Host behavior modification of Achaearanea tingo (Araneae: Theridiidae) induced by the parasitoid wasp Zatypota alborhombarta (Hymenoptera: Ichneumonidae)

Behavioral manipulation involving Zatypota (Ichneumonidae: Pimplinae) parasitoids and their spider hosts is usually associated with an increase in web complexity at the location where the parasitoid larva builds its cocoon. A higher number of web threads at this location may improve stability and provide a physical barrier against potential predators. However, we observed that parasitized individuals of Achaearanea tingo attacked by Z. alborhombarta change the three‐dimensional structure of their webs to a very simple and strong structure composed of two cables attached to the surrounding vegetation. This structure holds the curled leaf formerly used by the spider as a shelter. The parasitoid larva remains protected within this shelter after killing the host. The architectural pattern of the cocoon webs of A. tingo indicates that host manipulation is characterized by the repetition of one specific subroutine involved in web construction. Similar alterations have been previously described for cocoon webs constructed by parasitized orb‐weavers, but not for the three‐dimensional webs of theridiids.     

Epistatic partners of neurogenic genes modulate Drosophila olfactory behavior

The extent to which epistasis affects the genetic architecture of complex traits is difficult to quantify, and identifying variants in natural populations with epistatic interactions is challenging. Previous studies in Drosophila implicated extensive epistasis between variants in genes that affect neural connectivity and contribute to natural variation in olfactory response to benzaldehyde. In this study, we implemented a powerful screen to quantify the extent of epistasis as well as identify candidate interacting variants using 203 inbred wild‐derived lines with sequenced genomes of the Drosophila melanogaster Genetic Reference Panel (DGRP). We crossed the DGRP lines to P[GT1]‐element insertion mutants in Sema‐5c and neuralized (neur), two neurodevelopmental loci which affect olfactory behavior, and to their coisogenic wild‐type control. We observed significant variation in olfactory responses to benzaldehyde among F₁ genotypes and for the DGRP line by mutant genotype interactions for both loci, showing extensive nonadditive genetic variation. We performed genome‐wide association analyses to identify the candidate modifier loci. None of these polymorphisms were in or near the focal genes; therefore, epistasis is the cause of the nonadditive genetic variance. Candidate genes could be placed in interaction networks. Several candidate modifiers are associated with neural development. Analyses of mutants of candidate epistatic partners with neur (merry‐go‐round (mgr), prospero (pros), CG10098, Alhambra (Alh) and CG12535) and Sema‐5c (CG42540 and bruchpilot (brp)) showed aberrant olfactory responses compared with coisogenic controls. Thus, integrating genome‐wide analyses of natural variants with mutations at defined genomic locations in a common coisogenic background can unmask specific epistatic modifiers of behavioral phenotypes.     

Genome-wide survey of prokaryotic O-protein phosphatases

Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokaryotic genomes. The availability of complete genome sequence information for several prokaryotes permits a genome-wide survey of O-protein phosphatases. The distribution of the various protein phosphatase families has been observed to be mosaic, with the exception of the members of the phospho protein family P (PPP), which is consistent with previous studies. The PPP family is ubiquitous in the prokaryotic world and undergoes the highest sequence divergence within a genome amongst phosphatases studied. The co-occurrence of low molecular mass tyrosine phosphatase (LMWPc) and PPP domain in a single polypeptide suggests that the protein present in Archaeoglobus fulgidus might represent the progenitor for all protein phosphatases. The curation of data on prokaryotic protein phosphatases provides a convenient framework for the analysis of domain architectures and for characterising structural and functional properties of this important family of signalling proteins.     

A dynamic, architectural plant model simulating resource-dependent growth

BACKGROUND AND AIMS: Physiological and architectural plant models have originally been developed for different purposes and therefore have little in common, thus making combined applications difficult. There is, however, an increasing demand for crop models that simulate the genetic and resource-dependent variability of plant geometry and architecture, because man is increasingly able to transform plant production systems through combined genetic and environmental engineering. MODEL: GREENLAB is presented, a mathematical plant model that simulates interactions between plant structure and function. Dual-scale automaton is used to simulate plant organogenesis from germination to maturity on the basis of organogenetic growth cycles that have constant thermal time. Plant fresh biomass production is computed from transpiration, assuming transpiration efficiency to be constant and atmospheric demand to be the driving force, under non-limiting water supply. The fresh biomass is then distributed among expanding organs according to their relative demand. Demand for organ growth is estimated from allometric relationships (e.g. leaf surface to weight ratios) and kinetics of potential growth rate for each organ type. These are obtained through parameter optimization against empirical, morphological data sets by running the model in inverted mode. Potential growth rates are then used as estimates of relative sink strength in the model. These and other 'hidden' plant parameters are calibrated using the non-linear, least-square method. KEY RESULTS AND CONCLUSIONS: The model reproduced accurately the dynamics of plant growth, architecture and geometry of various annual and woody plants, enabling 3D visualization. It was also able to simulate the variability of leaf size on the plant and compensatory growth following pruning, as a result of internal competition for resources. The potential of the model's underlying concepts to predict the plant's phenotypic plasticity is discussed.     

