“dendRoAnalyst”: A tool for processing and analysing dendrometer data

Dendrometers are vital tools for studying the response of trees to intra-annual environmental changes in different temporal resolutions, ranging from hourly, daily to weekly time resolution. Dendrometers are increasingly used in forest management and tree physiological studies. Besides the data analysis, data processing is also challenging, time-consuming and potentially error-prone due to the immense number of measurements generated by self-registering electronic dendrometers. We present the package ‘dendRoAnalyst’ based on R statistical software to process and analyse dendrometer data using various approaches. This package offers algorithms for handling and pre-cleaning of dendrometer data before the application of subsequent data analytical steps. This includes identifying and erasing artefacts in dendrometer datasets not related to actual stem circumference change, identifying data gaps within records, and the possibility of change(s) in temporal resolution. Furthermore, the package can calculate different daily statistics of dendrometer data, including the daily amplitude of tree growth. The package dendRoAnalyst is therefore intended to facilitate researchers with a collection of functions for handling and analysing dendrometer data.     

Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

对新型冠状病毒肺炎继发真菌感染的思考

新型冠状病毒肺炎(coronavirus disease 2019,COVID-19)疫情十分严重,给民众的健康带来了巨大威胁。COVID-19患者可能继发侵袭性真菌感染,会严重威胁患者的生命,因此,在诊治策略上应该给予重视。除了加强高危患者中病原真菌的常规检查外,还应加大力度支持和扶持病原真菌先进检测技术的研发;此外,还应重点支持针对医疗单位、公共场所和家庭等常温环境以及体表和器物表面灭活病毒、细菌、真菌等病原体的新型技术和方法的研发。最终为国家战胜COVID-19和继发感染疫情提供新措施和新策略。     

A potential tradeoff between feeding rate and aversive learning determines intoxication in a Caenorhabditis elegans host-pathogen system

Despite being the first line of defense against infection, little is known about how host-pathogen interactions determine avoidance. Caenorhabditis elegans can become infected by chemoattractant-producing bacteria through ingestion. The worms can learn to associate these chemoattractants with harm through aversive learning. As a result, the worms will avoid the pathogen. Evolutionary constraints have likely shaped the attraction, intoxication and learning dynamics between bacteria and C. elegans, but these have not been explored. Using bacteria engineered to express an acylhomoserine lactone chemoattractant and a nematicidal protein, we explored how manipulating the amount of attractant produced by the bacteria affects learning and intoxication in mixed stage populations of C. elegans. We found that increasing the production rate of the chemoattractant increased the feeding rate in C. elegans, but decreased the time required for C. elegans to learn to avoid the chemoattractant. Learning generally coincided with a decreased feeding rate. We also observed that the percentage of intoxicated worms was maximized at intermediate production rates of the attractant. We propose that interactions between attractant driven feeding rate and aversive learning are likely responsible for this trend. Our results increase our understanding of behavioral avoidance in C. elegans and have implications in understanding host-pathogen dynamics that shape avoidance.     

Variation in the methods leads to variation in the interpretation of biodiversity–ecosystem multifunctionality relationships

生物多样性常常和生态系统多功能性(生态系统同时提供多个生态系统功能的能力)正相关。然而,生物多样性与生态系统多功能性的关系是否依赖于生态系统功能的数目有诸多争议。其中,生物多样性对生态系统多功能性的影响或许不随生态系统功能数目的变化而变化,或者随生态系统功能数目的增多而增强。我们期望通过研究不同生态系统多功能性指数的统计原理来解决这些争议。 我们使用了模型模拟和一系列来自不同空间尺度(从局域到全球)和不同生物群系(温带和高寒草地、森林和干旱地)的经验数据。我们回顾了量化生态系统多功能性的三种方法,包括平均值法、加和法和阈值法。我们发现随着生态系统功能数目的增加,生物多样性与生态系统多功能性的关系要么不变,要么增强。这些结果可由平均和加和的多功能性指数的统计原理来解释。具体来讲,当利用生态系统功能的平均值计算多功能性指数时,由于多样性对多功能性的效应等于多样性对单个生态系统功能效应的平均值,所以不会随生态系统功能数目的变化而变化。同样的道理,当利用单个生态系统的加和值计算多功能性指数时,多样性的效应会随着生态系统功能数目的增加而增强。我们提出了一个改进的多功能性指数,将平均或加和多功能性指数转化为标准化的多功能性指数, 以便于对不同研究的结果进行比较。此外,我们提出了基于变量数值范围的标准化方法来解决阈值法的数学假象问题(多样性效应随生态系统功能数目的增加而增强)。我们的研究结果表明,量化多功能性指数的方法不同,结果也不同。因此,有必要加深对不同方法数理基础的理解。而标准化的多功能性指数为比较不同研究中的生物多样性与生态系统多功能性的关系提供了有效的方法。     

