Computational and Experimental Investigation of the Antimicrobial Peptide Cecropin XJ and its Ligands as the Impact Factors of Antibacterial Activity

Cecropin XJ, as a heat stable antimicrobial peptide (AMP), displayed broad bacteriostatic activities, effectively inhibited proliferation of cancer cells and induced cell apoptosis in vitro. However, it exhibited little hemolytic activity and very low cytotoxicity to erythrocytes and normal cells. Although exerts multiple remarkable bioactivities, the refined molecular conformation of native Cecropin XJ remains unsolved. The aim of the present study is to comprehensively investigate the physicochemical characteristics and structure-function relationship of this antimicrobial peptide by using a series of bioinformatics and experimental approaches. In this study, we revealed that the mature Cecropin XJ consists of 41 amino acids, containing two α-helical structures from Lys⁷ to Lys²⁵ and from Ala²⁹ to Ile³⁹. The phylogenetic tree indicated that Cecropin XJ belongs to the Class I AMPs of cecropin family. Hydrophobic analysis showed Cecropin XJ is a typical amphiphilic molecule. The surface of Cecropin XJ was found to have a much wide range of electrostatic potential from ?83.243 to +83.243. The amphipathicity and surface potential of Cecropin XJ partially supported the AMP pore-forming hypothesis. Scanning electron microscopy experimentally confirmed the damages of Cecropin XJ to microbial membrane. Four predicted docking sites respectively for magnesium ion (Mg²⁺), adenosine diphosphate (ADP), bacteriopheophytin (BPH), and guanosine triphosphate (GTP) were found on the surface of Cecropin XJ. Thereinto, Mg²⁺ was experimentally proved to suppress the antibacterial activity of Cecropin XJ; both GTP and ADP enhanced the bactericidal activities to varying degrees. The present study provides a foundation for further investigation of molecular evolution, structural modification, and functional mechanisms of Cecropin XJ.     

Effect of a Low-Protein Diet Supplemented with Ketoacids on Skeletal Muscle Atrophy and Autophagy in Rats with Type 2 Diabetic Nephropathy

A low-protein diet supplemented with ketoacids maintains nutritional status in patients with diabetic nephropathy. The activation of autophagy has been shown in the skeletal muscle of diabetic and uremic rats. This study aimed to determine whether a low-protein diet supplemented with ketoacids improves muscle atrophy and decreases the increased autophagy observed in rats with type 2 diabetic nephropathy. In this study, 24-week-old Goto-Kakizaki male rats were randomly divided into groups that received either a normal protein diet (NPD group), a low-protein diet (LPD group) or a low-protein diet supplemented with ketoacids (LPD+KA group) for 24 weeks. Age- and weight-matched Wistar rats served as control animals and received a normal protein diet (control group). We found that protein restriction attenuated proteinuria and decreased blood urea nitrogen and serum creatinine levels. Compared with the NPD and LPD groups, the LPD+KA group showed a delay in body weight loss, an attenuation in soleus muscle mass loss and a decrease of the mean cross-sectional area of soleus muscle fibers. The mRNA and protein expression of autophagy-related genes, such as Beclin-1, LC3B, Bnip3, p62 and Cathepsin L, were increased in the soleus muscle of GK rats fed with NPD compared to Wistar rats. Importantly, LPD resulted in a slight reduction in the expression of autophagy-related genes; however, these differences were not statistically significant. In addition, LPD+KA abolished the upregulation of autophagy-related gene expression. Furthermore, the activation of autophagy in the NPD and LPD groups was confirmed by the appearance of autophagosomes or autolysosomes using electron microscopy, when compared with the Control and LPD+KA groups. Our results showed that LPD+KA abolished the activation of autophagy in skeletal muscle and decreased muscle loss in rats with type 2 diabetic nephropathy.     

