Pooled Protein Immunization for Identification of Cell Surface Antigens in Streptococcus sanguinis

Background

Available bacterial genomes provide opportunities for screening vaccines by reverse vaccinology. Efficient identification of surface antigens is required to reduce time and animal cost in this technology. We developed an approach to identify surface antigens rapidly in Streptococcus sanguinis, a common infective endocarditis causative species.

Methods and Findings

We applied bioinformatics for antigen prediction and pooled antigens for immunization. Forty-seven surface-exposed proteins including 28 lipoproteins and 19 cell wall-anchored proteins were chosen based on computer algorithms and comparative genomic analyses. Eight proteins among these candidates and 2 other proteins were pooled together to immunize rabbits. The antiserum reacted strongly with each protein and with S. sanguinis whole cells. Affinity chromatography was used to purify the antibodies to 9 of the antigen pool components. Competitive ELISA and FACS results indicated that these 9 proteins were exposed on S. sanguinis cell surfaces. The purified antibodies had demonstrable opsonic activity.

Conclusions

The results indicate that immunization with pooled proteins, in combination with affinity purification, and comprehensive immunological assays may facilitate cell surface antigen identification to combat infectious diseases.     

Prediction of functional phosphorylation sites by incorporating evolutionary information

Protein phosphorylation is a ubiquitous protein post-translational modification, which plays an important role in cellular signaling systems underlying various physiological and pathological processes. Current in silico methods mainly focused on the prediction of phosphorylation sites, but rare methods considered whether a phosphorylation site is functional or not. Since functional phosphorylation sites are more valuable for further experimental research and a proportion of phosphorylation sites have no direct functional effects, the prediction of functional phosphorylation sites is quite necessary for this research area. Previous studies have shown that functional phosphorylation sites are more conserved than non-functional phosphorylation sites in evolution. Thus, in our method, we developed a web server by integrating existing phosphorylation site prediction methods, as well as both absolute and relative evolutionary conservation scores to predict the most likely functional phosphorylation sites. Using our method, we predicted the most likely functional sites of the human, rat and mouse proteomes and built a database for the predicted sites. By the analysis of overall prediction results, we demonstrated that protein phosphorylation plays an important role in all the enriched KEGG pathways. By the analysis of protein-specific prediction results, we demonstrated the usefulness of our method for individual protein studies. Our method would help to characterize the most likely functional phosphorylation sites for further studies in this research area.     

林睡鼠幼鼠的活动规律和行为初步观察

本文通过红外线照相的方法,对发育期的林睡鼠幼鼠进行室内活动规律及行为观察,为充分了解林睡鼠越冬前的能量储备形式提供饲养参考。将鼠密度监测仪固定在饲养笼具上方,24h连续拍照,采集和分析6-9月年龄在10周内的幼鼠各种活动数据。结果显示：幼鼠一天中超过70%的时间都在窝内度过,大部分时间都蜷缩成一团少有动作;在窝外活动时间多在玩耍,如攀爬笼架。用于进食和饮水的时间不超过全天的2%。林睡鼠幼鼠主要活动时间在21:00-07:00,活动高峰在21:00-03:00之间。幼鼠出生3周后开始出窝活动,哺乳期30d后开始采食,5周后幼鼠有交配玩耍行为。随着日龄的增长,活动高峰从23：00提前到21：00,活动时间也逐渐延长,但9周龄后活动时间逐渐缩短,幼鼠的饮水进食时间与其活动的时间长短较为一致。10周体重可达成年体重的70%。研究表明,林睡鼠在夏秋季节基本是昼伏夜出动物。光照是影响其在外活动的重要因素之一。幼鼠6周后所需的饲料和水量大于成年林睡鼠,在此期间要注意饲料和水的补充。     

Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology

Background: Quantitative analysis of mitochondrial morphology plays important roles in studies of mitochondrial biology. The analysis depends critically on segmentation of mitochondria, the image analysis process of extracting mitochondrial morphology from images. The main goal of this study is to characterize the performance of convolutional neural networks (CNNs) in segmentation of mitochondria from fluorescence microscopy images. Recently, CNNs have achieved remarkable success in challenging image segmentation tasks in several disciplines. So far, however, our knowledge of their performance in segmenting biological images remains limited. In particular, we know little about their robustness, which defines their capability of segmenting biological images of different conditions, and their sensitivity, which defines their capability of detecting subtle morphological changes of biological objects. Methods: We have developed a method that uses realistic synthetic images of different conditions to characterize the robustness and sensitivity of CNNs in segmentation of mitochondria. Using this method, we compared performance of two widely adopted CNNs: the fully convolutional network (FCN) and the U-Net. We further compared the two networks against the adaptive active-mask (AAM) algorithm, a representative of high-performance conventional segmentation algorithms. Results: The FCN and the U-Net consistently outperformed the AAM in accuracy, robustness, and sensitivity, often by a significant margin. The U-Net provided overall the best performance. Conclusions: Our study demonstrates superior performance of the U-Net and the FCN in segmentation of mitochondria. It also provides quantitative measurements of the robustness and sensitivity of these networks that are essential to their applications in quantitative analysis of mitochondrial morphology.     

