Pseudogaps in the 2D half-filled Hubbard model
Bacillus spp.

• Modification in milk proteins • Extraction of malt infusion • Clarification of beer • Production of flavouring derived from soy • Production of animal feeds
strains well characterized – Study of gene regulation of the enzymes of
interest
Enhancing
• Enhancing of strains – increasing production to tens of g/l in processes of 50- 100 hours lasting
Commodity chemicals
• Amilases & Proteases • Bacillus:
– Good catalytic properties – High cellular density from low cost carbon and
nitrogen sources – Realise directly to the culture medium (low cost
• enzymes for human food industry (beverage,dairy products, bakery foods)
• enzymes for animal feeds
50-60% of this market are enzymes from Bacillus American, European, Japanese, Chinese companies (Novozymes, Danisco-Genencor, DSM)
法国海岸松树皮提取物碧萝芷对长链游离脂肪酸诱导的巨噬细胞perilipin2基因表达的影响

法国海岸松树皮提取物碧萝芷对长链游离脂肪酸诱导的巨噬细胞perilipin2基因表达的影响范斌;杜强;谷剑秋;张锦【摘要】Abstract Objective To investigate the effect of Pycnogenol on oleic acid-induced perilipin2 expression in macrophages. Methods Realtime PCR and Western blot were performed to detect perilipin2 expression. Transient transfection and luciferase assay were employed to measure perilipin2 promoter activity. Results Oleic acid significantly induced perilipiti2 expression in a dose-and time-dependent manner in macrophages; oleic acid markedly enhanced perilipin2 promoter activity; Pycnogenol significantly suppressed oleic acid-induced perihpin2 expression and promoter activity. Conclusion For the first time,we demonstrated that Pycnogenol significantly suppressed oleic acid-induced perilipin2 expression and promoter activity.%目的研究碧萝芷(PYC)对油酸诱导的巨噬细胞perilipin2表达的影响及其相关分子机制.方法应用Real-time PCR 和Western blot测定油酸及PYC对perilipin2 mRNA和蛋白水平表达影响.应用荧光素酶活性分析方法检测油酸及PYC时perilipin2启动子活性的影响.结果油酸以剂量和浓度依赖方式上调perilipin2 mRNA和蛋白水平表达,并促进perilipin2启动子活性.PYC以剂量依赖方式抑制了油酸诱导的perilipin2表达及启动子活性.结论PYC抑制了巨噬细胞中油酸诱导的perilipin2的表达.PYC通过抑制perilipin2启动子活性,从而直接抑制perilipin2的表达.【期刊名称】《中国医科大学学报》【年(卷),期】2011(040)007【总页数】5页(P611-615)【关键词】长链游离脂肪酸;泡沫细胞;碧萝芷;PAT家族蛋白【作者】范斌;杜强;谷剑秋;张锦【作者单位】中国医科大学附属盛京医院神经内科,沈阳110004;中国医科大学附属盛京医院内分泌科,沈阳110004;中国医科大学附属第一医院内分泌科,沈阳110001;中国医科大学附属第一医院内分泌科,沈阳110001【正文语种】中文【中图分类】R363单核细胞通过内皮细胞的间隙移入内膜下并分化成巨噬细胞,巨噬细胞吞噬体内过剩的脂质后变成泡沫细胞,泡沫细胞聚集并形成斑块是动脉粥样硬化发生、发展的主要病理基础[1,2]。
金线莲多糖抗衰老作用及其机制

疗组为阳性对照.6周后对小鼠进行行为学测试,8周后 检 测 小 鼠 的 大 脑 皮 层 p?NF?κBp65 表 达,以 及 大 脑 皮
层过氧化氢酶、超氧化物歧化酶及血清总抗氧化能力活性 和 丙 二 醛 浓 度,并 检 测 小 鼠 腹 腔 巨 噬 细 胞 的 吞 噬 情
况.结果表明:与衰老小鼠相比较,经金线莲多糖治疗后,小鼠的抗氧化酶活性显著提高,其大脑皮 层 p?NF?κB
p65表达下调,且运动、空间探索和学习记忆能力明 显 改 善;同 时,金 线 莲 多 糖 能 增 强 衰 老 小 鼠 清 除 抗 原 的 能 力;金线莲多糖抗衰老作用与其抗氧化、抑制 NF?κB 信号通路、增强衰老小鼠免疫能力有关.
关键词: 金线莲多糖;NF?κB 信号通路;抗氧化;认知能力;抗衰老
与衰老模型组小鼠相比经不同剂量金线莲多糖和ve治疗后小鼠的运动时间运动速度和站立次数均明显增加犘001犘005说明金线莲多糖和ve能使衰老小鼠的运动空间探索学习和记忆能力有明显改善
第 41 卷 第 1 期
2020年1月
华 侨 大 学 学 报 (自 然 科 学 版 ) JournalofHuaqiaoUniversity (NaturalScience)
衰老是生物体随着年龄增长在形态结构和生理功能 方面出 现的 一 系 列 退 行 性 变 化,是 正 常 且 自 然
收 稿 日 期 : 2019?07?22
通 信 作 者 : 刘 青 (1970?),女 ,副 教 授 ,博 士 ,主 要 从 事 天 然 药 物 的 提 取 及 活 性 的 研 究 .E?mail:yunliu@126.com. 基 金 项 目 : 福 建 省 自 然 科 学 基 金 资 助 项 目 (2013J01337)
Evolution of ATP-binding cassette transporter genes

ABC gene
Transported substrate
Arabinose Ri bose Maltose G3P Polysaccharides
believed to transport tryptophan and a White-Brown dimer guanine [12]. The sterile 6 (STE6) gene encodes an ABC protein that extrudes the yeast mating factor, a modified oligopeptide [13]. STE6 is similar in organization and in amino acid sequence to the P-glycoproteins (see below). Characterization o f ABC gene sequences from the expressed sequence tag (EST) database suggests that there are at least 25 human ABC genes (our unpublished data). The organization of ABC genes in eukaryotes also varies significantly. The most common combination consists of four domains in succession, T M - A T P - T M - A T E H o w ever, there are examples o f A T P - T M - A T P - T M (PDR5), T M - A T P (ALD, PMP70, TAP, MDLI, MDL2, ATM1, PXA) and ATP-ATP (OAB) genes (Fig. lb). The evolutionary history and functional significance of this diversity in gene organization remains unclear. As for the bacterial genes, the functional protein always appears to contain two ATP and two transmembrane domains, the only described exception being OAB, which binds to 2'-5' oligoadenylate as part of the ribonuclease L complex [14]. Other ABC genes that have functions other than transport will undoubtedly be described.
Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin

Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of thechromatin-remodeling factor DDM1Hidetoshi Saze*and Tetsuji KakutaniDepartment of Integrated Genetics,National Institute of Genetics,Mishima,Shizuoka,JapanEpigenetically silent transposons and repeats constitute a substantial proportion of eukaryotic genomes,but their impact on cellular gene function remains largely unex-plored.In Arabidopsis ,transposons are silenced by DNA methylation,and this methylation is often abolished by mutations in a chromatin-remodeling gene DDM1(DECREASE IN DNA METHYLA TION 1).The ddm1muta-tion induces various types of developmental abnormalities through de-repression of transposons and repeats.Here,we report a novel mechanism for a ddm1-induced syn-drome,called bonsai (bns ).We identified the gene respon-sible for the bns phenotypes by genetic linkage analysis and subsequent transcriptional analysis.The bns pheno-types are due to silencing of a putative Anaphase-Promoting Complex (APC)13gene.The BNS gene silencing was associated with DNA hypermethylation,which is in contrast to the ddm1-induced hypomethylation in the other genomic regions.This paradoxical BNS hy-permethylation was reproducibly induced during self-pol-lination of the ddm1mutant,and it was mediated by a long interspersed nuclear element (LINE)retrotransposon flanking the BNS gene.We discuss possible molecular mechanisms and the evolutionary implications of transpo-son-mediated epigenetic changes in the BNS locus.The EMBO Journal (2007)26,3641–3652.doi:10.1038/sj.emboj.7601788;Published online 12July 2007Subject Categories :chromatin &transcription;plant biology Keywords :anaphase promoting complex;BONSAI;epigenetic inheritance;heterochromatin;small RNAIntroductionMethylation of cytosine is a heritable epigenetic mark in-volved in several important biological processes,including genomic imprinting and transposon silencing (Jaenisch and Bird,2003;Rangwala and Richards,2004;Chan et al ,2005;Zilberman and Henikoff,2005).Transposons are methylated in diverse organisms,and loss of cytosine methylation leads to activation of transposons (Y oder et al ,1997;Walsh et al ,1998;Miura et al ,2001;Singer et al ,2001;Kato et al ,2003;Selker et al ,2003).Genome-wide mapping of DNA methyla-tion in the flowering plant Arabidopsis demonstrated that a majority of cytosine methylation is concentrated in hetero-chromatic regions,where transposons and repetitive se-quences accumulate (Lippman et al ,2004;Zhang et al ,2006;Zilberman et al ,2007).Unexpectedly,however,recent high-resolution mapping studies revealed that B 20–30%of expressed genes have methylation within their transcribed regions,although the methylation level is generally lower than that in transposons (Zhang et al ,2006;Zilberman et al ,2007).Interestingly,the proportion of those methylated genes increases toward heterochromatic pericentromeric regions,possibly reflecting direct or indirect interaction(s)of epige-netic states between euchromatic genes and heterochromatic sequences (Zilberman et al ,2007).In the large genomes of plants and vertebrates,transposons and repeats are also scattered among and within genes.However,the impact of such local heterochromatin on activity of cellular genes remained largely unexplored.The impact of epigenetic changes on transposon activity can be directly examined using Arabidopsis mutants with defective genomic DNA methylation.In plants,cytosine methylation is found in both CG and non-CG contexts.In Arabidopsis ,methylation at CG sites is maintained by DNA methyltransferase MET1,an ortholog of Dnmt1in mammals,while methylation at non-CG sites depends on DNA methyl-transferase genes,CMT3and DRM2(Finnegan et al ,1996;Ronemus et al ,1996;Bartee et al ,2001;Lindroth et al ,2001;Cao et al ,2003;Kankel et al ,2003).Another gene involved in maintenance of methylation and silencing of heterochroma-tin loci is a chromatin-remodeling ATPase gene DDM1(DECREASE IN DNA METHYLA TION 1),which is involved in both CG and non-CG methylation (Vongs et al ,1993;Jeddeloh et al ,1998).In addition,chromatin and RNAi components involved in de novo DNA methylation have recently been identified using several reporter transgene systems (Aufsatz et al ,2002;Kanno et al ,2004,2005;Chan et al ,2005;Herr et al ,2005;Onodera et al ,2005;Pontier et al ,2005;Pontes et al ,2006).Notably,many of the putative endogenous targets of this pathway are located near transpo-son sequences,which might epigenetically regulate adjacent genes (Huettel et al ,2006).Several examples of developmental variants were recov-ered in both met1and ddm1mutant lines (Finnegan et al 1996;Kakutani et al ,1996,2004;Ronemus et al ,1996;Kankel et al ,2003;Saze et al ,2003).Genetic analysis of some of these ddm1-induced developmental variants revealed that each of the abnormalities is due to a heritable change in a locus other than DDM1(Kakutani et al ,1996).For example,a ddm1-induced dwarf phenotype named bal is produced by the overexpression of a cluster of disease resistance genes (Stokes et al ,2002).Another ddm1-induced developmental variation,characterized by a delay in flowering onset,is dueReceived:28April 2007;accepted:13June 2007;published online:12July 2007*Corresponding author.Department of Integrated Genetics,National Institute of Genetics,Y ata 1111,Mishima,Shizuoka 411-8540,Japan.T el.:þ81559816805;Fax:þ81559816804;E-mail:hsaze@lab.nig.ac.jpThe EMBO Journal (2007)26,3641–3652|&2007European Molecular Biology Organization |All Rights Reserved 0261-4189/07to ectopic expression of the imprinted homeobox gene FW A (Kakutani,1997;Soppe et al ,2000;Kinoshita et al ,2004).Although these abnormalities behave as dominant traits,some of the ddm1-induced abnormalities behave as heritable recessive traits,suggesting that a different mechanism is responsible (Kakutani et al ,2004).Here,we report the identification of the target gene of a ddm1-induced loss-of-function epigenetic abnormality called bns (Kakutani,1997;Kakutani et al ,2004).The loss of BONSAI gene function was due to gene silencing associated with DNA hypermethylation and small RNA accumulation.The de novo methylation of the BONSAI gene was induced reproducibly in independent ddm1mutant lines.This ectopic methylation depends on the presence of a long interspersed nuclear element (LINE)retrotransposon insertion within the 30non-coding region.The LINE insertion,which is found in the majority of natural accessions,generates a potential trigger for epigenetic variation with strong developmental effects.ResultsRepeated self-pollination of a ddm1mutant induced a combination of phenotypes named bnsRepeated self-pollination of the DNA hypomethylation mu-tant