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.     

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.     

Inter‐individual variation in colour patterns in noctuid moths characterizes long‐distance dispersers and agricultural pests

A high capacity for long‐distance dispersal is a key to success for species confronted with environmental heterogeneity, habitat modification, fragmentation and loss. However, dispersal capacity is difficult to quantify and therefore poorly known in most taxa. Here, we report on a test for an association of variation in dispersal capacity with variable colouration of noctuid moths. First, using data from 12 experienced lepidopterologists, we showed that despite variation among experts in average assessments, different species are consistently classified as having non‐variable, variable or highly variable colour patterns when assessed by different experts. We then compared the incidence of non‐resident species with high inter‐individual variation in colour patterns recorded on the isolated island Utklippan (n = 47), with that in a species pool of potential long‐distance dispersers from the nearest mainland (n = 295). Species with high inter‐individual colour pattern variation were over‐represented on the island compared with species having non‐variable colouration. This finding constitutes rare evidence from the wild of long‐distance dispersal, measured on a spatial scale relevant for moths when tracking habitats in fragmented and changing landscapes or when keeping pace with environmental challenges associated with climate change. Finally, we showed that Swedish noctuid moths classified as agricultural pests (n = 28) had more variable colour patterns compared with non‐pests (n = 368). The majority of agricultural pests were also recorded on the isolated island, an outcome that is indicative of pest species having high dispersal capacity. Data on colour pattern variation may thus offer a simple and cost‐effective proxy to estimate dispersal capacity and can also help identify potential pest species. Our findings are potentially useful when modelling and predicting population and range dynamics of species in spatiotemporally heterogeneous environments, with direct implications for conservation biology and pest management.     

The use of natural language to communicate the perception of vibrotactile stimuli

This study explores the subjective use of adjectives to verbally communicate vibrotactile stimulation across multiple frequencies. In total, nine different vibrotactile stimulus frequencies (10–300?Hz) were utilized, and subjective evaluation methods, which involved adjectives, were used to assess the sensory representations of the participants (18 healthy male participants; mean age, 22.9 years; standard deviation, 3.5). Sensory terms such as ‘slow,’ ‘protruding,’ and ‘thick’ were used as representative expressions to describe low-frequency (10–100?Hz) vibrotactile stimulations, while ‘fast,’ ‘shallow,’ and ‘tickly’ were used to describe high-frequency (225–300?Hz) vibrotactile stimulations. At the frequencies of 150 and 200?Hz, no characteristic word was found because there was no difference in subjective evaluation scores from other low or high frequencies. The results suggest that vibrotactile stimulation at different frequencies induce diverse sensory representations, owing to not only the motion and shape of the stimuli but also the subjective responses of the perceivers. The results of this study could be utilized in developing affective haptic devices in the future.     

基于机器学习的风景园林智能化分析应用研究

机器学习使实现数据的智能化处理及充分利用数据中蕴含的知识与价值成为可能。探索基于机器学习在风景园林领域智能化分析应用的途径,开展3个实验。其中2个与数据分析研究相关,提出基于调研图像色彩聚类分析的城市色彩印象和基于图像识别技术的景观视觉质量评估与网络应用平台部署实验。最后1个实验与数字化设计创作相关,提出用于设计方案遴选的地形生成方法,包括2个子项目：应用深度学习生成对抗网络（GAN）的地形生成和建立遮罩、预测未知区域的高程。3个实验应用到机器学习中分类、聚类和回归3个主要方向中的算法以及深度学习的生成对抗网络,对传统的研究问题提出了基于机器学习新的研究方法。因此,在应用机器学习风景园林领域,可以有效地从多源数据中学习相互增强的知识,发现问题,并提出解决问题的新方法。     

乙基多杀菌素和联苯肼酯对地熊蜂的毒性及风险评估

【目的】明确乙基多杀菌素和联苯肼酯对地熊蜂Bombus terrestris的毒性, 探讨这两种农药亚致死浓度对地熊蜂体内乙酰胆碱酯酶(AchE)、谷胱甘肽-S-转移酶(GST)和羧酸酯酶(CarE) 3种解毒酶活性的影响。【方法】采用饲喂法测定60 g a.i./L乙基多杀菌素和43%联苯肼酯对地熊蜂采集蜂的急性经口毒性,依据农药对蜜蜂生态风险的危害熵(hazard quotient, HQ)值评估这两种农药对地熊蜂的风险。同时测定了这两种农药亚致死剂量(LD₅₀和LD₈₀)处理后地熊蜂AchE, GST和CarE的活性变化。【结果】60 g a.i./L乙基多杀菌素和43%联苯肼酯对地熊蜂采集蜂的急性经口毒性测定48 h时LD₅₀值分别为3.590和1 447 μg a.i./蜂,其中60 g a.i./L乙基多杀菌素表现为中毒,43%联苯肼酯表现为低毒。两种农药对地熊蜂采集蜂的HQ值均低于50,表现为低风险。LD₅₀和LD₈₀剂量的乙基多杀菌素处理组与对照组相比,3 h时地熊蜂AchE活性被激活,显著高于对照组(P＜0.05),分别为对照组的1.45和1.23倍,24 h后活性受到抑制,两个剂量处理组AchE活性均显著低于对照组(P＜0.05);CarE活性3 h时同样被激活,显著高于对照组(P＜0.05),LD₅₀和LD₈₀剂量处理组CarE活性分别为对照组的1.24和1.53倍, 24 h后活性受到抑制,其中LD₅₀剂量处理组CarE活性显著低于对照组(P＜0.05),LD₈₀剂量处理组CarE活性与对照组差异不显著(P＞0.05);LD₅₀和LD₈₀剂量处理组GST活性3 h被激活,显著高于对照组(P＜0.05),分别为对照组的2.24和2.58倍,24 h后活性降低,但两个剂量处理组GST活性仍显著高于对照组(P＜0.05)。43%联苯肼酯处理后,与对照组相比3 h时LD₅₀和LD₈₀剂量处理组AchE活性与对照组差异不显著(P＞0.05),24 h后AchE活性降低,显著低于对照组(P＜0.05),分别是对照组的75%和80%;CarE活性3 h时被抑制,LD₅₀剂量处理组CarE活性显著低于对照组(P＜0.05),LD₈₀剂量处理组CarE活性低于对照组,但差异不显著(P＞0.05),24 h后CarE活性被激活,其中LD₅₀剂量处理组CarE活性高于对照组,但差异不显著(P＞0.05),LD₈₀剂量处理组CarE活性显著高于对照组(P＜0.05);LD₅₀剂量处理组GST活性3 h时被激活,显著高于对照组(P＜0.05),24 h后活性降低,但仍显著高于对照组(P＜0.05),3 h和24 h的活性分别为对照组的2.04和1.72倍,LD₈₀剂量处理组3 h的GST活性与对照组无显著差异(P＞0.05),24 h后活性降低,显著低于对照组(P＜0.05)。【结论】乙基多杀菌素和联苯肼酯对地熊蜂的HQ 评估均表现为低风险,其中联苯肼酯对地熊蜂的安全性较高,在熊蜂授粉过程中可以按照推荐剂量应用,但过量施用或者长期施用可能会造成熊蜂体内药剂积累引起生理或者行为的变化,乙基多杀菌素在温室及大田授粉期的使用剂量和方法有待进一步研究。