Profile-based string kernels for remote homology detection and motif extraction

We introduce novel profile-based string kernels for use with support vector machines (SVMs) for the problems of protein classification and remote homology detection. These kernels use probabilistic profiles, such as those produced by the PSI-BLAST algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. By use of an efficient data structure, the kernels are fast to compute once the profiles have been obtained. For example, the time needed to run PSI-BLAST in order to build the profiles is significantly longer than both the kernel computation time and the SVM training time. We present remote homology detection experiments based on the SCOP database where we show that profile-based string kernels used with SVM classifiers strongly outperform all recently presented supervised SVM methods. We further examine how to incorporate predicted secondary structure information into the profile kernel to obtain a small but significant performance improvement. We also show how we can use the learned SVM classifier to extract "discriminative sequence motifs"--short regions of the original profile that contribute almost all the weight of the SVM classification score--and show that these discriminative motifs correspond to meaningful structural features in the protein data. The use of PSI-BLAST profiles can be seen as a semi-supervised learning technique, since PSI-BLAST leverages unlabeled data from a large sequence database to build more informative profiles. Recently presented "cluster kernels" give general semi-supervised methods for improving SVM protein classification performance. We show that our profile kernel results also outperform cluster kernels while providing much better scalability to large datasets.     

萝藦科马利筋族植物化学成分研究进展(Ⅱ)

综述了到目前为止,从马利筋族植物中发现的黄酮、强心甙、生物碱、萜类、苯衍生物类等成分的种类及其分布,并介绍了一些化合物的药理作用以及黄酮类和C21甾体化合物在鹅绒藤属化学分类中的作用.     

A novel method to harvest <Emphasis Type="Italic">Chlorella</Emphasis> sp. by co-flocculation/air flotation

Objectives

To develop a more effective dissolved air flotation process for harvesting microalgae biomass, a co-flocculation/air flotation (CAF) system was developed that uses an ejector followed by a helix tube flocculation reactor (HTFR) as a co-flocculation device to harvest Chlorella sp. 64.01.

Results

The optimal size distribution of micro-bubbles and an air release efficiency of 96 % were obtained when the flow ratio of inlet fluid (raw water) to motive fluid (saturated water) of the ejector was 0.14. With a reaction time of 24 s in the HTFR, microalgae cells and micro-bubbles were well flocculated, and these aerated flocs caused a fast rising velocity (96 m/h) and high harvesting efficiency (94 %).

Conclusions

In a CAF process, micro-bubbles can be encapsulated into microalgae flocs, which makes aerated flocs more stable. CAF is an effective approach to harvesting microalgae.

     

水分胁迫对甘薯叶肉细胞光合电子传递的影响

水分胁迫降低了甘薯叶肉细胞的光合能力。在有解偶联剂存在时,水分胁迫对叶肉细胞的光合电子传递没有影响,但在无解偶联剂存在下,水分胁迫促进了甘薯叶肉细胞的光合电子传递,表现出明显的解偶联效应。水分胁迫伤害了甘薯叶绿体偶联因子结构,使ATP合成受阻,叶肉细胞的光合滞后期加长。     

微菌落观察法快速检测和鉴别结核杆菌培养物的研究

将取自肺结核患者的219例痰标本接种匡氏琼脂平板,共分离到112例结核菌生长物。其中培养法104例(92.8％)阳性,微菌落观察法108例(96.4％)阳性,微菌落法阳性率稍高。培养法和微菌落法阳性标本首次检出时间分别为18.6d和11d,微菌落检出时间更短(P<0.01)。常规菌型鉴别方法与微菌落法对结核杆菌菌型鉴别的符合率为99％。     

