GENUS ANTROPHYUM KAULF.FROM CHINA AND NEIGHBORING REGIONS

ＧＥＮＵＳＡＮＴＲＯＰＨＹＵＭＫＡＵＬＦ．ＦＲＯＭＣＨＩＮＡＡＮＤＮＥＩＧＨＢＯＲＩＮＧＲＥＧＩＯＮＳＸ．Ｃ．ＺＨＡＮＧ（Ｔｈｅｈｅｒｂａｒｉｕｍ（ＰＥ）,ＩｎｓｔｉｔｕｔｅｏｆＢｏｔａｎｙ,ＣｈｉｎｅｓｅＡｃａｄｅｍｙｏｆＳｃｉｅｎｃｅｓ,Ｂｅｉ...     

SELF-TRAINING NEURAL NETWORK MODEL FOR REAL TIME TOMOGRAPHY DATA PROCESSING

ＳＥＬＦ—ＴＲＡＩＮＩＮＧＮＥＵＲＡＬＮＥＴＷＯＲＫＭＯＤＥＬＦＯＲＲＥＡＬＴＩＭＥＴＯＭＯＧＲＡＰＨＹＤＡＴＡＰＲＯＣＥＳＳＩＮＧＹｕ．Ｋｕｌｃｈｉｎ;Ｏ．Ｋａｍｅｎｅｙ（Ｄｅｐａｒｔｍｅｎｔｏｆｐｈｙｓｉｃｓ,ＦａｒＥａｓｔｅｒｎＳｔａｔｅＴｅｃ...     

大肠杆菌精氨酰—tRNA合成酶的变种ArgRS306KR的纯化…

本文从含ＡｒｇＲＳ３０６ＫＲ基因ａｒｇｓ３０６ＫＲ的ｐＵＣ１８重组质粒的大肠杆菌ＴＧ１转化子中经ＤＥＡＥ－Ｓｅｐｈａｃｅｌ和Ｂｌｕｅ－Ｓｅｐｈａｒｏｓｅ两步柱层析,得到电泳一条带的ＡｒｇＲＳ３０６ＫＲ。纯酶的比活为２７９０单位／毫克。该酶氨酰化和ＡＴＰ－ＰＰｉ交换活力的最适ＰＨ分别为ＰＨ８．３和ＰＨ７．５。氨酰化活力对ＡＴＰ、Ａｒｇ和ｔＲＮＡ的Ｋｍ分别２．６ｍｍｏｌ／Ｌ、１４．０μｍｏｌ／Ｌ和５．     

大肠杆菌精氨酰－tRNA合成酶的变种ArgRS306KR的纯化和基本性质

本文从含ＡｒｇＲＳ３０６ＫＲ基因ａｒｇｓ３０６ＫＲ的ｐＵＣ１８重组质粒的大肠杆菌ＴＧ１转化子中经ＤＥＡＥ－Ｓｅｐｈａｃｅｌ和Ｂｌｕｅ－Ｓｅｐｈａｒｏｓｅ两步柱层析,得到电泳一条带的ＡｒｇＲＳ３０６ＫＲ。纯酶的比活为２７９０单位／毫克。该酶氨酰化和ＡＴＰ～ＰＰｉ交换活力的最适ｐＨ分别为ｐＨ８．３和ｐＨ７．５。氨酰化活力对ＡＴＰ、Ａｒｇ和ｔＲＮＡ的Ｋｍ分别为２．６ｍｍｏｌ／Ｌ、１４．０μｍｏｌ／Ｌ和５．０μｍｏｌ／Ｌ：Ｖｍａｘ为７６３０单位／毫克;ｋｏａｔ为９Ｓ－１。ＡＴＰ～ＰＰｉ交换活力对ＡＴＰ和Ａｒｇ的Ｋｍ分别为８．３ｍｍｏｌ／Ｌ和９９μｍｏｌ／Ｌ;Ｖｍａｘ为１６３２０单位／毫克;ｋｃａｔ为１８Ｓ－１。     

用蛋白质工程方法改变葡萄糖异构酶最适pH和最适温度

用寡核苷酸诱导的定点突变方法构建了葡萄糖异构酶基因的突变体（Ｎ１８４Ｄ和Ａ１９８Ｃ）。含突变体的重组质粒ｐＴＫＤ－ＧＩ１（Ｎ１８４Ｄ）和ｐＴＫＤ－ＧＩ２（Ａ１９８ｃ）在Ｅ．ｃｏｌｉＫ３８菌株中表达,用ＤＥＡＥ－Ｓｅｐｈａｒｏｓｅ ＦＦ和Ｓｅｐｈａｃｒｙｌ Ｓ－３００ＨＲ柱层析分离纯化突变酶。与野生型葡萄糖异构酶比较实验表明：（１）突变酶Ｎ１８４Ｄ的最适ｐＨ值下降了１个单位;等电点下降了０．６个单位     

