产酸克雷伯氏杆菌发酵产2，3-丁二醇的培养基优化

采用不同设计方法相结合的策略对耐高糖产酸克雷伯氏杆菌（Klebsiella oxytoca）ME—UD-3-4发酵产2,3-丁二醇的培养基进行优化。首先在单因素实验的基础上采用Plackett—Burrnan设计法对影响ME—UD-3-4发酵产2,3-丁二醇的相关因素进行研究,筛选到3种有显著效应的因素（P〈0．05）：葡萄糖、玉米浆和MgSO4·7H2O。然后利用响应曲面法（Response Surface Methodology,RSM）对这3种因素的最佳水平范围进一步探讨;对得到的回归模型进行分析,得最佳条件（g／L）：葡萄糖220、玉米浆19和MgSO4·7H2O 0．4;在最佳条件下,发酵80h,2,3-丁二醇产量从原来的57．3 g／L提高到86．1 g／L,生产强度由0．72g／（L·h）提高到1．08g/（L·h）。     

氨基功能化整体材料在磷酸化肽快速可控富集中的应用

针对质谱在磷酸化肽分析过程中检测灵敏度低的问题,本文在移液器吸头尖端原位制备了氨基功能化整体材料,并将其应用于磷酸化肽的快速富集.基于该材料所建立的磷酸化肽富集方法操作简便、分析时间短,并且能够有效避免富集过程中材料与溶液分离不完全所导致的样品损失等问题.而在不同组成的上样溶液条件下,氨基功能化整体材料对单磷酸化肽和多磷酸化肽表现出了不同的磷酸化肽富集选择性,因而借助于对上样溶液组成的调控,该材料可以分别实现对磷酸化肽的全富集以及对多磷酸化肽的选择性富集.     

液质联用多反应监测法定量目标多肽或蛋白质

为建立优化的血浆内源性多肽提取方法,并且构建目标多肽和蛋白质的质谱定量方 法,本研究考察了超滤法、有机溶剂沉淀法和固相萃取法对血浆内源性多肽的提取效果 ,并通过Tricine-SDS-PAGE对提取效果进行比较.通过液相色谱串联质谱多反应监测 （MRM）分析,建立了多肽标准品ESAT-6定量方法,并将ESAT-6定量建立的液相色谱和质谱条件应用于蛋白质的定量,对多肽和蛋白质MRM定量的标准曲线进行了考 察.Tricine-SDS-PAGE结果表明,乙腈沉淀法是最佳的血浆内源性多肽提取方法,低分子量的多肽可以得到很好的富集,且能有效地去除高分子蛋白质的污染.液相色谱串联 质谱MRM法检测血浆内提取的多肽,标准曲线的线性较好,相关系数为0.999.另外,采 用MRM法对胶内分离的蛋白质进行定量,标准曲线的线性相关系数为0.995.综上所述, 本研究构建了一种简单有效的血浆多肽提取方法,通过液质联用MRM法成功地实现了目标多肽和蛋白质定量测定.该定量方法可以推广应用于复杂样品中的多肽和蛋白质的定 量分析.     

质谱技术解析磷酸化蛋白质组

蛋白质磷酸化是生物体内存在的一种普遍的调节方式,在细胞信号传递中占有极重要的地位.质谱已逐渐被人们认为是挑战这一领域的有利工具.综述了目前利用质谱技术分析磷酸化蛋白质的方法,包括利用固定化的金属亲和层析柱、抗体和化学标签技术富集目的分子,肽片段质量图和前体离子扫描（precusor ion scans）等技术检测磷酸化肽段,串联质谱对磷酸化肽段测序鉴定磷酸化位点,以及引入质量标签对蛋白质的磷酸化水平进行定量等.虽然现在已经有很多可行的方法用于分析磷酸化蛋白质,但要达到从少量生物样品中解析其全部磷酸化蛋白质仍需要有很多技术上的突破.     