川产淫羊藿属（Epimedium）药用植物的无性系构件特征和生物量配置比较

在构件水平上,对川产的3种药用淫羊藿属植物（淫羊藿（Epimedium brevicornu）、箭叶淫羊藿（E.sagittatum）、柔毛淫羊藿（E.pubescens））的无性系构件特征、克隆构型及构件生物量配置进行比较,结果表明在野生状态下：该属3个种无性系构件的形态特征差异显著,且存在较大的变异性,变异系数范围在29.29%~48.31%之间;箭叶淫羊藿更趋于“游击型”克隆构型,而淫羊藿和柔毛淫羊藿则更趋于“密集型”克隆构型;该属3个种都将高比例生物量配置到叶片或者根茎,其次为茎,再其次为根。柔毛淫羊藿具有更强的克隆繁殖能力,单位面积上各构件生物量均最大,应作为人工引种栽培的首选种。     

放牧干扰对青藏高原东缘窄叶鲜卑花空间结构的影响

在四川西北部松潘县卡卡沟对青藏高原东缘高海拔地区3个不同放牧强度下的窄叶鲜卑花灌丛的空间结构进行了研究,结果表明：放牧干扰对卡卡沟东南坡的窄叶鲜卑花空间结构影响显著,植株的总生物量、总叶面积和茎的边材面积在重度放牧下显著低于轻度和中度放牧梯度样地。中度和重度放牧情况下叶片长度、宽度以及面积均比轻度放牧显著提高;植株高度随放牧强度增加出现先升后降的现象,而顶部枝叶生物量分配则出现与之相反的情况。虽然植物空间结构发生变化,但是单位边材面积上支持的叶面积并没有变化,中度放牧使植株枝叶生物量更加均匀分布。放牧干扰下植物空间结构的塑性变化依然受到Huber数的制约,使叶片蒸腾耗水与茎的供水能力上维持平衡。     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.     

阿拉善高原2种荒漠植物根系构型及生态适应性特征

根系构型决定了植物对资源的吸收方式,根系构型的变化是植物对环境的生态适应和有效生存策略。在阿拉善高原西南缘红砂（Reaumuria soongarica）-珍珠猪毛菜（Salsola passerina）混生群落采用传统挖掘法收集两种植物根系,基于量化的根系形态指标,利用几何拓扑学及分形理论分析了根系构型特征,探讨了该地区2种植物对干旱生境的生态适应策略。结果表明：红砂和珍珠猪毛菜根系均以水平分布占优,根系浅层化分布明显,混生的两种植物占据不同的生态位;2种荒漠植物均具有较大的比根长（SRL）和比表面积（SRA）,红砂SRL=21.3 cm/g,SRA=7.6 cm²/g,珍珠SRL=22.4 cm/g,SRA=6.5 cm²/g,有利于水分和养分的获取;红砂根系拓扑指数（TI）、修正拓扑参数（q_a和q_b）分别为0.86、0.52、0.49,珍珠猪毛菜对应参数分别为0.93、0.76、0.73,表明2种植物根系均趋向于鱼尾形分支结构;根系分形维数值（FD_红=1.488、FD_珍=1.422）较小,而分形丰度值（lgK_红=1.855、lgK_珍=1.774）较大,表明2种植物分支相对简单,但空间拓展能力强,有利于对营养空间的占有。上述特征可能是阿拉善西南缘红砂-珍珠猪毛菜群落2种荒漠植物植物对干旱贫瘠生境的重要生态适应策略。     

学生参与的大学校园景观设计研究—以清华大学为例

校园通过环境育人的作用潜移默化地影响着学生的成长,校园景观设计研究已成为设计类专业学生学位论文及设计课选题的主要对象之一。清华大学的教学与实践中,设计类专业学生参与校园景观营造的过程主要与其专业学习相结合,本科生与研究生各有侧重。非设计类专业学生是校园学生使用者中的多数,其参与过程以公众参与理论为指导,通过多种形式进行。合理进行资源整合与计划协调,校园景观设计研究可以成为学生价值塑造、能力培养、知识传授的理想平台。     

口述史方法在风景园林教学中的应用探讨

风景园林专业的教学中,园林历史文化的传承与研习是一个漫长的过程。而高校教育中,除了历史知识、文化内涵的传授、讲解外,如何发挥高等教育及当代“人”在历史与文化中的主动性亦是一个重要课题。“口述史”方法有别于传统历史建构及研究方式,为学习者提供了解、认知、参与风景园林历史脉络的梳理及文化传承中的新可能。因此,以华南农业大学风景园林专业教学中的2项实践“口述工艺”及“广州市城市公园建设与发展研究”为例,探讨口述史在专业教学操作过程中的课程设计方法、应用范围以及与传统历史研习思路的差异。认为“口述史”的教学应用更多地以学生主导、以实践操作为主,推进学生多视角的历史认知、参与风景园林历史脉络的梳理、培养独立思考能力,推动风景园林历史教学改革与职业教育。