Visualization of comparative genomic analyses by BLAST score ratio

Background  

The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.     

Conformational changes of membrane-bound (Na+−K+)-ATPase as revealed by antibody inhibition

Summary As different structural states of the (Na⁺–K⁺)-ATPase (EC 3.6.1.3) may lead to a changed reactivity to antibodies, the influence of Na⁺, K⁺, Mg⁺⁺, P_i and ATP on the reaction between highly purified (Na⁺–K⁺)-ATPase and antibodies directed against the membrane-bound enzyme was measured. The antigen antibody reaction was registered by measuring the antibody inhibition of (Na⁺–K⁺)-ATPase activity.In themembrane-bound but not in thesolubilized enzyme four different degrees of antibody inhibition were obtained at equilibrium of the antigen antibody reaction if different combinations of Na⁺, K⁺, Mg⁺⁺ and ATP were present during the incubation with the antibodies. Corresponding to the different degrees of inhibition, different rates of enzyme inhibition were measured. (a) The smallest degree of enzyme inhibition was obtained when (i) only Mg⁺⁺, (ii) Mg⁺⁺ and Na⁺ or (iii) Mg⁺⁺ and K⁺ were present during the antigen antibody reaction. (b) The enzyme activity was inhibited more strongly if Na⁺, Mg⁺⁺ and ATP were present together. (c) It was inhibited even more if only (i) Na⁺, (ii) K⁺, (iii) ATP or both (iv) ATP and Na⁺, (v) ATP and K⁺, (vi) ATP and Mg⁺⁺, or if (vii) no ATP and activating ions were present. (d) The highest degree of antibody inhibition was obtained if Mg⁺⁺, ATP and K⁺ were present together.In the presence of Mg⁺⁺ plus ADP and in the presence of Mg⁺⁺ plus the ATP analog adenylyl (--methylene) diphosphonate, Na⁺ and K⁺ did not influence the degree of antibody inhibition as they did in the presence of Mg⁺⁺ plus ATP. It was further found that the degree of antibody inhibition in the presence of Mg⁺⁺, ATP and K⁺ was affected by the sequence in which K⁺ and ATP were added to the enzyme prior to the addition of the antibodies.It is suggested that by antibody inhibition different conformations of the (Na⁺–K⁺)-ATPase could be detected. These conformations may possibly not occur in the solubilized enzyme and therefore do not seem to be necessarily linked to the intermediary steps of the ATP hydrolysis of the enzyme. The structural changes which are induced by Na⁺ and K⁺ in the presence of Mg⁺⁺ plus ATP are proposed to occur during the Na⁺–K⁺ transport.     

Characterization and histochemical localization of the rat intestinal Na(+)-D-glucose cotransporter by monoclonal antibodies

The localization of the Na(+)-D-glucose cotransporter in rat small intestine was investigated with four monoclonal antibodies which were raised against porcine renal brush-border membrane proteins. The antibodies alter high affinity phlorizin binding or Na+ gradient-dependent D-glucose uptake in kidney and intestine. In both organs, the antibodies react with polypeptides with apparent molecular weights of 75,000 and 47,000. In pig kidney, these polypeptides were identified as components of the Na(+)-D-glucose cotransporter (Koepsell, H., K. Korn, A. Raszeja-Specht, S. Bernotat-Danielowski, D. Ollig, J. Biol. Chem. 263, 18419-18429 (1988)). The electron microscopic localization of antibody binding was investigated by immunogold labeling of ultrathin plastic sections. In villi and crypts of duodenum, jejunum and ileum the antibodies bound specifically to brush-border membranes of enterocytes and did not react with the basolateral membranes. The density of antigenic sites in brush-border membranes was highest in jejunum, intermediate in ileum and lowest in duodenum. On the tip, the middle and the basis of the villi the density of antigenic sites was similar. The data demonstrate homologous Na(+)-D-glucose cotransporters in kidney and intestine. They suggest that during maturation of the enterocytes when the total area of brush-border membrane increases, the concentration of the Na(+)-D-glucose cotransporter in the brush-border membrane remains constant. However, we found that different segments of small intestine not only contain different surface areas of the transporter-containing brush-border membrane per intestinal length but also different densities of the transporter within the brush-border membrane.     

GeneKeyDB: A lightweight,gene-centric,relational database to support data mining environments

Background  

The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration.     

Staphylococcus aureus primase has higher initiation specificity, interacts with single-stranded DNA stronger, but is less stimulated by its helicase than Escherichia coli primase

The study of primases from model organisms such as Escherichia coli , phage T7 and phage T4 has demonstrated the essential nature of primase function, which is to generate de novo RNA polymers to prime DNA polymerase. However, little is known about the function of primases from other eubacteria. Their overall low primary sequence homology may result in functional differences. To help understand which primase functions were conserved, primase and its replication partner helicase from the pathogenic Gram-positive bacteria Staphylococcus aureus were compared in detail with that of E. coli primase and helicase. The conserved properties were to primer initiation and elongation and included slow kinetics, low fidelity and poor sugar specificity. The significant differences included S. aureus primase having sixfold higher kinetic affinity for its template than E. coli primase under equivalent conditions. This naturally higher activity was balanced by its fourfold lower stimulation by its replication fork helicase compared with E. coli primase. The most significant difference between the two primases was that S. aureus helicase stimulation did not broaden the S. aureus primase initiation specificity, which has important biological implications.     