磷酸化蛋白质组学研究中磷酸化肽段富集与分离方法研究进展

对磷酸化蛋白质组（phosphoproteome）进行系统深入的研究依赖于高重复性和特异性的磷酸化肽段富集与分离方法。目前发展了多种不同原理的磷酸化肽段富集方法,它们往往具有不同的选择性和特异性,因此,根据不同的研究目的选择最适合的富集方法显得尤为重要。本文综述了基于亲和色谱法（affinity chromatography）、免疫沉淀法（immunoprecipitation）、化学衍生法（chemical derivatization）、色谱法（chromatography）和其他新发展方法的磷酸化肽段富集方法,详细介绍了各自的优缺点及相关的优化与改进策略。此外,还简单介绍了磷酸化肽段富集与预分方法的不同组合的研究进展。     

虎纹捕鸟蛛毒素-X的化学合成及其鉴定

应用芴甲氧羰基（Fmoc）固相方法化学合成了虎纹捕鸟蛛毒素-X（huwentoxin-X,HWTX-X）,并在含5mmol／LGSH和0．5mmol／LGSSG的0．1mol／L Tris-HCl溶液（pH8．0）中氧化复性：复性产物与天然多肽具有相同的分子质量,在反相HPLC上共洗脱,其一维核磁共振谱规则分散,表明合成多肽形成了3对二硫键和稳定的空间结构,并与天然多肽相同：此合成的多肽能专一性抑制大鼠背根神经节细胞上N-型电压敏感钙离子通道．其IC50约40nmol／L. HWTX-X的成功合成和鉴定为进一步研究HWTX-X的结构与功能关系、药理学性质以及新型镇痛药物研发奠定了基础．     

益母草（Leonurus artemisia）灭螺效果研究

本实验研充分别采用益母草的根、茎、叶的0．10、0．25、0．50、2．00、1．00g／L和水苏碱的0．20、0．40、0．60、0．80、1．00g/L 5个不同浓度梯度的处理液处理钉螺,设清水和0．001g／L浓度的氯硝柳胺溶液为对照。结果表明：（1）益母草各部分的水浸液均有很好的灭螺效果。用不同浓度的处理液浸杀钉螺,在不同时间的处理下,钉螺死亡率存在差异,其钉螺死亡率是随处理浓度的增加和时间的延长呈上升趋势,0．5g／L以上的益母草根、茎、叶、化水浸液和浓度达0．60g／L以上的水苏碱处理液均可达到100％的明显毒杀钉螺致死效果,与通常使用浓度0．0001g／L氯硝柳胺溶液的灭螺效果相当,不过益母苹根、茎、叶水浸液的毒效较氯硝柳胺略慢,用0．0001g／L氯硝柳胺溶液处理钉螺2—3d可达100％的死亡率,而用0．5g／L以上的益母草根、茎、叶水浸液水溶液处理需要3—5d才能达到同样的效果;灭螺效果顺序依次为：叶〉茎〉根。（2）钉螺趋避性研究表明水苏碱和益母草根、茎和叶的处理液对钉螺具有明显的驱逐作用,而盐酸益母草碱几乎没有作用。由此获得化感作用植物益母草灭螺的化学生态学证据。为研制新的具中国特色的植物成份灭螺剂打下了基础。并为合成仿生灭螺剂以及最终构建生态工程中强化感作用植物群落灭螺提供理论依据。     

