Raft microdomain localized in the luminal leaflet of inner membrane complex of living Toxoplasma gondii

Membrane microdomains or rafts, sterol- and sphingolipid-rich microdomains in the plasma membrane have been studied extensively in mammalian cells. Recently, rafts were found to mediate virulence in a variety of parasites, including Toxoplasma gondii. However, it has been difficult to examine a two-dimensional distribution of lipid molecules at a nanometer scale. We tried to determine the distribution of glycosphingolipids GM1 and GM3, putative raft components in the T. gondii cell membrane in this study, using a rapid-frozen and freeze-fractured immuno-electron microscopy method. This method physically stabilized molecules in situ, to minimize the probability of artefactual disruption. Labeling of GM3, but not GM1, was observed in the exoplasmic (or luminal), but not the cytoplasmic, leaflet of the inner membrane complex (IMC) in T. gondii infected in human foreskin fibroblast-1 (HFF-1). No labeling was detected in any leaflet of the T. gondii plasma membrane. In contrast to HFF-1, T. gondii infected in mouse fibroblast (MF), labelings of both GM1 and GM3 were detected in the IMC luminal leaflet, although GM1′s gold labeling density was very low. The same freeze-fracture EM method showed that both GM1 and GM3 were expressed in the exoplasmic leaflet of the MF plasma membrane. However, labeling of only GM3, but not GM1, was detected in the exoplasmic leaflet of the HFF-1 plasma membrane. These results suggest that GM1 or GM3, localized in the IMC, is obtained from the plasma membranes of infected host mammalian cells. Furthermore, the localization of microdomains or rafts in the luminal leaflets of the intracellular confined space IMC organelle of T. gondii suggests a novel characteristic of rafts.     

Enhanced Device Efficiency of Bilayered Inverted Organic Solar Cells Based on Photocurable P3HTs with a Light‐Harvesting ZnO Nanorod Array

Periodically patterned zinc oxide nanorod (P‐ZnO NR) layers are directly prepared from a pre‐patterned ZnO seed layer using a polydimethylsiloxane (PDMS) elastomeric stamp and then applied in inverted organic photovoltaic devices (IOPVs). The IOPV is assembled with a hydrothermally grown zinc oxide nanorod patterns with a (100) preferential crystal orientation as an electron transport buffer layer (ETBL) and photoactive bilayer consisting of methacylate end‐functionalized poly(3‐hexylthiophene) (P3HT‐MA), phenyl‐C₆₀‐butyric acid methyl ester (PC₆₀BM) and indene‐C₆₀ bis‐adduct (IC₆₀BA). In te IOPVs, the P‐ZnO NR is found to induce efficient light harvesting and the photocrosslinkable P3HTs afford solution‐processed bilayer architecture in IOPVs to show improved device stability and performance (PCE_max= 5.95%), as the bilayered structure allowed direct exciton splitting, thus reducing the charge recombination.     

Spirosoma profusum sp. nov., and Spirosoma validum sp. nov., radiation-resistant bacteria isolated from soil in South Korea

Two novel Gram-negative, rod-shaped bacterial strains BT702^T and BT704^T were isolated from soil collected in Jeongseon (37° 22′ 45″ N, 128° 39′ 53″ E), Gangwon province, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT702^T and BT704^T belong to distinct lineage within the genus Spirosoma (family Cytophagaceae, order Cytophagales, class Cytophagia and phylum Bacteroidetes). The strain BT702^T was closely related to Spirosoma flavus 15J11-2^T (96.7% 16S rRNA gene similarity) and Spirosoma metallilatum TX0405^T (93.3%). The strain BT704^T was closely related to Spirosoma koreense 15J8-5^T (94.6%), Spirosoma endophyticum DSM 26130^T (93.8%) and Spirosoma humi S7-4-1^T (93.8%). The genome sizes of type strains BT702^T and BT704^T are 8,731,341 bp and 8,221,062 bp, respectively. The major cellular fatty acids of strains BT702^T and BT704^T were C_16:1 ω5c and summed feature 3 (C_16:1 ω6c/C_16:1 ω7c). The strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strain BT702^T was identified to be phosphatidylethanolamine (PE), aminophospholipid (APL) and aminolipid (AL), while that of strain BT704^T consisted of phosphatidylethanolamine (PE) and aminophospholipid (APL). Based on the polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT702^T and BT704^T can be suggested as two new bacterial species within the genus Spirosoma and the proposed names are Spirosoma profusum and Spirosoma validum, respectively. The type strain of Spirosoma profusum is BT702^T (=?KACC 22028^T?=?NBRC 114859^T) and type strain of Spirosoma validum is BT704^T (=?KACC 22030^T?=?NBRC 114966^T).

