中国生物多样性在线数据处理平台的构建

高质量的生物多样性数据能够为生物多样性的研究与保护提供数据支撑。目前研究人员开发了大量的生物多样性数据处理软件或工具, 包括工作流系统、R语言包、Python语言包和Excel工具等, 但是使用这些软件或工具需要用户安装相应的软件客户端, 并掌握一定的编程语言、软件开发和复杂的Excel公式等知识和技能。为降低用户的学习成本和使用门槛, 本文采用了Browser/Server模式设计技术、Web技术、可视化技术、响应式开发技术、网络爬虫技术、数据处理技术和Solr智能检索技术等, 针对不同维度的生物多样性数据设计和开发了相应的数据处理模块, 构建了中国生物多样性在线数据处理平台(http://dp.iflora.cn/)。该平台能够有效地帮助科研人员对物种名称、地理位置、时间日期和经纬度等数据进行处理, 并提供数据格式转换、数据质量评测和资源统计分析等辅助功能, 帮助科研人员实现零代码和低门槛地处理生物多样性数据, 提供便捷、高效和简单的数据清洗、校正、转换和整合等数据处理渠道, 为生物多样性研究和保护提供信息化技术支持与服务。     

综述与专论: 针对严重急性呼吸综合征冠状病毒2变异株Omicron的疫苗研究进展

2021年底,严重急性呼吸综合征冠状病毒2 Omicron变异株迅速取代Delta突变株在世界范围内广泛流行,其S蛋白具有36个位点突变,导致致病力和传播力发生明显变化,并且具备了免疫逃逸的能力。疫苗接种是目前疫情防控最普适的手段,研究发现,现有疫苗针对Omicron突变株的保护效果明显下降。新的免疫策略或特异性疫苗/多价疫苗针对Omicron有效性的评估均需要动物模型的支撑。在实验室条件下,利用动物模型进行活病毒攻击实验,是在体内验证保护性中和抗体、疫苗有效性的关键技术手段,本文将从动物模型方向综述国内外针对Omicron变异株的疫苗研究进展。     

4种种子处理剂对菜心安全性及保护作用评价

为评价4种种子处理剂对菜心种子的安全性以及对黄曲条跳甲Phyllotreta striolata (Fabricius)的防治效果和保苗作用,本研究开展了室内、田间安全性试验以及田间保护试验。室内安全性试验结果显示,40%溴酰·噻虫嗪种子处理悬浮剂、600 g/L吡虫啉悬浮种衣剂、18%噻虫胺种子处理悬浮剂、54%吡虫·氟虫腈悬浮种衣剂用量分别低于5 120、9 600、2 880、7 040 g(a.i.)/100 kg种子时,对菜心种子发芽和生长无影响。田间安全性及保护作用结果显示,40%溴酰·噻虫嗪种子处理悬浮剂和54%吡虫·氟虫腈悬浮种衣剂保护作用显著,菜心出苗后25 d的株高和鲜重与对照组相比均有增加,且差异显著。结果表明40%溴酰·噻虫嗪种子处理悬浮剂和54%吡虫·氟虫腈悬浮种衣剂对菜心种子具有较好的安全性,且对菜心苗期有良好的保护作用。     

鲫幼鱼耳石荧光标记效果

为确认茜素络合物对鲫（Carassius auratus）耳石进行有效标记的可行性,以便为鲫甚至其他鲤科鱼类标志放流技术的开发及效果评估提供一定的借鉴,本研究以孵出后90 d的鲫幼鱼为研究对象,设置单一浓度（100 mg/L）的茜素络合物浸泡标记5 d,分析茜素络合物在耳石上的沉积情况以及不同耳石在不同后续饲养天数的动态变化。结果表明,矢耳石、微耳石和星耳石上在可见光、绿色和蓝色激发光下都检测到了良好的茜素络合物标记环,标记率和存活率均为100%。但不同耳石的茜素络合物标记效果不同,荧光下,星耳石的标记效果最显著,微耳石次之;可见光下,微耳石的标记效果最好,星耳石次之。随着后续饲养天数的延长,可见光下标记逐渐减弱,至20 d时基本消失,而在绿色和蓝色激光下标记环荧光强度无减弱迹象,能长久保持,且在蓝色激发光下标记环更易被观测到。上述结果结合鲫生长、存活和行为正常等情况综合显示,在100 mg/L茜素络合物溶液中浸泡标记鲫幼鱼5 d,其耳石可以获得满意的标记效果。     

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。     

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.     

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.     

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.