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.     

Recent advances in synthesis and surface modification of lanthanide-doped upconversion nanoparticles for biomedical applications

Lanthanide (Ln)-doped upconversion nanoparticles (UCNPs) with appropriate surface modification can be used for a wide range of biomedical applications such as bio-detection, cancer therapy, bio-labeling, fluorescence imaging, magnetic resonance imaging and drug delivery. The upconversion phenomenon exhibited by Ln-doped UCNPs renders them tremendous advantages in biological applications over other types of fluorescent materials (e.g., organic dyes, fluorescent proteins, gold nanoparticles, quantum dots, and luminescent transition metal complexes) for: (i) enhanced tissue penetration depths achieved by near-infrared (NIR) excitation; (ii) improved stability against photobleaching, photoblinking and photochemical degradation; (iii) non-photodamaging to DNA/RNA due to lower excitation light energy; (iv) lower cytotoxicity; and (v) higher detection sensitivity. Ln-doped UCNPs are therefore attracting increasing attentions in recent years. In this review, we present recent advances in the synthesis of Ln-doped UCNPs and their surface modification, as well as their emerging applications in biomedicine. The future prospects of Ln-doped UCNPs for biomedical applications are also discussed.     

Pyrazolo[3,4-d]pyrimidine derivatives containing a Schiff base moiety as potential antiviral agents

A series of pyrazolo[3,4-d]pyrimidine derivatives containing a Schiff base moiety were synthesized, characterised, and evaluated for their activity against tobacco mosaic virus (TMV). Biological assays indicated that several of the derivatives exhibited significant activity against TMV. In particularly, compounds 5y and 5aa displayed excellent inactivating activity against TMV, with half maximal effective concentration (EC₅₀) values of 70.3 and 53.65?μg/mL, respectively, which were much better than that of ribavirin (150.45?μg/mL), and 5aa was superior to ningnanmycin (EC₅₀?=?55.35?μg/mL). Interactions of compounds 5y and 5aa with TMV coat protein (TMV-CP) were investigated using microscale thermophoresis and molecular docking. Compounds 5y and 5aa displayed strong binding capability to TMV-CP with dissociation constant (K_d) values of 22.6 and 9.8?μM, respectively. These findings indicate that pyrazolo[3,4-d]pyrimidine derivatives containing a Schiff base may be potential antiviral agents.     

Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL

PINK1 is a mitochondrial kinase mutated in some familial cases of Parkinson's disease. It has been found to work in the same pathway as the E3 ligase Parkin in the maintenance of flight muscles and dopaminergic neurons in Drosophila melanogaster and to recruit cytosolic Parkin to mitochondria to mediate mitophagy in mammalian cells. Although PINK1 has a predicted mitochondrial import sequence, its cellular and submitochondrial localization remains unclear in part because it is rapidly degraded. In this study, we report that the mitochondrial inner membrane rhomboid protease presenilin-associated rhomboid-like protein (PARL) mediates cleavage of PINK1 dependent on mitochondrial membrane potential. In the absence of PARL, the constitutive degradation of PINK1 is inhibited, stabilizing a 60-kD form inside mitochondria. When mitochondrial membrane potential is dissipated, PINK1 accumulates as a 63-kD full-length form on the outer mitochondrial membrane, where it can recruit Parkin to impaired mitochondria. Thus, differential localization to the inner and outer mitochondrial membranes appears to regulate PINK1 stability and function.     

小G蛋白在植物抗病性中的作用(英文)

小G蛋白一类是低分子量GTP结合蛋白,其分子量大约20～30 kDa。小G蛋白作为重要的分子开关参与了细胞许多重要生理信号途径的调控。近几年在植物中的研究、尤其是对模式植物水稻抗病分子机制的研究发现,Rho家族的小G蛋白在植物抗病信号传导途径的调控中起了关键的作用。本文对植物特有的Rho家族小G蛋白在植物免疫反应中的最新研究进展进行了综述。     

小RNA病毒和小DNA病毒的三维结构模型

本文综述了小RNA病毒和小DNA病毒的主要结构特征,绘制出了它们的三维结构模型,从中找出了两者间的共同点和差异,为进一步研究两种病毒提供了依据。     

人胃粘膜G、D细胞与肠化生关系的研究

用免疫细胞化学和原位杂交技术探讨G、D细胞及胃泌素mRNA与肠化生的关系。标本来自胃镜活检的胃粘膜。结果显示,在与大肠化生区相邻的胃粘膜,G细胞突变消失,假幽门腺化生也缺乏G细胞,而淖肠化生仍保留少数G细胞;D细胞不仅见于小肠化生,而且也出现在假幽门腺化生以及某些大肠化生区。胃泌素mRNA仅限于G细胞分布区,未出现在大肠化生区和假幽门腺化生区,G细胞及胃泌素mRNA在大肠化生区的消失,可能由于局部杯状细胞分泌的硫酸粘蛋白改变了局部的微环境,从而影响了G细胞的分化与发育,至于假幽门腺化生区G细胞及胃泌素mRNA消失的原因还不清楚,应继续研究。