蚯蚓-秸秆及其交互作用对黑麦草修复Cu污染土壤的影响

以高沙土为供试土壤,加入Cu^2＋以模拟成：0,100,200,400mg／kgCu^2＋的Cu污染土壤,设置接种蚯蚓（E）、表施秸秆（M）,同时加入蚯蚓和秸秆（ME）及不加蚯蚓和秸秆的对照（CK）4个处理,并种植黑麦草。研究蚯蚓、秸秆相互作用对黑麦草吸收、富集铜的影响。结果表明：加入秸秆显著提高了蚯蚓的生物量,一定程度上缓解了重金属对蚯蚓的毒害,同时蚯蚓显著提高了秸秆的分解率,较无蚯蚓对照提高了58．11％～77．32％。接种蚯蚓（E,ME）还提高了土壤有效态重金属（DTPA-Cu）含量,秸秆处理（M）则降低了土壤有效态重金属含量。研究还发现,E处理促进了黑麦草地上部生长,而M和ME处理均显著提高了黑麦草地下部的生物量。E和ME处理同时提高了植物地上部和地下部的Cu浓度及Cu吸收量,M处理则只对植物的地下部Cu浓度和Cu吸收量有显著促进作用。总体来看,E处理、M处理及ME处理分别使黑麦草地上部Cu富集系数提高了31．22％～121．07％．2．12％～61．28％和25．56％～132．64％。     

脱脂沙棘籽制备活性多肽的研究北大核心CSCD

本文比较了用巯基蛋白酶酶解沙棘籽蛋白所得酶解多肽对乙醇脱氢酶（ADH）的激活率效果。结果表明,木瓜蛋白酶的酶解产物对ADH的激活效果最好。该活性多肽的最佳制备条件为,酶解pH为6．5,温度为50℃,酶解时间3．5h,加酶量为4000U／g。体外实验表明,木瓜蛋白酶水解产物中ADH激活率较高的为500—2000Da的多肽,达57．52％,与未分级的酶解液相比,活性提高显著（P〈0．01）。分子量在2000～3000Da的沙棘多肽也具有一定的ADH激活率,为35．09％,说明具有ADH激活率的活性多肽分子量为500～3000Da。木瓜蛋白酶酶解液经膜分离处理后,收集得到的500—3000Da的多肽组成占总肽及氨基酸质量的66．50％。     

正交设计优化东亚砂藓DDRT-PCR反应体系

利用正交实验设计L25（5^6）对东亚砂藓（Racomitrium japonicum）DDRT—PCR反应体系的6因素（Mg^2＋、dNTP、锚定引物、随机引物、模板DNA、Taq酶）在5个水平上进行优化实验。结果筛选出各反应因素的最佳体系（20μL）为：Mg^2＋2．25mmol／L、dNTP0．4mmol／L、锚定引物1．0μmol／L、随机引物0．7μmol／L、模板DNA1．6μL、Taq酶2．5U。对东亚砂藓DDRT—PCR最佳反应体系进行梯度PCR引物退火温度筛选,得到的最佳退火温度为45．4℃。该优化体系的建立,为进一步进行东亚砂藓抗旱基因的筛选与克隆等一系列分子研究提供了重要参考依据。     

Kinetic analysis of the interaction between amphotericin B and human serum albumin using surface plasmon resonance and fluorescence spectroscopy.

The binding interaction between amphotericin B and human serum albumin (HSA) has been studied using surface plasmon resonance (SPR) spectroscopy combined with a fluorescence quenching method to confirm the binding kinetic results. In this paper, the SPR method used to study the drug-protein interaction has been described in detail. The association rate constant, dissociation rate constant and the equilibrium association constant of amphotericin B binding to HSA were obtained using this method. To confirm the feasibility of the SPR method, a fluorescence quenching method was performed to obtain the equilibrium constant. In order to obtain more accurate results, experiment design was used to optimize the fluorescence quenching process. The two equilibrium association constants obtained using the two methods were 4.017 x 10(4) M(-1) (SPR) and 3.656 x 10(4) M(-1) (fluorescence quenching method) respectively.     

Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking

In single-particle analysis, a three-dimensional (3-D) structure of a protein is constructed using electron microscopy (EM). As these images are very noisy in general, the primary process of this 3-D reconstruction is the classification of images according to their Euler angles, the images in each classified group then being averaged to reduce the noise level. In our newly developed strategy of classification, we introduce a topology representing network (TRN) method. It is a modified method of a growing neural gas network (GNG). In this system, a network structure is automatically determined in response to the images input through a growing process. After learning without a masking procedure, the GNG creates clear averages of the inputs as unit coordinates in multi-dimensional space, which are then utilized for classification. In the process, connections are automatically created between highly related units and their positions are shifted where the inputs are distributed in multi-dimensional space. Consequently, several separated groups of connected units are formed. Although the interrelationship of units in this space are not easily understood, we succeeded in solving this problem by converting the unit positions into two-dimensional (2-D) space, and by further optimizing the unit positions with the simulated annealing (SA) method. In the optimized 2-D map, visualization of the connections of units provided rich information about clustering. As demonstrated here, this method is clearly superior to both the multi-variate statistical analysis (MSA) and the self-organizing map (SOM) as a classification method and provides a first reliable classification method which can be used without masking for very noisy images.     

Resolution of the enantiomers of ibuprofen; comparison study of diastereomeric method and chiral stationary phase method

In this study, an indirect diastereomeric method and a direct method utilizing a chiral stationary phase (CSP) were investigated for the resolution of ibuprofen enantiomers. In the indirect method, ethylchloroformate (ECF) and 2-ethoxy-1-1-ethoxycarbonyl-1,2-dihydroquinoline (EEDQ) were utilized as first-step derivatizing reagents in acetonitrile or toluene. In the direct CSP method, ibuprofen enantiomers were derivatized to p-nitrobenzyl ureides and then resolved on an (R)-(−)-(1-naphthyl)ethylurea CSP column. The derivatization procedure took place in 10 min with an overall inversion efficiency of 90.3%. Racemization was not observed under the derivatization conditions used. The HPLC-CSP method was utilized to study the pharmacokinetics of ibuprofen enantiomers in dog plasma after a single oral administration of 200 mg of ibuprofen racemate.     

A Comparative Study on the Efficiency of Two Enucleation Methods in Pig Somatic Cell Nuclear Transfer: Effects of the Squeezing and the Aspiration Methods

In this study, two enucleation methods, the squeezing and the aspiration methods, were compared. The efficiency of these two methods to enucleate pig oocytes and the in vitro and in vivo viability of somatic cell nuclear transfer (SCNT) pig embryos, were evaluated. In the squeezing method, the zona pellucida was partially dissected and a small amount of cytoplasm containing metaphase II (MII) chromosomes and the first polar body (PB) were pushed out. In the aspiration method, the PB and MII chromosomes were aspirated using a beveled micropipette. After injection of fetal fibroblasts into the perivitelline space, reconstructed oocytes were fused and activated electrically, and then cultured in vitro for 6 days or transferred to surrogates. The squeezing method resulted in a higher proportion of degenerated oocytes than the aspiration method (14% vs. 5%). The squeezing method took longer to enucleate 100 oocytes (306 minutes) than the aspirating method (113 minutes). Fusion rate (72–78%) and cleavage rate (67%) were not influenced by the enucleation method but blastocyst formation was improved (P < 0.05) in oocytes enucleated by the aspiration method (5 vs. 9%). When SCNT embryos were transferred to recipients, pregnancy rates to term were similar (27%, 3/11 and 27%, 3/11) in both methods with the birth of 10 piglets/3 litters and 16 piglets/3 litters in the squeezing and the aspiration methods, respectively. Our results indicate that the aspiration method for oocyte enucleation is more efficient than the squeezing method in producing a large number of pig SCNT embryos with normal in vivo viability.     

A comparative study on the efficiency of two enucleation methods in pig somatic cell nuclear transfer: effects of the squeezing and the aspiration methods