黑线姬鼠肥满度的研究

黑线姬鼠肥满度的研究ＳＴＵＤＹＯＮＴＨＥＲＥＬＡＴＩＶＥＦＡＴＮＥＳＳＯＦＴＨＥＳＴＲＩＰＥＤＦＩＥＬＤＭＯＵＳＥ（ＡＰＯＤＥＭＵＳＡＧＲＡＲＩＶＳ）ＫｅｙｗｏｒｄｓＳｔｒｉｐｅｄｆｉｅｌｄｍｏｕｓｅ（Ａｐｏｄｅｍｕｓ：ａｇｒａｒｉｕｓ）;Ｒｅｌａｔ...     

重组FAS分子的表达、纯化及抗体制备

用ＰＣＲ法扩增出编码人ＦＡＳ分子胞外区的ｃＤＮＡ片段,直接克隆到ｐＧＥＭ－Ｔ载体上,经ＤＮＡ序列测定后,再插入到谷胱甘肽转硫酶（ＧＳＴ）融合蛋白表达载体ｐＧＥＸ－ＫＧ的ＥｃｏＲⅠ和ＳａｌⅠ位点之间,构成重组质粒ｐＫＧ－ｈＦＡＳ,将此质粒导入大肠杆菌,经ＩＰＴＧ诱导后获得ＧＳＴ－ｈＦＡＳ重组融合蛋白的表达,用谷胱甘肽偶联的Ｓｅｐｈａｒｏｓｅ４Ｂ经亲合层析获得纯化的ＧＳＴ－ｈＦＡＳ蛋白,经凝血酶酶切和二次亲合层析去除ＧＳＴ部分,得到纯化的ＦＡＳ蛋白．用纯化的ＦＡＳ抗原免疫家兔制备了抗ＦＡＳ抗体,经检测发现抗ＦＡＳ抗体能诱导Ｕ９３７细胞发生细胞凋亡     

系统感染TMV的番茄叶胞外β-1,3-葡聚糖酶

系统感染ＴＭＶ （ｔｏｂａｃｃｏ ｍ ｏｓａｉｃ ｖｉｒｕｓ）的番茄（Ｌｙｃｏｐｅｒｓｉｃｏｎ ｅｓｃｕｌｅｎｔｕｍ Ｍｉｌｌ．）叶胞外蛋白提取液经冰冻干燥浓缩、－ ２０℃丙酮沉淀、ＣＭ－Ｓｅｐｈａｄｅｘ Ｃ－２５离子交换层析、ＤＥＡＥ－Ｓｅｐｈａｄｅｘ Ａ－２５离子交换层析和Ｓｅｐｈａｄｅｘ Ｇ－７５凝胶层析纯化,获得ＰＡＧＥ均一的β－１,３－葡聚糖酶．ＳＤＳ－ＰＡＧＥ证明,它包含分子量为３６ ｋＤ 和２７ ｋＤ的两个同工酶．以昆布多糖为底物,酶的最适ｐＨ 在４．８—５．２之间,在ｐＨ ４—８稳定;酶的最适温度在３０—４０℃之间,在４０℃保温１ｈ 后酶活性不变;Ｋｍ 值为９．２ ｍ ｇ／ｍ Ｌ．在系统感染ＴＭＶ 的番茄叶胞外蛋白提取液中,有分子量为２２ ｋＤ、２７ ｋＤ和３６ ｋＤ的３个β－１,３－葡聚糖酶同工酶     

重组人干细胞因子在大肠杆菌中的表达及活性鉴定

采用ＰＣＲ方法从重组载体ｐＫＫＳＣＦ扩增出人干细胞因子（ＳＣＦ）基因ｃＤＮＡ片段,经亚克隆构建成表达载体ｐＥＴ１１ｄＳＣＦ,经限制性酶谱分析鉴定证实．继用ＩＰＴＧ诱导重组ｐＥＴ１１ｄＳＣＦ在大肠杆菌ＨＭＳ１７４（ＤＥ３）中表达,经初步纯化获得重组人ＳＣＦ蛋白质,经检测具有生理活性,对脐带血ＣＦＵ－ＣＭ和ＨＰＰ－ＣＦＣ增殖有明显刺激作用,为进一步的生物工程研究奠定了基础．     