JosD1, a Membrane-targeted Deubiquitinating Enzyme,Is Activated by Ubiquitination and Regulates Membrane Dynamics,Cell Motility,and Endocytosis

The functional diversity of deubiquitinating enzymes (DUBs) is not well understood. The MJD family of DUBs consists of four cysteine proteases that share a catalytic “Josephin” domain. The family is named after the DUB ATXN3, which causes the neurodegenerative disease Machado-Joseph disease. The two closely related Josephin domain-containing (JosD) proteins 1 and 2 consist of little more than the Josephin domain. To gain insight into the properties of Josephin domains, we investigated JosD1 and JosD2. JosD1 and JosD2 were found to differ fundamentally in many respects. In vitro, only JosD2 can cleave ubiquitin chains. In contrast, JosD1 cleaves ubiquitin chains only after it is monoubiquitinated, a form of posttranslational-dependent regulation shared with ATXN3. A significant fraction of JosD1 is monoubiquitinated in diverse mouse tissues. In cell-based studies, JosD2 localizes to the cytoplasm whereas JosD1 preferentially localizes to the plasma membrane, particularly when ubiquitinated. The membrane occupancy by JosD1 suggests that it could participate in membrane-dependent events such as cell motility and endocytosis. Indeed, time-lapse imaging revealed that JosD1 enhances membrane dynamics and cell motility. JosD1 also influences endocytosis in cultured cells by increasing the uptake of endocytic markers of macropinocytosis while decreasing those for clathrin- and caveolae-mediated endocytosis. Our results establish that two closely related DUBs differ markedly in activity and function and that JosD1, a membrane-associated DUB whose activity is regulated by ubiquitination, helps regulate membrane dynamics, cell motility, and endocytosis.     

Diversity of the intestinal microbiota in different patterns of feeding infants by Illumina high-throughput sequencing

The gastrointestinal microbiota plays a crucial role in the health and disease of the host through its impact on nutrition. Gut microbial composition is related to different diets, but an association of microbiota with different diets in infant has not yet been shown. In this work, we compared the fecal microbiota of breast-fed (BF) and formula-fed infants (FF). By using Illumina high-throughput sequencing and biochemical analyses, we found differences in gut microbiota between the two groups. BF infants showed a significant enrichment of Actinobacteria and Firmicutes and depletion of Proteobacteria (P < 0.05), the abundance of Bacteroidetes in the two groups was very low (P > 0.05). Enterobacteriaceae (Proteobacteria) were the dominant bacteria in FF infant fecal microbiota, and Veillonellaceae (Firmicutes) and Enterobacteriaceae (Proteobacteria) were the dominant bacteria in the BF infant fecal microbiota. The number of genera (percentage of sequences >0.1 %) in BF and FF infants was 17 and 15 respectively, and Streptococcus was the dominant bacterial genus in both groups.     

微杆菌Sneb159杀线虫活性物质的分离与鉴定

【目的】有关Microbacterium maritypicum在植物线虫生物防治方面的研究较少,探究菌株M. maritypicum Sneb159的杀线虫活性,明确菌株发酵液中具有杀线虫活性的物质,为生物农药的开发提供理论依据。【方法】本研究检测了菌株Sneb159发酵液对大豆胞囊线虫二龄幼虫的触杀活性;并以触杀活性为追踪,采用有机溶剂萃取、硅胶柱层析及半制备高效液相色谱等技术对菌株Sneb159发酵滤液中的活性物质进行分离纯化;采用核磁共振波谱对纯化物进行结构鉴定。【结果】菌株Sneb159具有杀线虫活性,在24 h和48 h处理组中线虫的死亡率均显著高于对照组。从菌株Sneb159发酵滤液中分离得到杀线虫活性物质A6,经结构鉴定确定该物质为苯乙酰胺。【结论】首次发现M. maritypicum对大豆胞囊线虫的触杀作用,并且明确活性物质为苯乙酰胺。结果表明菌株M. maritypicum Sneb159和苯乙酰胺在大豆胞囊线虫的生物防治方面具有较好的应用潜力。     

Probiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China

The purpose of this study was to evaluate the probiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China. Four Enterococcus isolates showed high cholesterol removal ability in media were identified as Enterococcus durans (KLDS 6.0930 and 6.0933) and Enterococcus faecalis (KLDS 6.0934 and 6.0935) by 16S rRNA and pheS gene sequences, respectively, and selected for further evaluation. In order to assess the probiotic potential and safety of these strains, the property of four Enterococcus strains were examined, including acid and bile tolerance, adherence to Caco‐2 cells and antibiotics susceptibility. All four strains showed potential cholesterol assimilation, de‐conjugation of bile salts and/or cholesterol degradation to remove cholesterol in vitro. In addition, the potential effect of E. durans KLDS 6.0930 on serum cholesterol levels was evaluated in Sprague‐Dawley rats. After 4 weeks administration, compared with rats fed a high‐cholesterol diet without lactic acid bacteria supplementation, there was a significant (P < 0.05) decrease in the total cholesterol and low‐density lipoprotein cholesterol levels in the serum of rats treated with KLDS 6.0930. Furthermore, total bile acid level in the feces was significantly (P < 0.05) increased after KLDS 6.0930 administration. These observations suggested that the strain E. durans KLDS 6.0930 may be used in the future as a good candidate for lowering human serum cholesterol levels.     

A Multi-Atlas Labeling Approach for Identifying Subject-Specific Functional Regions of Interest

The functional region of interest (fROI) approach has increasingly become a favored methodology in functional magnetic resonance imaging (fMRI) because it can circumvent inter-subject anatomical and functional variability, and thus increase the sensitivity and functional resolution of fMRI analyses. The standard fROI method requires human experts to meticulously examine and identify subject-specific fROIs within activation clusters. This process is time-consuming and heavily dependent on experts’ knowledge. Several algorithmic approaches have been proposed for identifying subject-specific fROIs; however, these approaches cannot easily incorporate prior knowledge of inter-subject variability. In the present study, we improved the multi-atlas labeling approach for defining subject-specific fROIs. In particular, we used a classifier-based atlas-encoding scheme and an atlas selection procedure to account for the large spatial variability across subjects. Using a functional atlas database for face recognition, we showed that with these two features, our approach efficiently circumvented inter-subject anatomical and functional variability and thus improved labeling accuracy. Moreover, in comparison with a single-atlas approach, our multi-atlas labeling approach showed better performance in identifying subject-specific fROIs.     

反硝化基因工程菌株YP4S的构建及对污水除氮特性研究

从养殖场污泥中筛选出菌株YP4,经16S rDNA分子发育树的同源序列比对,确定为克雷伯什菌属(Klebsiella sp.)。由NCBI数据库查编码亚硝酸还原酶(Nir)的基因nirS序列,设计引物,以铜绿假单胞菌PAOI基因组DNA为模板,应用PCR技术扩增目的片段nirS,经过双酶切、克隆和转化,得到重组质粒pYP4S,然后转化野生菌株YP4,构建反硝化基因工程菌YP4S。菌株生长曲线测定表明,工程菌株YP4S与YP4的生长特性基本一致。工程菌株YP4S对模拟污水COD、TN、NH_4^+-N和NO_3^--N具有较高的去除率,YP4S与YP4相比,对NO_2^--N积累的减少量为(32.44±3.96)%,明显减少了NO_2^--N的积累。通过正交试验获得工程菌株YP4S在C/N=10、T=30℃、r=200 r/min和pH=7.0的最佳组合条件下,对模拟污水TN去除率较高。应用工程菌株YP4S处理猪场沉淀池的实际污水,COD、TN、TP、NH_4^+-N和NO_3^--N去除率分别为(95.87±0.82)%、(76.38±3.84)%、(97.13±0.54)%和(75.35±2.57)%,NO_2^--N积累量为(3.31±1.24) mg/L,表明工程菌株YP4S具有较好反硝化作用,对含氮量高的实际污水修复具有潜在的应用前景。