ddm1results in a variety of developmental abnormalities (Kakutani et al ,1996).Genetic analyses of some of the phenotypes have revealed that they are caused by gain-of-function alleles,which reflect overexpression of the respon-sible genes (Soppe et al ,2000;Stokes et al ,2002).However,not all of the developmental abnormalities are gain-of-func-tion alleles.An example is a ddm1-induced developmental syndrome that we named bns .The bns phenotypes were characterized by short,compact inflorescence,resulting in reduced plant height (Figure 1A and B).The bns variant showed disrupted phyllotaxis,re-duced apical dominance and production of clusters of bracts and flowers at the apex of the inflorescence (Figure 1C and D).These phenotypes seem to reflect the inhibition of inter-node elongation and the termination of shoot growth at the apical meristems (Figure 1;Kakutani,1997;Kakutani et al ,2004).After backcrossing to the parental wild-type (WT)Columbia (Col),the bns phenotype was not detectable in the F 1population,suggesting that the abnormal phenotypes are not due to a gain-of-function mutation.In the self-pollinated progeny of an F 1plant,we recovered F 2plants showing the bns phenotype.The phenotypic plants included both ddm1/ddm1and DDM1/-genotypes.This observation suggests that the bns phenotypes are produced by a heritable change in a locus (or loci)other than DDM1.Identification of the BNS geneT o further understand the basis of the heritable bns pheno-types,we examined their inheritance in the F 2progeny from a cross of a ddm1plant with bns phenotypes (Col)to a WT Landsberg erecta (L er )plant.The genotype was determined for 531F 2plants with clear bns phenotypes,which comprised about 10%of the F 2population.Characterization of Col/L er polymorphisms throughout the genome revealed that all of the phenotypic plants were homozygous for the Col haplo-type in one locus in the bottom arm of chromosome 1,suggesting that a loss-of-function allele in this locus is responsible for the bns trait.This locus was narrowed to an interval between genetic markers NGA111and BW54(five recombinants and two recombinants,respectively,out of the 1062chromosomes examined).We compared the transcript levels of 54predicted genes in this genetically defined BNS region between WT and bns plants (backcrossed to DDM1/DDM1),using a reverse transcription (RT)–PCR assay.We found that one gene (AT1G73177)showed a severe reduction in its expression in bns DDM1compared to WT plants (Figure 2A).The AT1G73177transcript was also reduced in the self-pollinated ddm1plants with the bns phenotypes (data not shown).The identified gene consists of four exons and encodes a predicted 63-amino acid (aa)protein (Figure 2B),and this annotation is supported by the presence of full-length cDNA in nucleotide sequence databases (GenBank:A Y088589).A truncated non-LTR-type retrotran-sposon (LINE,long interspersed nuclear elements)sequence (AT1G73175)was found in the 30UTR in the WT Col genome (Figure 2B and see below).T wo flanking genes,AT1G73170and AT1G73180,did not show a detectable reduction in their transcript level in bns plants (Figure 2A).T o test whether the bns phenotypes are due to the repres-sion of AT1G73177,this gene was knocked down by RNAi in WT Col plants by transformation with a transgenic construct producing double-stranded RNA (dsRNA)of the gene se-quence (Figure 2C).The transgenic lines showed the bns -like phenotypes (i.e.,reduced plant height and clustered flowers)associated with a reduction in AT1G73177transcript abundance (Figure 2C and D).In addition,we analyzed the effect of a T -DNA insertion in the upstream non-coding region in the first exon (SALK_027397).In the insertion mutant,a transcript was still detectable by RT–PCR,but the levelwasFigure 1The bns phenotypes.(A )WT Col plants (two on the left)and bns plants in a DDM1/DDM1background (two on the right;hereafter referred to as bns ).Both are six weeks old.(B )A close-up image of bns .(C )Inflorescences of bns .(D )A cluster of flowers produced in bns .Epigenetic mutation of a transposon-flanked gene H Saze and T Kakutaniless than that observed in WT plants(Figure2B and C).The plants homozygous for the T-DNA insertion showed similar phenotypes,although they were much milder(Figure2D), further confirming that the reduction in AT1G73177transcript induces the bns phenotypes.From these results,together with the recessive nature of the bns mutation,we concluded that the loss or reduction in AT1G73177function is most likely to be responsible for the bns phenotypes.The BNS gene product has similarity to a subunit of the Anaphase-Promoting Complex/Cyclosome(APC/C) The predicted BNS protein has a high similarity to the mammalian Swm1/Apc13,a subunit of Anaphase-Promoting Complex/Cyclosome(APC/C)(Figure2E).The APC/C is a large ubiquitin–protein ligase complex that reg-ulates cell cycle progression in eukaryotic cells(Castro et al, 2005).Swm1/Apc13was originally identified for its role in spore wall assembly in Saccharomyces cerevisiae(Ufano et al, 1999),and was later found to be a core subunit of the APC/C (Y oon et al,2002;Hall et al,2003).The protein is evolution-arily conserved in a wide range of organisms(Schwickart et al,2004)(Figure2E).We detected BNS expression in all tissues examined in WT plants(Supplementary Figure1). bns is an epigenetic mutation associated with DNA hypermethylationDespite the marked reduction in BNS expression in the bns line,the nucleotide sequence of the BNS gene in the bnslineAT1G73170AT1G73177AT1G73180ACT2ACT2 (RT−)WT bns ddm1AT1G73170AT1G73177AT1G73180ACT2ACT2 (RT−)WT bns RNAi T-DNAMDS----EVQRDGRILDLIDDAWREDKLPYEDVAI-----PLNELPEP--EQDNG---GTMDS----EVQRDGRILDLIDDAWREDKLPYEDVAI-----PLSELPEP--EQDNG---GTMGGVEQEQLLSLGVLIDIVDEQWMRDTLPADDVPV-----PPAMAVKT--EEAEDPAPANMSGLELELGLSLGVLIDVVDEQWMRDTLPADDIPV-----PPAMAVKT--EDAEDPAPANMA------EVSLGMLIDIVDEEWMRDTLPDDDLPL-----PPVLAVKT--DDTEE---TNMA------ELSLGILIDIVDEEWMRDTLPDDDLPL-----PPTLVVRT--DDTED---SNMDSNYNYVHMNKPGVV-LFASDWLKDRLPVDDVEVRVEHLPPVTEDEMTIQHSSANLILM*:::..*.***:*::*.:..TESVKEQEMKWTDLALQYLHENVPPIGN74TESVKEQEMKWTDLALQGLHENVPPAGN74QESQPAQGDVWRDFTLENL---------72QESQPAQGDVWRDFALENL---------72QETQQADAETWRDLALDTQ---------63QETQQVNLDAWHDLAFGQE---------63KNKQLRHEPAWKDLELEDLVNAFAFIQ-86:..**:: Hs_APC13MmOsZmBNSGmSp_APC13Figure2Identification of the BNS gene.(A)RT–PCR for the BNS gene(AT1G73177)and neighboring genes(AT1G73170and AT1G73180).T otal RNA isolated from wild-type Col(WT),bns(backcrossed to DDM1)and ddm1plants(before repeated self-pollination)was used.The BNS transcript was also reduced in ddm1lines after repeated self-pollination(not shown).Actin2(ACT2)was used as a control.