中华姬鼠种群生态的初步分析

中华姬鼠种群生态的初步分析ＴＨＥＰＲＥＬＩＭＩＮＡＲＹＡＮＡＬＹＳＩＳＯＮＴＨＥＰＯＰＵＬＡＴＩＯＮＥＣＯＬＯＧＹＯＦＣＨＩＮＥＳＥＦＩＥＬＤＭＯＵＳＥ（ＡＰＯＤＥＭＵＳＤＲＡＣＯ）ＫｅｙＷｏｒｄｓＣｈｉｎｅｓｅＦｉｅｌｄＭｏｕｓｅ（Ａｐｏｄｅｍｕｓ...     

The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination

Several variants of RB69 DNA polymerase (RB69 pol) with single-site replacements in the nascent base-pair binding pocket are less discriminating with respect to noncomplementary dNMP incorporation than the wild-type enzyme. To quantify the loss in base selectivity, we determined the transient-state kinetic parameters for incorporation of correct and all combinations of incorrect dNMPs by the exonuclease-deficient form of one of these RB69 pol variants, L561A, using rapid chemical quench assays. The L561A variant did not significantly alter the k(pol) and K(D) values for incorporation of correct dNMPs, but it showed increased incorporation efficiency (k(pol)/K(D)) for mispaired bases relative to the wild-type enzyme. The incorporation efficiency for mispaired bases by the L561A variant ranged from 1.5 x 10(-)(5) microM(-)(1) s(-)(1) for dCMP opposite templating C to 2 x 10(-)(3) microM(-)(1) s(-)(1) for dAMP opposite templating C. These k(pol)/K(D) values are 3-60-fold greater than those observed with the wild-type enzyme. The effect of the L561A replacement on the mutation frequency in vivo was determined by infecting Escherichia coli harboring a plasmid encoding the L561A variant of RB69 pol with T4 phage bearing a mutant rII locus, and the rates of reversions to rII(+) were scored. The exonuclease-proficient RB69 pol L561A displayed a weak mutator phenotype. In contrast, no progeny phage were produced after infection of E. coli, expressing an exonuclease-deficient RB69 pol L561A, with either mutant or wild-type T4 phage. This dominant-lethal phenotype was attributed to error catastrophe caused by the high rate of mutation expected from combining the pol L561A and exo(-) mutator activities.     

Kinetics of error generation in homologous B-family DNA polymerases

The kinetics of forming a proper Watson–Crick base pair as well incorporating bases opposite furan, an abasic site analog, have been well characterized for the B Family replicative DNA polymerase from bacteriophage T4. Structural studies of these reactions, however, have only been performed with the homologous enzyme from bacteriophage RB69. In this work, the homologous enzymes from RB69 and T4 were compared in parallel reactions to determine the relative abilities of the two polymerases to incorporate correct nucleotides as well as to form improper pairings. The kinetic rates for three different exonuclease mutants for each enzyme were measured for incorporation of an A opposite T and an A opposite furan as well as for the formation of A:C and T:T mismatches. The T4 exonuclease mutants were all ~2- to 7-fold more efficient than the corresponding RB69 exonuclease mutants depending on whether a T or furan was in the templating position and which exonuclease mutant was used. The rates for mismatch formation by T4 were significantly reduced compared with incorporation opposite furan, much more so than the corresponding RB69 mutant. These results show that there are kinetic differences between the two enzymes but they are not large enough to preclude structural assumptions for T4 DNA polymerase based on the known structure of the RB69 DNA polymerase.     

Purification and characterization of porcine liver DNA polymerase gamma: utilization of dUTP and dTTP during in vitro DNA synthesis.