     

超声引导经皮微波消融治疗邻近血管的原发性肝癌的疗效分析

探讨超声引导经皮微波消融治疗邻近血管的原发性肝癌的疗效。2010年1月至2013年6月期间,回顾性分析在我院采用超声引导下微波消融技术治疗的213例(267个病灶)原发性肝癌患者的病例资料,根据患者病灶位置分为邻近血管组(76例,91个病灶)和对照组(137例,176个病灶),比较两组患者的微波消融次数、微波消融时间、完全消融率、局部肿瘤进展率、累计存活率及并发症。邻近血管组和对照组的原发性肝癌患者消融次数均为1~3次,两组平均微波消融次数无显著差异(p<0.05)。两组微波消融时间为5~28 min,其中邻近血管组显著高于对照组(p>0.05)。微波消融1个月后,邻近血管组的完全消融率与对照组无显著差异(p<0.05)。两组患者在3个阶段(1随访1年,3年和5年)的的局部肿瘤进展率和累计生存率无统计学差异(p<0.05)。两组患者5年随访时间内分别有29例和53例患者死亡。主要死亡原因包括肝癌进展、肝功能衰竭、血管曲张破裂、脑出血、急性肺栓塞、心肌梗死等。邻近血管组共有25例出现术后并发症,对照组有44例。主要并发症类型为腹腔积液、膈疝、出血、肝脓肿、气胸、肝区疼痛和发热。两组之间并发症发生率无统计学意义(p=0.907)。微波消融治疗邻近血管的原发性肝癌具有较好的局部肿瘤控制率,可对邻近血管的危险病灶区域进行有效治疗。     

Steered molecular dynamics simulation of the binding of the bovine auxilin J domain to the Hsc70 nucleotide-binding domain

The Hsp70 and Hsp40 chaperone machine plays critical roles in protein folding, membrane translocation, and protein degradation by binding and releasing protein substrates in a process that utilizes ATP. The activities of the Hsp70 family of chaperones are recruited and stimulated by the J domains of Hsp40 chaperones. However, structural information on the Hsp40–Hsp70 complex is lacking, and the molecular details of this interaction are yet to be elucidated. Here we used steered molecular dynamics (SMD) simulations to investigate the molecular interactions that occur during the dissociation of the auxilin J domain from the Hsc70 nucleotide-binding domain (NBD). The changes in energy observed during the SMD simulation suggest that electrostatic interactions are the dominant type of interaction. Additionally, we found that Hsp70 mainly interacts with auxilin through the surface residues Tyr866, Arg867, and Lys868 of helix II, His874, Asp876, Lys877, Thr879, and Gln881 of the HPD loop, and Phe891, Asn895, Asp896, and Asn903 of helix III. The conservative residues Tyr866, Arg867, Lys868, His874, Asp876, Lys877, and Phe891 were also found in a previous study to be indispensable to the catalytic activity of the DnaJ J domain and the binding of it with the NBD of DnaK. The in silico identification of the importance of auxilin residues Asn895, Asp896, and Asn903 agrees with previous mutagenesis and NMR data suggesting that helix III of the J domain of the T antigen interacts with Hsp70. Furthermore, our data indicate that Thr879 and Gln881 from the HPD loop are also important as they mediate the interaction between the bovine auxilin J domain and Hsc70.     

Efficient remote homology detection using local structure

MOTIVATION: The function of an unknown biological sequence can often be accurately inferred if we are able to map this unknown sequence to its corresponding homologous family. At present, discriminative methods such as SVM-Fisher and SVM-pairwise, which combine support vector machine (SVM) and sequence similarity, are recognized as the most accurate methods, with SVM-pairwise being the most accurate. However, these methods typically encode sequence information into their feature vectors and ignore the structure information. They are also computationally inefficient. Based on these observations, we present an alternative method for SVM-based protein classification. Our proposed method, SVM-I-sites, utilizes structure similarity for remote homology detection. RESULT: We run experiments on the Structural Classification of Proteins 1.53 data set. The results show that SVM-I-sites is more efficient than SVM-pairwise. Further, we find that SVM-I-sites outperforms sequence-based methods such as PSI-BLAST, SAM, and SVM-Fisher while achieving a comparable performance with SVM-pairwise. AVAILABILITY: I-sites server is accessible through the web at http://www.bioinfo.rpi.edu. Programs are available upon request for academics. Licensing agreements are available for commercial interests. The framework of encoding local structure into feature vector is available upon request.