(B)A schematic representation of the BNS locus.Boxes represent exons(coding sequences in black and UTRs in white for BNS and the neighboring genes,and in gray for the LINE sequence).Black arrows indicate the annotated transcription start sites and transcript orientation(). Horizontal white arrowheads represent the target site duplications of the LINE insertion.The position of the T-DNA insertion in thefirst exon of BNS in SALK_027397line is also indicated.The positions of primer pair,F2and R3,used for RT–PCR of AT1G73177,are also shown.(C)Knockdown of BNS transcripts in the RNAi lines and in the T-DNA insertion line.RT–PCR was performed with total RNA from wild-type Col (WT),bns,transgenic plants expressing dsRNA of BNS gene(RNAi)and SALK_027397line homozygous for the T-DNA insertion(T-DNA).(D)Phenotypes of a BNS RNAi line(left panel),and an inflorescence in a plant homozygous for the T-DNA insertion(right panel).(E)Multiple aa sequence alignment of BNS(Arabidopsis thaliana;AT1G73177)and APC13homologs in Homo sapiens(Hs,NP_056206),Mus musculus (Mm,NP_852059),Oryza sativa(Os,NP_001060376),Zea mays(Zm,A Y105005),Glycine max(Gm,CX701269)and Schizosaccharomyces pombe(Sp,NP_595754).The sequences were aligned using the ClustalW program that highlights the identical and conserved aa with asterisks and dots,respectively.Epigenetic mutation of a transposon-flanked geneH Saze and T Kakutaniwas identical to that in the WT progenitor strain,Col(from À825toþ946;data not shown).These results suggested that the silencing of the BNS gene has an epigenetic basis.We therefore examined the level of DNA methylation in this region.T o detect DNA methylation,we used the following two methods:digestibility by methylation-sensitive restriction enzymes and bisulfite genomic sequencing.Bisulfite genomic sequencing revealed that the BNS gene in the WT Col genome was almost free of DNA methylation(WT Col in Figure3A). On the other hand,theflanking LINE sequence was heavily methylated,especially at CG sites(Figure3A and B).In the bns line,the BNS gene region was also heavily methylated (bottom diagram in Figure3A),which is in contrast to the situation in WT Col plants.The hypermethylation at the BNS locus was found at both CG and non-CG sites.The methylation status of the BNS region was confirmed by digestion with methylation-sensitive restriction enzymes and subsequent PCR.WT Col samples did not show a PCR signal,reflecting the complete digestion of the genomic DNA (left panel in Figure3C).Samples derived from bns plants showed bands reflecting incomplete digestion due to methy-lation.These results are consistent with the results of the bisulfite sequencing.Repeated self-pollination of ddm1mutant reproducibly induced de novo DNA methylation in the BNS gene The hypermethylation in the BNS gene contrasts with the global DNA hypomethylation induced by the ddm1.We examined whether this paradoxical DNA hypermethylation in the BNS locus reflected one single purely stochastic event, or BNS hypermethylation could be reproducibly induced in a ddm1mutant background.In order to see the initial effect of the ddm1mutation, ddm1homozygotes were selected from progeny derived by self-pollination of a DDM1/ddm1heterozygote.This DDM1/ ddm1parent was generated by backcrossing a ddm1mutant six times to WT Col parent,in order to remove heritable effects from the original ddm1/ddm1mutant(Kakutani et al, 1996,1999).ddm1/ddm1plants segregated in the self-polli-nated progeny of the backcrossed DDM1/ddm1parent did not show signs of BNS gene hypermethylation(ddm1(1stG) in Figure3).In order to see the effect of repeated self-pollination of the ddm1mutant,seven ddm1homozygotes in the segregating family were independently self-pollinated seven times.The hypermethylation of the BNS gene was detected in all seven independent ddm1lines(ddm1(8thG) in Figure3).The ddm1mutation reproducibly induced BNS methylation,but this process was slow and required multiple generations.As a control,BNS methylation was also exam-ined in four DDM1/DDM1sibling lines segregated from the same DDM1/ddm1parent and self-pollinated seven times in parallel(DDM1(8thG)in Figure3).BNS methylation was not detected in any of the four DDM1control lines.The lack of methylation in the DDM1sibling families further confirmed that the ddm1mutation was responsible for the de novo methylation of the BNS gene.Theflanking LINE sequence showed a reduction in DNA methylation in the self-pollinated ddm1plants(ddm1(8thG) in Figure3A and B).This result is consistent with the previous observations that DDM1activity is required for the maintenance of DNA methylation and silencing of endogen-ous transposons(Miura et al,2001;Singer et al,2001; Lippman et al,2004).The hypomethylation of the LINE was found only after repeated self-pollination,which is similar to the situation for the SINE-related sequence in the FW A promoter,which remains methylated in the initial gen-erations of ddm1inbreeding,but loses methylation stochas-tically in subsequent inbred generations(Soppe et al,2000). Interestingly,the LINE sequence was methylated to the WT level in the bns mutant line backcrossed into a DDM1/DDM1 background(Figure3A and B),suggesting de novo methyla-tion in the DDM1background.The hypermethylation and silencing of BNS gene is associated with small RNAsEpigenetic silencing of transposons and repeats are fre-quently associated with the production of small RNAs, which could be involved in RNA-directed DNA methylation (Zilberman et al,2003;Chan et al,2004;Matzke and Birchler, 2005).Because the BNS gene was methylated de novo in a ddm1background,we examined small RNAs corresponding to this region.As shown in Figure4,BNS gene silencing was associated with the accumulation of small RNA in the size of 24–25nt,the length of small RNA species often detected for heterochromatic sequences(Hamilton et al,2002;Xie et al, 2004;Henderson et al,2006;Pontes et al,2006).Small RNAs (24–25nt)were also detected in the ddm1mutant sample.A hybridization probe covering the30region of the BNS gene near the boundary with the LINE(BNS30probe)detected a weak but significant signal in the WT Col sample(Figure4B and C),although the signal increased in the sample carrying a silent BNS allele.As is the case for many other silent transposons,small RNA was also detected for the LINE sequence(Figure4B)in the WT Col sample.Interestingly,the amount of the small RNA for this family of LINE increased in the ddm1and bns plants.The increase in the small RNA signal might mediate the de novo methylation of this LINE element,and that may explain the partial methylation of the LINE in the ddm1 mutant,and the de novo methylation of the element after introduction into a background with a WT DDM1allele (Figure3A and B).The LINE insertion was found at the BNS locus in