Evolution of the secondary haustoria to a primary haustorium in the parasiticScrophulariaceae/Orobanchaceae

In the parasiticScrophulariaceae andOrobanchaceae, two types of contact organs exist: secondary and primary haustoria. Secondary haustoria are lateral organs, developing in large numbers and only when the seedling is fully established. In contrast, a primary haustorium represents the first developmental stage of the seedling itself. In the root system of the parasiticLesquereuxia syriaca (=Siphonostegia syriaca) there are only secondary haustoria, but a few of them apparently develop in a terminal position. This is achieved by transferring the haustorial initiation region closer to the root apex. One can interpret this as a transformation of the apical meristem into a meristematic haustorial tissue. On the condition that an extreme shortening (abbrevation) of the primary root could happen, we discuss the transformation of the terminal secondary into a primary haustorium.     

Anatomical Studies of Haustorium Ontogeny and the Remarkable Mode of Penetration of the Haustorium in Nuytsiafloribunda (Labill.) R. Br.

The development and structure of secondary haustoria of Nuytsia floribunda are described and compared with other Santalalean haustoria. After establishing contact with the host root, cortical folds of the haustorium grow around the root in separate directions and fuse forming a ring around it. At an early stage of development, meristematic tissue differentiates in the interior proximal part of the haustorium. Zones of collapsed layers are present in the outer cortical region. Subsequently, in the proximal part, two vascular cores, two lysigenous cavities and extensive masses of sclerenchyma develop prior to penetration of the host root. The sclerenchymatous cells form a characteristic structure, described as the sclerenchyma prong. During penetration the intrusive part of the haustorium reaches not only the host xylem but continues growing downwards until it entirely splits the host root. Comparable to a guillotine, the sclerenchyma prong is directly involved in this remarkable process. The sclerenchyma prong finally lies in the distal part of the haustorium. Following this mechanical slicing of the host root, tube-like cells of the intrusive part actively penetrate the host xylem in an axial direction.     

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.     

基于三类特征融合的O-糖基化位点预测

糖基化是蛋白质翻译后的主要修饰,O-糖基化的固定模式未知,高精度识别O-糖基化位点是机器学习面临的挑战性问题.以迄今最大的人O-糖基化位点Steentoft数据集为基础,本文首次提出了基于位置的卡方差表特征χ~2-pos,融合伪氨基酸序列进化信息Pse PSSM以及无方向的k间隔氨基酸对组分Undirected-CKSAAP表征序列,构建5个正负样本均衡的支持向量机分类器,经加权投票,独立测试准确率、Matthew相关系数及ROC曲线下面积,分别达到了89.62%、0.79、0.96,明显优于文献报道结果.χ~2-pos、Pse PSSM与Undirected-CKSAAP三种特征的融合在蛋白质糖基化、磷酸化等位点预测中有广泛应用前景.     

Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells

Viruses can reproduce their progenies only within a host cell, and their actions depend both on its destructive tendencies toward a specific host cell and on environmental conditions. Therefore, knowledge of the subcellular localization of viral proteins in a host cell or virus-infected cell is very useful for in-depth studying of their functions and mechanisms as well as designing antiviral drugs. An analysis on the Swiss-Prot database (version 50.0, released on May 30, 2006) indicates that only 23.5% of viral protein entries are annotated for their subcellular locations in this regard. As for the gene ontology database, the corresponding percentage is 23.8%. Such a gap calls for the development of high throughput tools for timely annotating the localization of viral proteins within host and virus-infected cells. In this article, a predictor called "Virus-PLoc" has been developed that is featured by fusing many basic classifiers with each engineered according to the K-nearest neighbor rule. The overall jackknife success rate obtained by Virus-PLoc in identifying the subcellular compartments of viral proteins was 80% for a benchmark dataset in which none of proteins has more than 25% sequence identity to any other in a same location site. Virus-PLoc will be freely available as a web-server at http://202.120.37.186/bioinf/virus for the public usage. Furthermore, Virus-PLoc has been used to provide large-scale predictions of all viral protein entries in Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The results thus obtained have been deposited in a downloadable file prepared with Microsoft Excel and named "Tab_Virus-PLoc.xls." This file is available at the same website and will be updated twice a year to include the new entries of viral proteins and reflect the continuous development of Virus-PLoc.     

Modeling continuous auxiliary covariate data in generalized linear mixed models using the kernel smoother

Auxiliary covariate data are often collected in biomedical studies when the primary exposure variable is only assessed on a subset of the study subjects. In this study, we investigate a semiparametric‐estimated likelihood estimation for the generalized linear mixed models (GLMM) in the presence of a continuous auxiliary variable. We use a kernel smoother to handle continuous auxiliary data. The method can be used to deal with missing or mismeasured covariate data problems in a variety of applications when an auxiliary variable is available and cluster sizes are not too small. Simulation study results show that the proposed method performs better than that which ignores the random effects in GLMM and that which only uses data in the validation data set. We illustrate the proposed method with a real data set from a recent environmental epidemiology study on the maternal serum 1,1‐dichloro‐2,2‐bis(p‐chlorophenyl) ethylene level in relationship to preterm births.     

Self-assembly of Pseudomonas fluorescens lipase into bimolecular aggregates dramatically affects functional properties

It has been found that lipase from Pseudomonas fluorescens (PFL) is able to aggregate into bimolecular structures (MW around 66 kD) even at moderate enzyme concentrations. At very low enzyme concentrations and in the presence of detergents, the same enzyme displayed a unimolecular structure with a molecular weight of 33 kD. Both enzyme structures displayed different functional properties. First, the bimolecular structure was much more stable than the unimolecular species (the bimolecular structure maintained over 80% of initial activity after 72 hours at 45 degrees C, while the unimolecular structure retained only around 30% of initial activity after 4 hours of incubation under the same experimental conditions); and the bimolecular form presented a higher optimal T. Second, the unimolecular form showed a much lower K(M) for ethyl butyrate than the bimolecular form. Third, the interfacial activation in biphasic substrate-aqueous milieu was higher for the bimolecular form. Fourth, the unimolecular structure was less active but much more enantioselective than the unimolecular species in the model reaction used. It is proposed that the bimolecular aggregates of PFL might be formed by two open lipase molecules (mutual interfacial activation), in intimate contact, and that the bimolecular form represents an example of "pseudo-quaternary" structure.