms and supporting discovery of effective treatments.

关键词： neuropsychiatric disorders iPSCs brain organoid schizophrenia autism spectrum disorder bipolar disorder

China and the United States： The Contest for global Economic Leadership

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China & World Economy 2018年第5期26卷 12-37页

作者： C. fred Bergsten Peterson Institute for International Economics USA

This paper considers whether there is a ＂Thucydides trap ＂＇ in the world economy, referring to the inherent conflict between incumbent and challenger It assesses the impact of President Trump ~ alienation of traditional US allies, which threatens to splinter the ＂hegemonic coalition ＇＂ and even push China and Europe together, and his convergence toward some Chinese norms on trade and even polities. It outlines three possible systemic scenarios： a ＂gO＂ in which the US is no longer willing to lead but China is not yet able or willing, and whether such a （likely） regime will be stable or unstable; a new ＂g1, ＂＇ sooner or later, led by China; and a cooperative ＂g2 ＂＂ in which the US and China agree to share leadership. It traces the evolution of actual leadership initiatives of the two countries in recent years. It compares US and Chinese attitudes on key systemic issues and concludes with an appraisal of ＂＇an international economic order with Chinese characteristics, ＂＂ a worm in which the state plays a greater role relative to market economics, the rule of law defers increasingly to voluntary arrangements, and politics tilt toward central ~overnment control more than democracy.

关键词： g2 global leadership hegemonic coalition trade war