Porcine liver DNA polymerase gamma has been demonstrated to preferentially incorporate dTMP over dUMP during in vitro DNA synthesis. When polymerase activity was measured in standard reactions containing saturating levels of either dTTP or dUTP, the polymerization rate was slightly faster in the reaction containing dTTP. However, under conditions where both dTTP and dUTP competed, at an equal molar concentration, approximately 3-times more thymine residues were incorporated than uracil residues into DNA. Similarly, preferential incorporation of dTMP was observed on several substrates including poly (dA).oligo p(dT), poly (rA).oligo p(dT) and poly (dA-dT). The discrimination against dUMP incorporation was even more apparent with reduced levels of dUTP. These observations were consistent with the finding that the Km for DNA polymerase gamma was about 3-fold lower for dTTP (0.4 microM) than for dUTP (1.1 microM). On the other hand, the Vmax for these two reactions was very similar. Discrimination against dUMP incorporation was also observed during inhibition of polymerase gamma by dideoxyribonucleoside triphosphates. Dideoxythymidine triphosphate preferentially inhibited dUMP incorporation compared to that of dTMP, whereas ddATP, ddCTP and ddGTP inhibited both reactions equally.     

噬菌体RB69 DNA聚合酶以不正确的核苷酸为底物的聚合反应的稳态动力学研究

测定了ＲＢ６９ ＤＮＡ 聚合酶以不正确的核苷酸（ｒＮＴＰ、ｄｄＮＴＰ以及碱基不配对的ｄＮＴＰ）为底物进行聚合反应的稳态动力学常数,并与Ｋｌｅｎｏｗ 酶进行了比较．结果表明,ＲＢ６９ ＤＮＡ 聚合酶在以不正确的核苷酸为底物进行聚合反应时,其Ｋｍ 值与正确底物参入时相比有大幅度提高,而ｋｃａｔ保持不变或下降幅度较小．而Ｋｌｅｎｏｗ 酶在利用不正确的核苷酸为底物时,与正确底物参入时相比,其ｋｃａｔ大幅度下降,而Ｋｍ （或ＫＤ）基本保持不变或上升较小幅度．两种酶不同的动力学特点反映出它们不同的底物选择机制．     

Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity

Changing a highly conserved amino acid in motif A of any of the four yeast family B DNA polymerases, DNA polymerase alpha, delta, epsilon or zeta, results in yeast strains with elevated mutation rates. In order to better understand this phenotype, we have performed structure-function studies of homologous mutants of RB69 DNA polymerase (RB69 pol), a structural model for family B members. When Leu415 in RB69 pol is replaced with phenylalanine or glycine, the mutant polymerases retain high-catalytic efficiency for correct nucleotide incorporation, yet have increased error rates due to increased misinsertion, increased mismatch extension and inefficient proofreading. The Leu415Phe mutant also has increased dNTP insertion efficiency opposite a template 8-oxoG and opposite an abasic site. The 2.5 A crystal structure of a ternary complex of RB69 L415F pol with a correctly base-paired incoming dTTP reveals that the phenylalanine ring is accommodated within a cavity seen in the wild-type enzyme, without steric clash or major change in active site geometry, consistent with retention of high-catalytic efficiency for correct incorporation. In addition, slight structural differences were observed that could be relevant to the reduced fidelity of L415F RB69 pol.     

Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue

We have recently challenged the widely held view that 2,4-difluorotoluene (dF) is a nonpolar isosteric analogue of the nucleotide dT, incapable of forming hydrogen bonds (HBs). To gain a further understanding for the kinetic preference that favors dAMP insertion opposite a templating dF, a result that mirrors the base selectivity that favors dAMP insertion opposite dT by RB69 DNA polymerase (RB69pol), we determined presteady-state kinetic parameters for incorporation of four dNMPs opposite dF by RB69pol and solved the structures of corresponding ternary complexes. We observed that both the F2 and F4 substituent of dF in these structures serve as HB acceptors forming HBs either directly with dTTP and dGTP or indirectly with dATP and dCTP via ordered water molecules. We have defined the shape and chemical features of each dF/dNTP pair in the RB69pol active site without the corresponding phosphodiester-linkage constraints of dF/dNs when they are embedded in isolated DNA duplexes. These features can explain the kinetic preferences exhibited by the templating dF when the nucleotide incorporation is catalyzed by wild type RB69pol or its mutants. We further show that the shapes of the dNTP/dF nascent base pair differ markedly from the corresponding dNTP/dT in the pol active site and that these differences have a profound effect on their incorporation efficiencies.     

