BacStalk: A comprehensive and interactive image analysis software tool for bacterial cell biology

Prokaryotic cells display a striking subcellular organization. Studies of the underlying mechanisms in different species have greatly enhanced our understanding of the morphological and physiological adaptation of bacteria to different environmental niches. The image analysis software tool BacStalk is designed to extract comprehensive quantitative information from the images of morphologically complex bacteria with stalks, flagella, or other appendages. The resulting data can be visualized in interactive demographs, kymographs, cell lineage plots, and scatter plots to enable fast and thorough data analysis and representation. Notably, BacStalk can generate demographs and kymographs that display fluorescence signals within the two-dimensional cellular outlines, to accurately represent their subcellular location. Beyond organisms with visible appendages, BacStalk is also suitable for established, non-stalked model organisms with common or uncommon cell shapes. BacStalk, therefore, contributes to the advancement of prokaryotic cell biology and physiology, as it widens the spectrum of easily accessible model organisms and enables highly intuitive and interactive data analysis and visualization.     

Sensitive monitoring of riboflavin in commercial multivitamins using poly (chitosan)‐based nanocomposite

The rapid and sensitive determination of riboflavin (RF) is important for the treatment of seborrheic and glossitis dermatitis, sunlight sensitivity, mucosal, and skin disorders. In this work, an electrochemical sensor was developed by electrodes modification using poly (chitosan) to sensitive detection of RF in commercial multivitamin. Electrodeposition of chitosan on the surface of glass carbon electrode was performed using cyclic voltammetry technique in the range of ?1 to +1 V. The modified electrode surface morphology was characterized using a high‐resolution field emission scanning electron microscope. The modified electrode was used as an effective electrical interface for the detection of RF using cyclic, differential pulse, and square wave voltammetry techniques. Finally, the sensor was applied to determine RF in commercial multivitamins. In optimum conditions, the linear range for the standard sample of RF and commercial multivitamins 94 to 333μM and 24.6 to 176μM were obtained, respectively. Low limit of quantification (LLOQ) were obtained as 24.6μM.     

Model‐assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways

Efficient approaches to increase plant lipid production are necessary to meet current industrial demands for this important resource. While Jatropha curcas cell culture can be used for in vitro lipid production, scaling up the system for industrial applications requires an understanding of how growth conditions affect lipid metabolism and yield. Here we present a bottom‐up metabolic reconstruction of J. curcas supported with labeling experiments and biomass characterization under three growth conditions. We show that the metabolic model can accurately predict growth and distribution of fluxes in cell cultures and use these findings to pinpoint energy expenditures that affect lipid biosynthesis and metabolism. In addition, by using constraint‐based modeling approaches we identify network reactions whose joint manipulation optimizes lipid production. The proposed model and computational analyses provide a stepping stone for future rational optimization of other agronomically relevant traits in J. curcas.     

Variation in phosphorus and sulfur content shapes the genetic architecture and phenotypic associations within the wheat grain ionome

Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur‐containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two‐trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.     

Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.     

蝴蝶兰PhNAC1基因序列分析及对低温胁迫的响应

为探讨NAC转录因子在蝴蝶兰低温胁迫响应中的分子调控机理,该研究以蝴蝶兰的叶片为材料,运用RT-PCR及RACE技术克隆得到一条蝴蝶兰的NAC转录因子基因完整的cDNA序列,命名为PhNAC1(GenBank登录号MF797909),并分析了其在两种低温条件下的表达模式。结果表明:PhNAC1基因cDNA序列全长1 442 bp,ORF全长942 bp,编码313个氨基酸。预测其蛋白分子量为35.22 kDa,等电点为6.95,属于稳定亲水性蛋白。二级结构预测表明,无规则卷曲和延伸链为该蛋白的主要结构元件,与三级结构预测结果基本相符。PhNAC1编码的氨基酸序列与其他已登录的兰科植物NAC蛋白进行同源序列比对,表明与小兰屿蝴蝶兰(XP_0205763790)亲缘关系较近,序列一致性达97%,其次为铁皮石斛(XP_020695081),一致性为84%。实时荧光定量PCR分析表明,PhNAC1基因在营养器官和生殖器官中均有表达,在蕊柱中的表达量最高。在11℃/6℃低温条件下,PhNAC1基因的转录表达水平在前5天随着处理时间逐渐升高,到第7天开始下降;在4℃低温条件下,PhNAC1基因的表达水平在处理0.5 h时表达量有所下降,1 h后表达量上升至对照水平,之后无明显变化,在处理24至48 h又逐渐升高,推测PhNAC1基因参与蝴蝶兰低温胁迫响应。     