Cell free expression and functional reconstitution of eukaryotic drug transporters

Polyspecific organic cation and anion transporters of the SLC22 protein family are critically involved in absorption and excretion of drugs. To elucidate transport mechanisms, functional and biophysical characterization of purified transporters is required and tertiary structures must be determined. Here, we synthesized rat organic cation transporters OCT1 and OCT2 and rat organic anion transporter OAT1 in a cell free system in the absence of detergent. We solubilized the precipitates with 2% 1-myristoyl-2-hydroxy- sn-glycero-3-[phospho- rac-(1-glycerol)] (LMPG), purified the transporters in the presence of 1% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) or octyl glucoside, and reconstituted them into proteoliposomes. From 1 mL reaction vessels 0.13-0.36 mg of transporter proteins was purified. Thus, from five to ten 1 mL reaction vessels sufficient protein for crystallization was obtained. In the presence of 1% LMPG and 0.5% CHAPS, OCT1 and OAT1 formed homo-oligomers but no hetero-oligomers. After reconstitution of OCT1, OCT2, and OAT1 into proteoliposomes, similar Michaelis-Menten K m values were measured for uptake of 1-methyl-4-phenylpyridinium and p-aminohippurate (PAH (-)) by the organic cation and anion transporters, respectively, as after expression of the transporters in cells. Using the reconstituted system, evidence was obtained that OAT1 operates as obligatory and electroneutral PAH (-)/dicarboxylate antiporter and contains a low-affinity chloride binding site that stimulates turnover. PAH (-) uptake was observed only with alpha-ketoglutarate (KG (2-)) on the trans side, and trans-KG (2-) increased the PAH (-) concentration in voltage-clamped proteoliposomes transiently above equilibrium. The V max of PAH (-)/KG (2-) antiport was increased by Cl (-) in a manner independent of gradients, and PAH (-)/KG (2-) antiport was independent of membrane potential in the absence or presence of Cl (-).     

实验动物屏障系统微生物动态状况

目的研究运行中的实验动物屏障系统微生物的情况。方法采用沉降菌法、棉拭子法等方法,研究运行中的屏障系统不同区域、不同环境指标下屏障系统内微生物的状况。结果动态下的屏障系统微生物情况与国标GB14925-2001中静态环境有较大不同,动物饲养室和动物实验室沉降菌浓度远高于静态要求;辅助区域在规范化消毒及严格管理的情况下,能达到国标要求。屏障系统的微生物情况存在一定的昼夜变化规律,在晚间出现峰值。结论合适的换气次数可有效控制实验动物屏障系统的沉降菌浓度;加强消毒及硬件的管理,是屏障系统内环境稳定的保障。     

外源亚精胺对盐胁迫下白刺幼苗叶片抗氧化酶系统的影响

为进一步阐明盐生植物白刺耐盐性与多胺的关系,通过水培试验研究了叶面喷施亚精胺(Spd)对不同浓度NaCl胁迫下西伯利亚白刺幼苗叶片丙二醛(MDA)和超氧阴离子(O2)产生速率,以及抗氧化物酶系统和根系活力的影响.结果表明:叶面喷施0.1 mmol·L1 Spd 5 d后,可显著提高100和200 mmol·L1 NaCl胁迫下白刺幼苗叶片超氧化物歧化酶(SOD)、过氧化物酶(POD)和过氧化氢酶(CAT)的活性以及根系活力,降低了叶片MDA含量和O2的产生速率;而在0、50、300 mmol·L-1 NaC1处理下,外施Spd对白刺幼苗叶片上述指标无显著影响.研究结果证实,在100～200 mmol·L-1 NaCl胁迫范围内,外施亚精胺可能通过增强体内保护酶活性来显著降低活性氧水平,有效减轻盐胁迫对盐生植物白刺幼苗造成的过氧化伤害,从而增强白刺对盐环境的适应性.     

冷蒿草原土壤可萌发种子库特征及其对放牧的响应

（１）采用萌发试验法对内蒙古冷蒿（Ａｒｔｅｍｉｓｉａ ｆｒｉｇｉｄａ）草原土壤种子特征及其在不同放牧压力下的变化进行了研究。（２）冷蒿草原可萌发种子库由４种多年生禾草,１１种种多年生杂草及３种１年生植物所组成。（３）每样中的可萌发种子是变化于４５到３０５之间,平均１０２／样。多年生禾草、多年生杂类草及１年生植物的土壤中种子量分别占总可萌发种子库的４６．５７％、５１．９６％和１．５７％。多年和禾 草