光敏核不育水稻61kD特异性蛋白质的纯化和N—端序列分析

用制备型聚丙烯酰胺凝胶电泳和制备型等电聚焦纯化了曾报道的光敏核不育水稻 (Oryza sativa)农垦 58S叶绿体的特异性蛋白质 P2 ,得到 SDS- PAGE和等电聚焦 (IEF )纯的 P2。经 SDS- PAGE和 IEF测定 ,该纯蛋白质的分子量是 61 k D,等电点是 5.8。现称 P2为 P61。氨基酸序列分析表明 P61的 N-端氨基酸序列与水稻和大麦叶绿体 ATPaseβ亚基的 N-端氨基酸序列同源。     

从超声波破碎的蓝藻类囊体膜中分离的叶绿素蛋白复合物

当蓝藻的类囊体膜用超声波进行破碎,并在4℃下用聚丙烯酰胺凝胶电泳进行分离,有6条叶绿素带被分离出来,它们分别是 CPIa,CPIb,CP1,CPa1 CPa2,FC。CP1 在红区和蓝区的吸收峰分别位于674和435 nm 处。在液氮甲该组分在725和680 nm 处有两个荧光发射带。CPa1和 CPa2的吸收光谱相似,其红峰和蓝峰的位置分别位于667和431.5nm 处。它们在77 K 的荧光发射峰都位于684 nm 处。用超声破碎法分离的叶绿素蛋白复合物的光谱特性,除 CPa1和 CPa2在红峰和蓝峰的吸收位置蓝移了3—5 nm 之外,其余与用 SDS 增溶法分离的相应复合物相似。属于光系统Ⅰ的 CPIa-CPI 的叶绿素含量占总叶绿素的40.93%,而属于光系统Ⅱ的 CPa1和 CPa2的叶绿素则占总叶绿素的38.78%,二者之差仅有2.15%。     

Oxidative stress-induced apoptosis is mediated by ERK1/2 phosphorylation

Oxidative stress is known to induce apoptosis in a wide variety of cell types, apparently by modulating intracellular signaling pathways. High concentrations of H2O2 have been found to induce apoptosis in L929 mouse fibroblast cells. To elucidate the mechanisms of H2O2-mediated apoptosis, ERK1/2, p38-MAPK, and JNK1/2 phosphorylation was examined, and ERK1/2 and JNK1/2 were found to be activated by H2O2. Inhibition of ERK1/2 activation by treatment of L929 cells with PD98059 or dominant-negative ERK2 transfection blocked H2O2-induced apoptosis, while inhibition of JNK1/2 by dominant-negative JNK1 or JNK2 or MKK4 or MKK7 transfection did not affect H2O2-mediated apoptosis. H2O2-mediated ERK1/2 activation was not only Ras-Raf dependent, but also both tyrosine kinase (PDGFbeta receptor and Src) and PKCdelta dependent. H2O2-mediated PKCdelta-dependent and tyrosine kinase-dependent ERK1/2 activations were independent from each other. Based on the above results, we suggest for the first time that oxidative damage-induced apoptosis is mediated by ERK1/2 phosphorylation which is not only Ras-Raf dependent, but also both tyrosine kinase and PKCdelta dependent.     

CO2倍增对不同基因型大豆光合色素含量和荧光诱导动力学参数的影响

研究了CO_2倍增对大豆(Glycine max L.)Bragg(野生型)及其不同单基因突变品系Nts 382(超结瘤突变体)和Nod 49(不结瘤突变体)某些光合特性的影响。结果表明,CO_2倍增能提高Bragg、Nts 382和Nod 49的叶绿素(Chl)和类胡萝卜素(Car)的含量,但不同品系提高的幅度有所不同。荧光诱导动力学测定结果表明,CO_2倍增均能提高其PSⅡ活性、PSⅡ原初光能转化效率和光合作用潜在量子转化效率。CO_2倍增更有利于提高Nts 382的荧光光化学猝灭系数(qp)和PSⅡ总的光化学量子产量,以及较大幅度地降低荧光非光化学猝灭系数(qN),有助于把所捕获的光能用于进行光合作用。这可能与Nts 382是超结瘤突变体,比Bragg和Nod 49能更充分地利用空气中的氮素有关。