以环境育人为理念的本科教学实验室管理模式探讨

本科教学实验室是开展本科生实验教学的主要场所,如何通过实验室的管理有效提升学生实验素养值得探索。文中主要介绍了将“6S (整理 (Seiri)、整顿 (Seiton)、清扫 (Seiso)、清洁 (Seiketsu)、素养 (Shitsuke)、安全 (Safety) 六项要素) 管理”理念引入本科教学实验室管理的应用实践与效果,特别是实验室环境管理、实验室安全管理、物品定位管理、试剂和耗材管理、学生培训和考核等方面的具体做法。通过实施“6S管理”,实验室环境得以改善,学生的实验素养得到提高,本科实验教学的质量得到改善和提高,达到环境育人的目的。这为高校教学实验室的建设和有效管理提供可推广、可操作的经验。     

污染场地土壤生态风险评估研究进展

随着我国快速城市化以及产业结构的调整,遗留下了大量的污染场地,发展和实施污染场地土壤生态风险评估是进行大规模污染场地修复行动的必要条件。本文围绕污染场地土壤生态风险评估的科学原理、框架构建及技术方法等方面的关键问题: 1)评估框架的场地实际针对性;2)概念模型的不确定性;3)土壤复合污染毒性机制;4)评估终点筛选;5)评估方法和框架构建等展开讨论,指出土壤复合污染的制毒机制,即污染物生物有效性和联合效应是污染场地土壤生态风险评估的关键科学问题。耦合美国环保局四步法和欧盟层级法的“证据-权重法”评估框架适用于野外复杂环境条件下的土壤污染生态风险评估。建议今后重点开展以下5个方面的工作: 1)污染场地土壤生态风险评估技术框架与风险管控技术框架之间的联合;2)概念模型研究;3)基于过程的场地土壤污染物反应运移模型研究;4)场地土壤复合污染生态毒理学机制研究;5)生态系统高水平生态风险评估终点研究。旨在为形成我国本土污染场地土壤生态风险评估技术指南提供理论基础和构架。     

疫情常态化下“发酵工程”线上线下混合式教学模式的改革与探索

新型冠状病毒肺炎疫情防控常态化下,线上线下混合式教学成为了许多高校课程采用的新型教学模式。本课程团队以学生为中心,结合传统教学法（Lecture-Based Learning,LBL）和慕课教学的优点,重新构建了“发酵工程”课程的教学过程,对课程的教学目标、教学要求、教学章节、教学考核、教学方法等进行了一系列的改革探索,并尝试了线上翻转课堂和课程思政融入课堂的教学模式,学生自主学习的积极性得以提高,促进、提升了课程的教与学效果。     

基于“抗疫精神”的“基因工程”课程思政教学设计与实践

课程思政是当前高校落实“立德树人”根本任务的重要形式。在抗击新型冠状病毒肺炎疫情中,中华民族同舟共济、守望相助,共同铸就了伟大的抗疫精神,为课程思政教学提供了最生动的元素。本文对“战疫”行动中的抗疫精神进行梳理和总结,将其内涵凝练为5项内容;以新型冠状病毒的“核酸检测、疫苗研制及其变异”中蕴含的“抗疫精神”为思政载体,甄选“基因工程”课程中对应的理论内容,开展聚焦抗疫精神的“基因工程”课程思政教学设计与实践研究,利用问卷法和深度访谈法对教学实施效果进行评价,旨在引导学生在学习专业理论知识的同时,感悟课程内容中蕴含的抗疫精神,并将其内化为价值追求,潜移默化中提升学生的思想意识和道德修养,同时为生物类其他专业课程思政教学提供参考和借鉴。