majority of Arabidopsis natural accessionsThe LINE(AT1G73175)at the BNS locus belongs to a pre-viously uncharacterized subfamily of LINE sequences in Arabidopsis(Wright et al,1996;Noma et al,2000,2001). The presence of16-bp target site duplication(TSD)followed by a9-bp poly(A)sequence proximal to BNS indicates that the LINE sequence is inserted in a tail-to-tail orientation relative to the BNS gene(Figure3A).In WT Col,BNS mRNA extends into the LINE sequence over the TSD and poly(A)sequences(Supplementary Figure2).The Col gen-ome contains two other members of this LINE subfamily, which share more than97%nucleotide sequence identity (AT1G17390and AT5G36935;Figure5A).The copy on chro-mosome5(AT5G36935)is likely to be the full-length copy (Figure5A).This copy encodes three open reading frames, with a structure similar to A TLN-L class LINEs(Noma et al, 2001).The presence of these three copies in the Col genome was confirmed by Southern blot analysis(Supplementary Figure3).Epigenetic mutation of a transposon-flanked gene H Saze and T KakutaniCpGCpNpG 100 bpAsymmetricLINE0.750.50.25(1stG)(8thG)(8thG)(DDM1)(1stG)(8thG)(8thG)(DDM1)(1stG)(8thG)(8thG)(DDM1)ddm1(1stG)ddm1(8thG)DDM1(8thG)bns UndigestSau 3AI Bg /II ***Col*Figure 3DNA methylation pattern in the BNS locus.(A )Schematic representations of the BNS locus and cytosine methylation level analyzed by bisulfite sequencing.After treatment with bisulfite,DNA fragments were amplified using four pairs of primers separately (the positions indicated as short horizontal black bars),and cloned for sequencing (12clones for each amplified region).The percentage of methylated cytosine is indicated by vertical bars (black,CG;blue,CNG;red,asymmetric cytosine).Boxes below represent exons (coding sequences in black and UTRs in white for BNS ,and in gray for the LINE sequence).(B )Proportion of methylated cytosines in the BNS locus,which is based on the results shown in panel A.(C )Methylation of the BNS region detected by restriction digestion.Genomic DNA was digested by methylation-sensitive restriction enzymes Bgl II (50-AGATCT -30)or Sau 3AI (50-GATC-30)(),and was subsequently used as template for PCR amplification.The positions of the restriction sites and primers used for the PCR are indicated in the bottom of panel A;primer pairs F2þR3and F3þR4were used after Bgl II and Sau 3AI digestion,respectively.Asterisks (*)indicate the samples used for bisulfite sequencing in panels A and B.Epigenetic mutation of a transposon-flanked geneH Saze and T KakutaniIn order to evaluate the impact of the LINE insertion in natural populations,we examined the presence of the LINE insertion at the BNS locus in 96natural accessions of Arabidopsis thaliana .Among them,83accessions have the LINE insertion in the BNS 30UTR,while 13did not have the insertion (Figure 5B).This was confirmed by Southern ana-lysis of the 96natural accessions (data not shown).Among the 13accessions without the LINE insertion,five contain sequences almost identical to Col apart from the LINE inser-tion (Figure 5C).In those accessions,the TSD sequence remained intact,suggesting that these are ancestral alleles before the LINE insertion.Presence of the LINE in the majority of natural accessions suggests that the LINE inser-tion per se does not have deleterious effects in natural populations.Dependence of the BNS hypermethylation on the flanking LINE sequenceUsing Cvi,which does not have the LINE insertion at the BNS locus (Figure 5C),we tested whether the LINE sequence is necessary for the ddm1-induced de novo methylation at the BNS locus.WT Cvi was crossed to a ddm1heterozygote,which had already been backcrossed six times in the hetero-zygous state (Kakutani et al ,1996).A DDM1/ddm1hetero-zygote originating from this cross was self-pollinated,and from the progeny,we selected ddm1homozygotes with the BNS allele from genome of Col (BNS LINE /BNS LINE ;homozy-gous for the LINE insertion)or Cvi (BNS À/BNS À;without the LINE insertion)(Figure 6A).After three rounds of self-polli-nation,DNA methylation of the BNS locus in these ddm1plants was examined using methylation-sensitive restriction enzymes.All of seven independent ddm1lines homozygous for the BNS LINE allele (from Col)showed de novo DNA methylation of the BNS locus,whereas none of the five ddm1lines homozygous for the BNS Àallele (from Cvi)showed ectopic DNA methylation (Figure 6B).This result suggests that ddm1-induced de novo methylation at the BNS gene depends on the presence of the LINE insertion in the 30UTR.DiscussionMechanism for BNS gene hypermethylation triggered by the ddm1mutationHere,we report the identification and characterization of a loss-of-function epigenetic developmental abnormality bns .The most striking feature of the bns trait is that the local hypermethylation of the BNS gene was induced in a back-ground of global DNA hypomethylation.The hypermethyla-tion of the BNS gene was not evident in newly segregated ddm1homozygous plants (1stG in Figure 3),but it was reproducibly induced in the self-pollinated progeny of ddm1mutants (8thG in Figure 3).These observations suggest that BNS hypermethylation may be due to an indirect effect of the globally hypomethylated ddm1background.Similar observa-tions have been previously reported for SUPERMAN (SUP )and AGAMOUS (AG )sequences;these sequences are stochas-tically hypermethylated in the absence of DDM1or MET1activity (Jacobsen and Meyerowitz,1997;Jacobsen et al ,2000).In both SUP and AG ,pyrimidine-rich sequences such as CT dinucleotide repeats are found in the hypermethylated target sequences,and the possible involvement of this sim-ple-sequence motif has been proposed (Jacobsen et al ,2000).However,a pyrimidine-rich sequence was not found in the BNS locus,suggesting that it is not the basis for BNS hyper-methylation (data not shown).Instead,our results suggest that BNS hypermethylation is mediated by the pre-existing LINE insertion in non-coding region of the BNS gene (Figure 6).The ectopic hypermethylation at BNS in ddm1background occurred in a spreading manner from the LINE into the BNS region (Figure 3A).Spread of heterochromatin into genic regions is also known in position-effect-variegation in Drosophila (Talbert and Henikoff,2006)and telomeric silen-cing in budding yeast (Grunstein,1997).Although the BNS locus resides in a euchromatic chromosomal arm,the dense DNA methylation on the LINE sequence at this locus suggests that the LINE sequence can function as local heterochroma-tin,which is maintained without affecting adjacent genes in the WT background.The DDM1gene is necessary for the maintenance of the heterochromatic characteristics of LINE and other transposons (Gendrel et al ,2002;Lippman et al ,2003,2004).DDM1might also be