Partner-specific prediction of RNA-binding residues in proteins: A critical assessment

RNA-protein interactions play essential roles in regulating gene expression. While some RNA-protein interactions are “specific”, that is, the RNA-binding proteins preferentially bind to particular RNA sequence or structural motifs, others are “non-RNA specific.” Deciphering the protein-RNA recognition code is essential for comprehending the functional implications of these interactions and for developing new therapies for many diseases. Because of the high cost of experimental determination of protein-RNA interfaces, there is a need for computational methods to identify RNA-binding residues in proteins. While most of the existing computational methods for predicting RNA-binding residues in RNA-binding proteins are oblivious to the characteristics of the partner RNA, there is growing interest in methods for partner-specific prediction of RNA binding sites in proteins. In this work, we assess the performance of two recently published partner-specific protein-RNA interface prediction tools, PS-PRIP, and PRIdictor, along with our own new tools. Specifically, we introduce a novel metric, RNA-specificity metric (RSM), for quantifying the RNA-specificity of the RNA binding residues predicted by such tools. Our results show that the RNA-binding residues predicted by previously published methods are oblivious to the characteristics of the putative RNA binding partner. Moreover, when evaluated using partner-agnostic metrics, RNA partner-specific methods are outperformed by the state-of-the-art partner-agnostic methods. We conjecture that either (a) the protein-RNA complexes in PDB are not representative of the protein-RNA interactions in nature, or (b) the current methods for partner-specific prediction of RNA-binding residues in proteins fail to account for the differences in RNA partner-specific versus partner-agnostic protein-RNA interactions, or both.     

Effects of various LED light spectra on circadian rhythm during starvation in the olive flounder (Paralichthys olivaceus)

In aquaculture, feeding is essential for the maintenance of metabolic processes and homoeostasis of fish. However, fasting acts as a stressor. In this study, we investigated the effect of circadian rhythm under various LED wavelengths [blue (460 nm), green (520 nm) and red (630 nm)] and two light intensities (0.3 and 0.6 W m^?2) over a 9-days period in the olive flounder (Paralichthys olivaceus). We analysed clock genes like period 2 (Per 2) and cryptochrome 1 (Cry 1), and serotonin and arylalkylamine-N-acetyltransferase 2 (AANAT 2), which control circadian rhythms. Per 2, Cry 1, serotonin and AANAT 2 were significantly decreased during the starvation period compared to the normal feeding group. Nevertheless, their levels increased in the groups exposed to green- and blue LED light during the experimental period. These results confirmed that green and blue wavelengths are effective in maintaining the circadian rhythm in olive flounder.     

Crystallization and preliminary X-ray crystallographic studies of ketosteroid isomerase from Pseudomonas putida biotype B

The Δ⁵-3-ketosteroid isomerase from Pseudomonas putida biotype B has been crystallized. The crystals belong to the space group P2₁2₁2₁ with unit cell dimensions of a = 36.48 Å, b = 74.30 Å, c = 96.02 Å, and contain one homodimer per asymmetric unit. Native diffraction data to 2.19 Å resolution have been obtained from one crystal at room temperature indicating that the crystals are quite suitable for structure determination by multiple isomorphous replacement.     

转录因子Foxo3a高表达对小鼠T淋巴瘤EL-4细胞周期和凋亡的影响

为了研究转录因子Foxo3a高表达对小鼠T淋巴瘤EL-4细胞周期和凋亡的影响,采用电穿孔法将真核表达载体pEGFP-N1/Foxo3a转染小鼠T淋巴瘤细胞系EL-4细胞,并通过聚合酶链式反应和免疫印迹法分别检测Foxo3a mRNA及蛋白表达。转录因子Foxo3a高表达后,采用细胞计数法绘制其细胞生长曲线;采用荧光显微镜法及流式细胞仪定性和定量观察典型EL-4细胞凋亡形态特征、细胞凋亡百分率及细胞周期变化情况。结果表明,转录因子Foxo3a真核表达质粒pEGFP-N1/Foxo3a经酶切鉴定及测序检测序列正确。转染pEGFP-N1/Foxo3a的小鼠EL-4细胞表达Foxo3a mRNA和蛋白水平显著升高。Foxo3a高表达明显抑制EL-4细胞的增殖能力,并使EL-4细胞发生明显G2期阻滞(P<0.001)。Foxo3a基因高表达后,荧光显微镜可以观察到典型凋亡的细胞形态。同时,EL-4细胞凋亡百分率显著升高(P<0.01)。结果提示,Foxo3a高表达可以有效抑制小鼠T淋巴瘤细胞体外细胞增殖,使细胞周期G2时相阻滞,并具有诱导细胞凋亡的作用。     

Associations of physical activity with gut microbiota in pre-adolescent children

[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children.[Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou’s evenness, and Faith’s phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2.[Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R² = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA.[Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.     

黄姜中薯蓣皂甙元的提取及定性定量分析

对黄姜中提取的薯蓣皂甙元进行红外和紫外可见波谱扫描,与标准品谱图对比分析,可知提取出的皂甙元与薯蓣皂甙元标准品有相同的结构。用分光光度法测定黄姜中薯蓣皂甙元的含量,以香荚兰醛-高氯酸-冰醋酸的加入顺序,在80℃水浴中加热15min,显色30min后,在542nm处测定吸收值能达到最佳值,最后得出皂甙元含量为2.27%,RSD为1.1%,回收率在97.2%~98.8%之间。     

Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18

Mobile genetic elements such as phages and plasmids have evolved anti-CRISPR proteins (Acrs) to suppress CRISPR-Cas adaptive immune systems. Recently, several phage and non-phage derived Acrs including AcrIIA17 and AcrIIA18 have been reported to inhibit Cas9 through modulation of sgRNA. Here, we show that AcrIIA17 and AcrIIA18 inactivate Cas9 through distinct mechanisms. AcrIIA17 inhibits Cas9 activity through interference with Cas9-sgRNA binary complex formation. In contrast, AcrIIA18 induces the truncation of sgRNA in a Cas9-dependent manner, generating a shortened sgRNA incapable of triggering Cas9 activity. The crystal structure of AcrIIA18, combined with mutagenesis studies, reveals a crucial role of the N-terminal β-hairpin in AcrIIA18 for sgRNA cleavage. The enzymatic inhibition mechanism of AcrIIA18 is different from those of the other reported type II Acrs. Our results add new insights into the mechanistic understanding of CRISPR-Cas9 inhibition by Acrs, and also provide valuable information in the designs of tools for conditional manipulation of CRISPR-Cas9.