In this study, two enucleation methods, the squeezing and the aspiration methods, were compared. The efficiency of these two methods to enucleate pig oocytes and the in vitro and in vivo viability of somatic cell nuclear transfer (SCNT) pig embryos, were evaluated. In the squeezing method, the zona pellucida was partially dissected and a small amount of cytoplasm containing metaphase II (MII) chromosomes and the first polar body (PB) were pushed out. In the aspiration method, the PB and MII chromosomes were aspirated using a beveled micropipette. After injection of fetal fibroblasts into the perivitelline space, reconstructed oocytes were fused and activated electrically, and then cultured in vitro for 6 days or transferred to surrogates. The squeezing method resulted in a higher proportion of degenerated oocytes than the aspiration method (14% vs. 5%). The squeezing method took longer to enucleate 100 oocytes (306 minutes) than the aspirating method (113 minutes). Fusion rate (72-78%) and cleavage rate (67%) were not influenced by the enucleation method but blastocyst formation was improved (P < 0.05) in oocytes enucleated by the aspiration method (5 vs. 9%). When SCNT embryos were transferred to recipients, pregnancy rates to term were similar (27%, 3/11 and 27%, 3/11) in both methods with the birth of 10 piglets/3 litters and 16 piglets/3 litters in the squeezing and the aspiration methods, respectively. Our results indicate that the aspiration method for oocyte enucleation is more efficient than the squeezing method in producing a large number of pig SCNT embryos with normal in vivo viability.     

检测人成纤维细胞增殖的XTT比色法

利用3种不同来源的成纤维细胞(大鼠肾上皮细胞,人胎肺成纤维细胞,人成纤维细胞)的活细胞线粒体脱氢酶在电子偶联剂硫酸酚嗪甲酯（phenazine methosulfate, PMS）的协同作用下,还原四氮唑复合物(XTT)形成可溶性的棕黄色甲簪（formazan）产物,测定细胞甲簪的生成量来反映细胞的生长与活性状态,并与传统的四甲基偶氮唑盐(MTT)方法作比较.结果表明,XTT方法直接测定水溶性的甲簪产物,敏感度高于MTT法,具有操作简单、快速、灵敏度高、结果准确的优点,为成纤维细胞的研究建立了新的检测方法.     

The evaluation of a laparoscopic insemination technique in ewes

Following synchronisation of oestrus using FGA and PMSG, ewes were inseminated by either the conventional cervical (CC) method or directly into the uterus by laparoscopy (LI). The CC method was carried out either at 48 and 60 hours following progestagen withdrawal with 480 x 10(6) spermatozoa per inseminate or once only at 56 hours with 600 x 10(6) spermatozoa. The laparoscopic method was performed at 52 hr using 48 x 10(6) spermatozoa per ewe. In the first two trials eggs were recovered at laparotomy. The egg recovery rate was significantly lower (P<0.05) for those ewes which had been inseminated by the LI method (74%) compared with those inseminated by the CC method (85%); fertilization rates were not significantly different (92% and 89% respectively). In the third trial 20 ewes were bled to determine their periovulatory LH concentrations and the timing of peak LH concentrations correlated with the outcome of each insemination. Ewes inseminated using laparoscopy did not conceive when their LH surge occurred >58 hr after progestagen withdrawal. In this and in the final experiment, the combined pregnancy rates and litter sizes (assessed radiographically) were 67% (n = 51) and 2.21 (n = 34) for the CC method and 75% (n = 48) and 1.97 (n = 36) for the LI method (P>0.05).     

Estimating species trees from unrooted gene trees

In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.     

Color standardization method and system for whole slide imaging based on spectral sensing

In the field of whole slide imaging, the imaging device or staining process cause color variations for each slide that affect the result of image analysis made by pathologist. In order to stabilize the analysis, we developed a color standardization method and system as described below. (1) Color standardization method based on RGB imaging and multi spectral sensing, which utilize less band (16 bands) than conventional method (60 bands). (2) High speed spectral sensing module. As a result, we confirmed the following effect. (1) We confirmed the performance improvement of nucleus detection by the color standardization. And we can conduct without training data set which is needed in conventional method. (2) We can get detection performance of H&E component equivalent to conventional method (60 bands). And measurement process is more than 255 times faster.     

Genotyping and annotation of Affymetrix SNP arrays

In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose–response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization it is indicated that our method is likely to be correct in majority of these cases. In addition, we demonstrate that our method produces more SNPs that are in concordance with Hardy–Weinberg equilibrium than the method by Affymetrix. Finally, we have validated our method on HapMap data and shown that the performance of our method is comparable to other methods.