necessary to define a heterochromatin boundary (Figure 7A).In mammals,the chromatin insulator CTCF has a barrier function that blocks the extension of heterochromatin.The CTCF-dependent in-sulator activity was abolished by loss of an SNF2-like chro-modomain helicase/ATPase protein,leading to a decrease in euchromatic histone modifications and DNA hypermethyla-tion around the boundary sequences (Ishihara et al ,2006).Interestingly,the spreading of DNA methylation was not found in the other side (opposite from the BNS gene)of the LINE sequence.On that side,the expression of the gene AT1G73170,which has the transcription start site approxi-mately 150bp away from the TSD of the LINE,was not affected in bns and self-pollinated ddm1lines (Figure 2A and B and data not shown).These results suggest thattheAT1G73177(BNS )Colbns ddm1100 bp24-nt 21-nt 24-nt 21-nt 24-nt 21-nt24-nt 21-nt BNS middle probe EtBrLINE probe miR171BNS 3′probe (LNA)Col CviBNS3′probe (LNA)EtBrprobeprobeprobe (LNA)Figure 4Small RNA northern analysis of the BNS locus.(A )The positions of three hybridization probes used are indicated.(B )Small RNA was examined in WT Col,bns in DDM1background and self-pollinated ddm1plants with reduced BNS expression.The same membrane was used for hybridization with each of the three probes and for the control miR171probe.Ethidium bromide staining of the major RNA is shown as a control (EtBr).(C )WT Col and Cvi samples on a different membrane.Epigenetic mutation of a transposon-flanked gene H Saze and T Kakutani。
光谱法研究药物小分子与蛋白质大分子的相互作用的英文

Spectroscopic Study of the Interaction between Small Molecules and Large Proteins1. IntroductionThe study of drug-protein interactions is of great importance in drug discovery and development. Understanding how small molecules interact with proteins at the molecular level is crucial for the design of new and more effective drugs. Spectroscopic techniques have proven to be valuable tools in the investigation of these interactions, providing det本人led information about the binding affinity, mode of binding, and structural changes that occur upon binding.2. Spectroscopic Techniques2.1. Fluorescence SpectroscopyFluorescence spectroscopy is widely used in the study of drug-protein interactions due to its high sensitivity and selectivity. By monitoring the changes in the fluorescence emission of either the drug or the protein upon binding, valuable information about the binding affinity and the binding site can be obt本人ned. Additionally, fluorescence quenching studies can provide insights into the proximity and accessibility of specific amino acid residues in the protein's binding site.2.2. UV-Visible SpectroscopyUV-Visible spectroscopy is another powerful tool for the investigation of drug-protein interactions. This technique can be used to monitor changes in the absorption spectra of either the drug or the protein upon binding, providing information about the binding affinity and the stoichiometry of the interaction. Moreover, UV-Visible spectroscopy can be used to study the conformational changes that occur in the protein upon binding to the drug.2.3. Circular Dichroism SpectroscopyCircular dichroism spectroscopy is widely used to investigate the secondary structure of proteins and to monitor conformational changes upon ligand binding. By analyzing the changes in the CD spectra of the protein in the presence of the drug, valuable information about the structural changes induced by the binding can be obt本人ned.2.4. Nuclear Magnetic Resonance SpectroscopyNMR spectroscopy is a powerful technique for the investigation of drug-protein interactions at the atomic level. By analyzing the chemical shifts and the NOE signals of the protein in thepresence of the drug, det本人led information about the binding site and the mode of binding can be obt本人ned. Additionally, NMR can provide insights into the dynamics of the protein upon binding to the drug.3. Applications3.1. Drug DiscoverySpectroscopic studies of drug-protein interactions play a crucial role in drug discovery, providing valuable information about the binding affinity, selectivity, and mode of action of potential drug candidates. By understanding how small molecules interact with their target proteins, researchers can design more potent and specific drugs with fewer side effects.3.2. Protein EngineeringSpectroscopic techniques can also be used to study the effects of mutations and modifications on the binding affinity and specificity of proteins. By analyzing the binding of small molecules to wild-type and mutant proteins, valuable insights into the structure-function relationship of proteins can be obt本人ned.3.3. Biophysical StudiesSpectroscopic studies of drug-protein interactions are also valuable for the characterization of protein-ligandplexes, providing insights into the thermodynamics and kinetics of the binding process. Additionally, these studies can be used to investigate the effects of environmental factors, such as pH, temperature, and ionic strength, on the stability and binding affinity of theplexes.4. Challenges and Future DirectionsWhile spectroscopic techniques have greatly contributed to our understanding of drug-protein interactions, there are still challenges that need to be addressed. For instance, the study of membrane proteins and protein-protein interactions using spectroscopic techniques rem本人ns challenging due to theplexity and heterogeneity of these systems. Additionally, the development of new spectroscopic methods and the integration of spectroscopy with other biophysical andputational approaches will further advance our understanding of drug-protein interactions.In conclusion, spectroscopic studies of drug-protein interactions have greatly contributed to our understanding of how small molecules interact with proteins at the molecular level. Byproviding det本人led information about the binding affinity, mode of binding, and structural changes that occur upon binding, spectroscopic techniques have be valuable tools in drug discovery, protein engineering, and biophysical studies. As technology continues to advance, spectroscopy will play an increasingly important role in the study of drug-protein interactions, leading to the development of more effective and targeted therapeutics.。
赝势的介绍

Vl(r)|l l|.
Traditionally PPs are split into a local part, long-ranged and behaving like −Zv e2/r for r → ∞, and a short-ranged semilocal term: ˆ ps = V ˆloc + V ˆSL, V ˆloc ≡ Vloc(r), V ˆSL ≡ V
2 d −2π (rφ(r)) d
d ln φ(r) dr
rc
= 4π
rc 0
|φ(r)|2r2dr
valid for any regular solution of the Schr¨ odinger equation at energy . – non local: there is one potential per angular momentum: V ps(r) =
ps 2 fl|φps l (r )| l
(fl is the occupancy of state with angular momentum l).