人脐带间充质干细胞微囊减轻小鼠急性肾损伤的研究

目的探讨人脐带间充质干细胞（MSCs）源性细胞外囊泡Oct-4 mRNA对受损的肾小管上皮细胞修复的作用及相关机制。 方法将培养的缺氧损伤肾小管上皮细胞置于含有人脐带MSCs细胞外囊泡及不同对照培养液的培养腔室玻片上孵育48?h,应用BrdU及TUNEL染色,检测各组细胞增殖或凋亡情况。将急性肾损伤模型小鼠分为4组：空白组、EVs组、Oct-4过表达组、Oct-4低敲组。并按照分组分别注射磷酸盐缓冲液（Vehicle）,人脐带MSCs细胞外囊泡（EVs）,过表达Oct-4基因的人脐带MSCs细胞外囊泡（EVs?+?Oct-4）及敲除Oct-4基因的人脐带MSCs外囊泡（EVs-Oct-4）,并在注射48?h及2周后采血测肌酐（Crea）及尿素氮（BUN）,了解肾功能变化;对各组上述处理后的肾组织应用TUNEL与增殖细胞核抗原表达量检测各组肾脏细胞凋亡与增殖情况;通过Masson染色检测了各组肾脏纤维化程度;通过PCR探索肾损伤后肾组织细胞Snail基因的表达变化。数据分析采用方差分析和SNK-q检验。 结果EVs?+ Oct-4处理缺氧的肾小管上皮细胞48?h后,TUNEL染色显示具有最少的凋亡细胞数（0~1）/?HPF,BrdU显示有最多的增殖细胞（7±2）/HPF。EVs,EV-Oct-4以及Vehicle对体外缺氧肾小管上皮细胞的上述作用依次减弱（P?相似文献   

Hypsodonty of Dipodidae (Rodentia) in Correlation with Diet Preferences and Habitats

The evolution of molar teeth from low-crowned (brachyodont) to high-crowned (hypsodont) has traditionally been recognized as a response to increasing tooth wear due to endogenous (e.g., fiber, silica) and/ or exogenous (e.g., dust, grit) properties of ingested food. Recent work indicates that the mean hypsodonty level of large herbivorous land mammalian communities is a strong predictor of precipitation in their habitats. For small mammals, however, the research is still in an early stage. This study performed comparative studies of hypsodonty on 26 extant dipodid species with and without consideration of phylogeny. The results confirm the role of diet in shaping the cheek tooth crown height in Dipodidae. The significant relationship of investigated environmental variables with hypsodonty may be partly due to phylogenetic effects. Nonetheless, the mean hypsodonty of dipodid communities has significant relationship with regional climatic variables. Hence, the hypsodonty of dipodids also has great potential to be a regional climate proxy.     

Remodeling of ER‐exit sites initiates a membrane supply pathway for autophagosome biogenesis

Autophagosomes are double‐membrane vesicles generated during autophagy. Biogenesis of the autophagosome requires membrane acquisition from intracellular compartments, the mechanisms of which are unclear. We previously found that a relocation of COPII machinery to the ER–Golgi intermediate compartment (ERGIC) generates ERGIC‐derived COPII vesicles which serve as a membrane precursor for the lipidation of LC3, a key membrane component of the autophagosome. Here we employed super‐resolution microscopy to show that starvation induces the enlargement of ER‐exit sites (ERES) positive for the COPII activator, SEC12, and the remodeled ERES patches along the ERGIC. A SEC12 binding protein, CTAGE5, is required for the enlargement of ERES, SEC12 relocation to the ERGIC, and modulates autophagosome biogenesis. Moreover, FIP200, a subunit of the ULK protein kinase complex, facilitates the starvation‐induced enlargement of ERES independent of the other subunits of this complex and associates via its C‐terminal domain with SEC12. Our data indicate a pathway wherein FIP200 and CTAGE5 facilitate starvation‐induced remodeling of the ERES, a prerequisite for the production of COPII vesicles budded from the ERGIC that contribute to autophagosome formation.     

转录调节因子σ~(38)介导铜绿假单胞菌绿脓菌素合成代谢调控

【目的】为了进一步鉴定铜绿假单胞菌转录调控因子σ~(38)对2个拷贝吩嗪合成基因簇(phz A1-G1和phz A2-G2)的具体调控方式并推定介导绿脓菌素合成代谢的可能调控机制。【方法】根据铜绿假单胞菌基因组信息,利用同源重组原理构建rpo S基因缺失突变株Δrpo S以及克隆全长rpo S基因作互补分析;再以单一吩嗪基因簇缺失突变株Δphz1和Δphz2为出发菌株,分别构建rpo S缺失突变株Δrpo Sphz1和rpo S插入突变株Δrpo Sphz2,测定并比较野生株及相关突变株的绿脓菌素合成量,初步推定σ~(38)因子对2个不同吩嗪基因簇表达的调控方式。【结果】在GA培养基中,突变株Δrpo S的绿脓菌素合成量比野生株显著增加;互补分析证实,σ~(38)可使突变株Δrpo S的绿脓菌素降低并接近野生株PAO1水平;与对照株Δphz1相比,突变株Δrpo Sphz1的绿脓菌素合成量因σ~(38)因子缺失而显著减少;而与对照株Δphz2相比,突变株Δrpo Sphz2的绿脓菌素合成量因σ~(38)因子缺失显著增加。【结论】转录调控因子σ~(38)对铜绿假单胞菌绿脓菌素的合成代谢的确具一定的负调控作用;结合已报道的研究结果,初步推定:σ~(38)因子通过负调控吩嗪基因簇phz1,正调控吩嗪基因簇phz2的表达实现对绿脓菌素合成代谢的调控。