马铃薯StMYB44基因对蔗糖的响应

MYB转录因子存在于所有真核生物中,是最具代表的转录因子家族之一,广泛参与植物发育、苯丙烷代谢、生物与非生物胁迫响应、激素响应以及细胞形态建成等过程。该研究从马铃薯品种‘青薯9号’中克隆得到StMYB44基因(GenBank登录号XM_006367359.2),该基因CDS长为963 bp,编码320个氨基酸,含有2个SANT结构域。实时荧光定量PCR结果显示,StMYB44基因在花中表达最高,在匍匐茎中表达最低;且StMYB44基因在无蔗糖处理下表达上调,在高浓度蔗糖处理下(6%、9%)表达下调。构建表达载体并进行遗传转化烟草发现,StMYB44基因突变体在无蔗糖条件下的长势明显好于野生型,而在高蔗糖浓度下(6%、9%)的长势弱于野生型,且蔗糖浓度越高,差异越大。研究表明,蔗糖浓度能够调节StMYB44基因的表达,推测StMYB44基因可能在植物响应蔗糖中起重要作用。     

玉米转基因技术专利权人合作态势分析

转基因玉米是最重要的转基因主粮作物之一,其转基因技术具有一定的代表性。为了更好地了解和掌握玉米转基因技术领域研发主体合作情况,文章构建了基于专利权人合作网络的目标技术领域专利权人合作态势分析框架,并基于社会网络分析方法与技术,以世界范围内的转基因玉米领域的重要专利权人为分析对象,构建合作网络、分析整体合作特征、挖掘合作子网、探测领域内重要专利权人,从而从宏观、中观和微观三个层面客观展现玉米转基因技术领域专利权人合作态势,为科技战略规划提供一定的决策支撑。     

大渡河中游干暖河谷区生境对植物群落分布格局和多样性的影响

大渡河中游干暖河谷区滑坡和泥石流灾害频发, 对该区域坡面植物群落的研究有助于揭示植被演替的方向, 为坡面植被生态恢复提供基本依据。本研究沿大渡河中游河谷区每隔约5 km设置典型样地, 调查了植被的物种组成和分布以及样地的地形、土壤等10个生境因子, 探讨河谷区植被的连续性变化, 并通过多元回归树(multivariate regression trees, MRT)、多样性指数和典范对应分析(canonical correspondence analysis, CCA)等方法对植物群落进行分类、比较和排序。结果表明: 大渡河中游干暖河谷植被以土壤碳含量、pH值和C : N等3个因子为节点, 可划分为多花胡枝子(Lespedeza floribunda)-荩草(Arthraxon hispidus)-香薷(Elsholtzia ciliate)(群落A)、地果(Ficus tikoua)-车桑子(Dodonaea viscosa)-川滇薹草(Carex schneideri)(群落B)、云南松(Pinus yunnanensis)-栓皮栎(Quercus variabilis)(群落C)和荩草-扭黄茅(Heteropogon contortus)(群落D)等4种群落。该区域以灌木和草本为主要植被类型(群落A、B、C), 间或有裸地分布, 易成为泥石流灾害产生的物源区; 以多花胡枝子为主的灌草群落A的物种丰富度、优势度与多样性表现一致, 均高于以乔木和草本为主的群落C和D, 但物种多样性优势并不显著, 灌草群落分布广而结构单一, 外来物种占比为8.33%, 是生态系统脆弱和不稳定的表现。多元回归树和典范对应分析结果表明, pH值、C : N、坡向和土壤容重等4个因子对植物群落组成和分布影响最大, 且土壤因子的影响大于地形因子。