Desirable characteristics of a Pseudopotential: • Transferability: can be estimated from atomic calculations on different configurations. In many cases simple unscreening produces an unacceptable loss of transferability. May require the nonlinear core correction: Vlps(r) = Vl(r) − VH (nps(r)) − Vxc(nc(r) + nps(r)) where nc(r) is the core charge of the atom (Froyen, Louie, Cohen 1982) • Softness: atoms with strongly oscillating pseudo-wavefunctions (first-row elements, elements with 3d and 4f valence electrons) will produce hard PPs requiring many PWs in calculations. Larger core radius means better softness but worse transferability. Various recipes to get optimal smoothness without compromising transferability: Troullier and Martins (1990), Rappe Rabe Kaxiras Joannopoulos (1990)
Tunneling Studies of Pseudogaps a Comment

a r X i v :co nd-mat/9802079v 1 [c o n d -m a t .s u p r -c o n ] 6 F e b 1998Tunneling Studies of Pseudogaps:a CommentR.S.Markiewicz and C.Kusko ∗Physics Department and Barnett Institute,Northeastern U.,Boston MA 02115The recent observation of the pseudogap in tunneling measurements on Bi 2Sr 2CaCu 2O 8+δ[1–3]should prove of great value in unravelling the mysteries of the ‘normal state’of the cuprates.However,several issues in these papers require clarification.Here,we discuss two impor-tant points.First,the gaps observed in the quasiparticle tunneling spectra are assumed to be superconducting gaps,and taken as evidence that the pseudogap is caused by super-conducting fluctuations.However,a normal-state gap (due,e.g.,to charge or spin density waves)will also show up in the tunneling spectra [4].For illustrative purposes,we use the pinned [5]Balseiro-Falicov (BF)[6]model of competition between a charge density wave (CDW)and (s-wave)superconductivity (SC),which gives a good ac-count of the doping dependence of the pseudogap [7]and is a simple model for striped phases [8].For a pure CDW,the spectral function is of BCS form:A (k,ω)=2π[u 2k δ(ω−E k +)+v 2k δ(ω−E k −)],(1)with u 2k =1−v 2k =(1+ǫk −/˜E k )/2,E k ±=(ǫk +±˜E k )/2,ǫk ±=ǫk ±ǫk +Q and ˜Ek =[1]Ch.Renner,et al.,Phys.Rev.Lett.80,149(1998).[2]Y.DeWilde,et al.,Phys.Rev.Lett.80,153(1998).[3]N.Miyakawa,et al.,Phys.Rev.Lett.80,157(1998).[4]A.M.Gabovich,Sov.J.Low Temp.Phys.18,490(1992).[5]R.S.Markiewicz,Physica C 193,323(1992).[6]C.Balseiro and L.Falicov,Phys.Rev.B 20,4457(1979).[7]R.S.Markiewicz,Phys.Rev.Lett.73,1310(1994).[8]R.S.Markiewicz,Phys.Rev.B 56,9091(1997).[9]I.Affleck and J.B.Marston,Phys.Rev.B 37,3774(1988).[10]A.Kampf and J.Schrieffer,Phys.Rev.B 42,7967(1990).[11]Summarized on p.1223of R.S.Markiewicz,J.Phys.Chem.Sol.58,1179(1997).1。
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a r X i v :c o n d -m a t /9910226v 1 [c o n d -m a t .s t r -e l ] 15 O c t 1999Pseudogaps in the 2D half-filled Hubbard modelC.Huscroft,M.Jarrell,Th.Maier,S.Moukouri,A.N.TahvildarzadehDepartment of Physics,University of Cincinnati,Cincinnati,OH 45221-0011(February 1,2008)We study the pseudogaps in the spectra of the half-filled 2D Hubbard model using both finite-size and dynamical cluster approximation (DCA)quantum Monte Carlo calculations.A charge pseudogap,accompanied by non-Fermi liquid behavior in the self energy,is shown to persist in the thermodynamic limit.The DCA (finite-size)method systematically underes-timates (overestimates)the width of the pseudogap.A spin pseudogap is not seen at half-filling.Introduction For over a decade it has been recognized that the normal state properties of high-T c superconduc-tors are unusual and appear to have non-Fermi liquid characteristics.[1]One of the most remarkable features of the normal state is a suppression of the density of states at the Fermi energy in a temperature regime above T c in underdoped samples.Angular resolved photoemis-sion experiments [2,3]show that this pseudogap in the spectral function has a d-wave anisotropy,the same sym-metry as the superconducting order parameter in these materials.This,along with theories that short-ranged spin fluctuations mediate pairing in the high-T c cuprates [4,5],emphasizes the importance of understanding the normal state,insulating phase.It is thought by many that the two-dimensional Hub-bard model,or closely related models,should capture the essential physics of the high-T c cuprates.[4]Yet,despite years of effort,neither the precursor pseudogap nor d-wave superconducting order have been conclusively seen in the Hubbard model.Intuitively,one may expect that the Hubbard model should show pseudogap behavior.At half-filling,the ground state of the 2D Hubbard model is an antifer-romagnetic insulator [6,7]and the spectrum is there-fore gapped.However,the Mermin-Wagner theorem pre-cludes any transition at finite T ,so as the temperature is lowered one may anticipate that a pseudogap will de-velop.[8]This question has been previously addressed in the 2D Hubbard insulator by finite-size lattice Quantum Monte Carlo (QMC)[9,10]and approximate many-body techniques [11–13].The results have been contradictory and inconclusive as to the existence of a pseudogap at low temperatures,due to limitations of these ing the recently developed Dynamical Cluster Ap-proximation (DCA)[14,15]we find that at sufficiently low temperatures a pseudogap opens in the single par-ticle spectral weight A (k ,ω)of the 2D Hubbard modelwith a simultaneous destruction of the Fermi liquid state due to critical fluctuations above the T =0transition temperature.This occurs in the weak-to-intermediate coupling regime U <W ,where U is the on-site Coulomb energy and W the non-interacting band width.Using finite-sized techniques,it is difficult to determine if a gap persists in the thermodynamic limit.At half fill-ing,finite-size QMC calculations display a gap in their spectra as soon as the correlation length exceeds the lat-tice size,so they tend to overestimate the pseudogap as it would appear in the thermodynamic limit.Finite-size scaling is complicated by the lack of an exact scaling ansatz for the gap and the cost of performing simula-tions of large systems.Calculations employing Dynami-cal Mean Field Approximation (DMFA)[16]in the para-magnetic phase do not display this behavior since they take place in the thermodynamic limit rather than on a finite-size lattice.However,the DMFA lacks the non-local spin fluctuations often believed to be responsible for the pseudogap.The Dynamical Cluster Approxima-tion (DCA)is a fully causal approach which systemati-cally incorporates non-local corrections to the DMFA by mapping the problem onto an embedded impurity clus-ter of size N c .N c determines the order of the approx-imation and provides a systematic expansion parameter 1/N c .While the DCA becomes exact in the limit of large N c it reduces to the DMFA for N c =1.Thus,the DCA differs from the usual finite size lattice calculations in that it is a reasonable approximation to the lattice prob-lem even for a “cluster”of a single site.Like the DMFA,the DCA solution remains in the thermodynamic limit,but the dynamical correlation length is restricted to the size of the embedded cluster.Thus the DCA tends to underestimate the pseudogap.Method The DCA is based on the assumption that the lattice self energy is weakly momentum dependent.This is equivalent to assuming that the dynamical inter-site correlations have a short spatial range b <∼L/2where L is the linear dimension of the cluster.Then,according to Nyquist’s sampling theorem [17],to reproduce these correlations in the self energy,we only need to sample the reciprocal space at intervals of ∆k ≈2π/L .Therefore,we could approximate G (K +˜k)by G (K )within the cell of size (π/L )D (see,Fig.1)centered on the cluster mo-mentum K (wherever feasible,we suppress the frequency labels)and use this Green function to calculate the self energy.Knowledge of these Green functions on a finer scale in momentum is unnecessary,and may be discarded to reduce the complexity of the problem.Thus the clus-1ter self energy can be constructed from the coarse-grained average of the single-particle Green function within the cell centered on the cluster momenta:¯G(K )≡Ncsa−10−50510ω−3−2−101Σ(π,0,ω)β=1.3β=2.6β=3.0β=4.0β=5.000.10.20.30.4A (π,0,ω)0123ω0.20.4χ’’(ω)/χ(T )ωIm Σ(k,ω)Re Σ(k,ω)FIG. 3.The spectral density A (k ,ω),and the real ReΣ(k ,ω)and imaginary ImΣ(k ,ω)parts of the self-energy for the 2D Hubbard model via the DCA with a paramagnetic host at k =(π,0)for a 64-site cluster (N c =64)at various temperatures.The on-site Coulomb repulsion U =5.2,the band width W =8,and the filling n =1.As the tem-perature is lowered,the system first builds a Fermi-liquid-like peak in A (k ,ω).By β=2.6,a pseudogap begins to develop in A (k ,ω)and simultaneously,ReΣ(k ,ω)develops a positive slope at ω=0,a signal of a non-Fermi liquid.The pseudogap deepens as the temperature is further lowered.The imaginary part of the dynamic spin susceptibility,divided by the static spin susceptibility is shown in the inset.No spin gap is seen.Results We study the 2D Hubbard Hamiltonian:H =−t i,j ,σ(c †iσc jσ+c †jσc iσ)+Ui(n i ↑−12)−µi,σn iσ.(4)where c †iσ(c iσ)creates (destroys)an electron at site i with spin σ,U is the on-site Coulomb potential,and n iσ=c †iσc iσis the number operator.We set the overlap integral t =1and measure all energies in terms of t .We work at µ=0where the system is half-filled ( n =1).We choose U =5.2,which is well below the value U >∼W believed to be necessary to open a Mott-Hubbard gap.We also calculate the angle integrated dynamical spin susceptibility shown in the inset.It does not have a pseudogap,as expected for the half-filled model since the spin-wave spectrum is gapless.Since a (spin)charge gap is generally defined as one which appears in the (spin)charge dynamics or thermodynamics,we conclude that the pseudogap is only in the charge response and is due to short-ranged antiferromagnetic spin correlations.Fig.3shows the spectral density A (k ,ω),and the real ReΣ(k ,ω)and imaginary ImΣ(k ,ω)parts of the self-energy for the 2D Hubbard model via the DCA with a paramagnetic host at the Fermi surface X pointk =(π,0)for a 64-site cluster (N c =64)at various temperatures.We obtain the spectral function A (k ,ω)via the Maximum Entropy Method (MEM).[21]As the temperature is lowered,the system first builds a Fermi-liquid-like peak in A (k ,ω).By β=2.6,a pseudogap begins to develop in A (k ,ω).The pseudogap builds as the temperature is further lowered.Fig.4shows the spectral function A (k ,ω)at the half-filled Fermi surface point k =(π/2,π/2).The qualitative features are similar to Fig.3,but the pseudogap opens at a lower temperature and the distance between the peaks is less than that seen at the X point.This behavior is reminiscent of the anisotropy of the pseudogap observed experimentally in the insulating [3]and in the supercon-ducting [5]cuprates,but is not large enough to be compa-rable with that seen experimentally.We speculate that the anisotropy seen here may be due to a difference in the number of states near the Fermi energy at these two points in the zone.−10−5510ω−3−2−101Σ(π/2,π/2,ω)β=1.3β=2.6β=3.0β=4.0β=5.000.10.20.30.4A (π/2,π/2,ω)Im Σ(k,ω)Re Σ(k,ω)FIG. 4.The spectral density A (k ,ω),and the real ReΣ(k ,ω)and imaginary ImΣ(k ,ω)parts of the self-energy for the 2D Hubbard model via the DCA at k =(π/2,π/2)and the same parameters as Fig.3.Again the system first builds a Fermi-liquid-like peak in A (k ,ω)and then develops a pseudogap in A (k ,ω)with a simultaneous non-Fermi liq-uid behavior in ReΣ(k ,ω).Here,though,the pseudogap first appears at a lower temperature than at k =(π,0).The DCA self-energy spectra Figs.3&4support the spectral evidence.At the X point,the slope of the real part ReΣ(k ,ω)becomes positive below β=2.6,the tem-perature at which we observed the opening of a pseudo-gap.This signals the appearance of two new solutions in the quasiparticle equation Re(ω−ǫk −Σ(k ,ω))=0in addition to the strongly damped solution at ω=0which is also present in the noninteracting system.These two new quasiparticle solutions for the same k -vector indi-cate precursor effects of the onset of antiferromagnetic ordering which entails a doubling of the unit cell.They3are referred as shadow states and are caused by antiferro-magnetic spin fluctuations in the paramagnetic state.At these temperatures,the imaginary part ImΣ(k ,ω)dis-plays a local minimum at ω=0indicating the break-down of the Fermi liquid behavior.We note that a differ-ent conclusion was previously reached in a FLEX study [11],which found that ImΣ(k ,ω)has a local minimum at ω=0which was not accompanied by an opening of a pseudogap.Since the pseudogap is due to short-range spin correlations,we conclude that FLEX underestimates these correlations.024ω0.10.20.30.40.50.6A (π,0,ω)N c =64N c =36N c =16N c =10246ωN=64N=16246N c1/20.10.20.3T *∆/5.2(a)(b)FIG.5.The spectral density A (k ,ω)at k =(π,0)for the 2D Hubbard model via (a)the DCA and (b)finite-size Quan-tum Monte Carlo (QMC)at an inverse temperature times the bandwidth βW =40on various size clusters.The tempera-ture T ∗at which the pseudogap first becomes apparent in the DCA spectra,as well as the full width ∆measured from peak to peak is plotted in the inset.The finite-size QMC over-estimates ∆and T ∗,whereas the DCA QMC systematically underestimates them.It is instructive to compare the DCA results with those obtained by finite-size QMC calculations.Fig.5shows the spectral density A (π,0,ω)obtained by analytically continuing both finite-size and DCA QMC data.In spite of the difference in the two methods,the information they provide is complimentary.In the finite-size results,(b),we see a similar opening of a pseudogap.However,as the length of the antiferromagnetic (AF)correlations reach the longest length on the finite-size lattice,the system develops a full gap.Thus,the finite-size QMC overesti-mates the size of the gap.In the DCA results,(a),the pseudogap emerges as soon as N c >1.The temperature T ∗at which the pseudogap first becomes apparent in the spectra,as well as the full width ∆measured from peak to peak is plotted in the inset.Both T ∗and ∆increase with N c .Since the DCA calculation remains in the ther-modynamic limit,a full gap due to antiferromagnetic cor-relations alone cannot open until their correlation length diverges.However,since these correlations are restrictedto the size of the cluster,the DCA systematically under-estimates the size of the gap.Thus,if a pseudogap exists in the DCA for finite N c ,it should persist in the limit as N c →∞.In summary,we have employed the recently developed DCA to study the long-open question of whether the half-filled Hubbard model has a pseudogap due to AF spin fluctuations.We find conclusive evidence of a pseudogap in the charge dynamics and have shown unambiguously that the T =0phase transition of the half-filled model is preceded by an opening of a pseudogap in A (k F ,ω)accompanied by pronounced non-Fermi liquid behavior in Σ(k F ,ω).Acknowledgments We would like to acknowledge use-ful conversations with P.van Dongen,B.Gyorffy,M.Hettler,H.R.Krishnamurthy R.R.P.Singh and J.Za-anen.This work was supported by the National Sci-ence Foundation grants DMR-9704021,DMR-9357199,and the Ohio Supercomputing Center.。