Base selectivity is impaired by mutants that perturb hydrogen bonding networks in the RB69 DNA polymerase active site

To investigate the molecular basis for the selective utilization of nucleoside triphosphates complementary to templating bases, by RB69 DNA polymerase (RB69 pol), we constructed a set of mutants that we predicted would perturb the "floor" of the nascent base-pairing interface in the enzyme. We then determined the pre-steady-state kinetic parameters for the incorporation of complementary and noncomplementary dNTPs by the exo(-) form of RB69 pol and its mutants. We found that the Y567A mutant had the same K(d) and k(pol) values for incorporation of C versus G as the wild-type exo(-) enzyme; however, the k(pol)/K(d) ratio for G versus G incorporation with the Y567A mutant was 10 times higher than the k(pol)/K(d) efficiency of G versus G incorporation using the exo(-) RB69 pol. The reduced level of discrimination by the Y567A mutant against incorporation of mismatched bases was also seen with the Y391A mutant. Stopped-flow fluorescence was also employed to monitor rates of putative conformational changes with the exo(-) RB69 pol and its mutants using a primer-template complex containing 2-aminopurine. The rates of fluorescence changes were equal to or greater than the rates of the rapid chemical quench, indicating that we were monitoring a process occurring before or during the phosphoryl transfer reaction. We have interpreted our results within the context of the crystal structure of the RB69 pol ternary complex [Franklin, M. C., et al. (2001) Cell 105, 657-667].     

(E)-5-(2-bromovinyl)-2'-deoxyuridine-5'-triphosphate as a DNA polymerase substrate.

Time course of incorporation and the effect of 5'-triphosphate of the selective antiherpetic agent (E)-5-(2-bromovinyl)-2'-deoxyuridine (bv5dUTP) on the incorporation of dTTP and dATP into template-primers of different structure were studied in E. coli DNA polymerase I Klenow fragment enzyme-catalyzed reactions. bv5dUTP could substitute for dTTP depending on the structure of template-primer. E.g. into calf thymus DNA incorporation of bv5dUMP was around 80% of that of dTMP at 30 minutes of incubation. The analog has also inhibited dTMP incorporation, net DNA synthesis, however, was hardly affected. The substrate properties of the analog were studied with [2-14C]-labelled bv5dUTP.     

Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates

We have used 2-aminopurine (2AP) as a fluorescent probe in the template strand of a 13/20mer primer/template (D) to detect deoxynucleoside triphosphates (N)-dependent conformational changes exhibited by RB69 DNA polymerase (ED) complexes. The rates and amplitudes of fluorescence quenching depend hyperbolically on the [dTTP] when a dideoxy-primer/template (ddP/T) with 2AP as the templating base (n position) is used. No detectable fluorescence changes occur when a ddP/T with 2AP positioned 5′ to the templating base (n + 1 position) is used. With a deoxy-primer/template (dP/T) with 2AP in the n position, a rapid fluorescence quenching occurs within 2 ms, followed by a second, slower fluorescence quenching with a rate constant similar to base incorporation as determined by chemical quench. With a dP/T having 2AP in the n + 1 position, there is a [dNTP]-dependent fluorescence enhancement that occurs at a rate comparable to dNMP incorporation. Collectively, the results favor a minimal kinetic scheme in which population of two distinct biochemical states of the ternary EDN complex precedes the nucleotidyl transfer reaction. Observed differences between dP/T and ddP/T ternary complexes indicate that the 3′ hydroxyl group of the primer plays a critical role in determining the rate constants of transitions that lead to strong deoxynucleoside triphosphate binding prior to chemistry.     

DNA fragmentation and cytotoxicity from increased cellular deoxyuridylate

Previous results from this laboratory have shown that thymidylate deprivation results in dramatic elevation of intracellular dUTP and incorporation of dUMP into DNA. The goal of the present studies was to determine whether the latter changes may play a part in the associated cytotoxicity ("thymineless death"), which is ordinarily assumed to be a direct result of reduced intracellular dTTP. The approach used here was to increase intracellular dUTP without allowing dTTP to diminish and observe the effects on cell viability. dUMP pools were expanded by exposure of cells to deoxyuridine [in cell growth medium containing hypoxanthine, methotrexate, and thymidine (HAT medium)], resulting in accumulation of dUTP to levels that approached those of dTTP, which were at, or higher than, the levels in untreated cells. In conjunction with this the cells became nonviable, and newly synthesized DNA was fragmented, both of which occur with thymidylate depletion and, we assume, result from the active process of excision repair at the many uracil-containing sites in DNA. The results indicate that, although the relative importance of low dTTP remains unknown, elevated dUTP can account for the cytotoxicity caused by thymidine starvation. Most of the "dTTP" measured by the DNA polymerase assay in cells treated with methotrexate (MTX) (plus purine supplement) was, in fact, dUTP, which may explain some previous observations of only modest depression of dTTP in cells treated with MTX or similarly acting drugs.