细菌萜类合成酶的生物信息学分析

【目的】目前对于萜类合成酶(Terpenoid synthase,TPS)的研究主要集中在植物和真菌中,而对细菌TPS的系统研究尚少。建立在大量已经被测序的细菌基因组基础上,利用生物信息学方法,对细菌TPS在全基因组范围内进行识别、分类和功能分析。【方法】利用TPS的隐马尔科夫模型(Pfam编号为PF03936)搜索自建的细菌蛋白质组数据库,预测出细菌TPS。对这些候选TPS的蛋白序列用MAFFT 7.130b进行多序列比对,并利用MEGA 6.0对多序列比对结果进行进化分析。利用MEME和PredictProtein分别进行细菌TPS的基序(Motifs)和点突变分析。【结果】建立在生物信息学分析的基础上,1 423条细菌TPS被识别,它们分布在8个门中,即放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、绿弯菌门(Chloroflexi)、酸杆菌门(Acidobacteria)和衣原体门(Chlamydiae)。进化分析表明细菌TPS可分为4大类,Motifs分析表明除了各类之间保守的基序(Motifs)外,还有特异的Motifs,这暗示着细菌TPS在不同类别之间的功能分化。点突变分析表明,细菌TPS不同位点的氨基酸突变对TPS功能的影响不同。【结论】细菌TPS主要分布于8个门中,其中在2个门中细菌TPS尚未见报道,即厚壁菌门(Firmicutes)与酸杆菌门(Acidobacteria)。基于进化分析,可以把细菌TPS分为4类,各类之间的差异可能是由类特异的Motifs决定的,另外细菌TPS不同氨基酸位点的突变分析为今后验证TPS的功能提供了很好的理论基础。     

Multi-Shell Copper Catalysts for Selective Electroreduction of CO2 to Multicarbon Chemicals

Electrocatalytic CO₂ reduction (CO₂R) coupled with renewable electricity has been considered as a promising route for the sustainability transition of energy and chemical industries. However, the unsatisfactory yield of desired products, particularly multicarbon (C₂₊) products, has hindered the implementation of this technology. This work describes a strategy to enhance the yield of C₂₊ product formation in CO₂R by utilizing spatial confinement effects. The finite element simulation results suggest that increasing the number of shells in the catalyst wil lead to a high local concentration of *CO and promotes the formation of C₂₊ products. Inspired by this, Cu nanoparticles are synthesized with desired hollow multi-shell structures. The CO₂ reduction results confirm that as the number of shells increase, the hollow multi-shell copper catalysts exhibit improved selectivity toward C₂₊ products. Specifically, the Cu catalyst with 4.4-shell achieved a high selectivity of over 80% toward C₂₊ at a current density of 900 mA cm⁻². Evidence from in situ attenuated total reflection surface-enhanced infrared absorption spectroscopy unveils that the multi-shell Cu catalyst exhibits an enhanced *CO_atop coverage and the stronger interaction with *CO_atop compared to commercial Cu, confirming the simulation results. Overall, the work promises an effective approach for boosting CO₂R selectivity toward value-added chemicals.     

Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs

Migration from rhizosphere to rhizoplane is a key selecting process in root microbiome assembly, but not fully understood. Rhizobiales members are overrepresented in the core root microbiome of terrestrial plants, and here we report a genome-wide transposon-sequencing of rhizoplane fitness genes of beneficial Sinorhizobium fredii on wild soybean, cultivated soybean, rice, and maize. There were few genes involved in broad-host-range rhizoplane colonization. The fadL mutant lacking a fatty acid transporter exhibited high colonization rates, while mutations in exoFQP (encoding membrane proteins directing exopolysaccharide polymerization and secretion), but not those in exo genes essential for exopolysaccharide biosynthesis, led to severely impaired colonization rates. This variation was not explainable by their rhizosphere and rhizoplane survivability, and associated biofilm and exopolysaccharide production, but consistent with their migration ability toward rhizoplane, and associated surface motility and the mixture of quorum-sensing AHLs (N-acylated-L-homoserine lactones). Genetics and physiology evidences suggested that FadL mediated long-chain AHL uptake while ExoF mediated the secretion of short-chain AHLs which negatively affected long-chain AHL biosynthesis. The fadL and exoF mutants had elevated and depleted extracellular long-chain AHLs, respectively. A synthetic mixture of long-chain AHLs mimicking that of the fadL mutant can improve rhizobial surface motility. When this AHL mixture was spotted into rhizosphere, the migration toward roots and rhizoplane colonization of S. fredii were enhanced in a diffusible way. This work adds novel parts managing extracellular AHLs, which modulate bacterial migration toward rhizoplane. The FadL-ExoFQP system is conserved in Alphaproteobacteria and may shape the “home life” of diverse keystone rhizobacteria.Subject terms: Microbial ecology, Functional genomics, Bacterial genetics     

Genetic diversity and inferred ancestry of Asian lotus (Nelumbo nucifera) germplasms in Thailand and Vietnam

Tropical lotus (Nelumbo) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively. Higher genetic diversity was revealed in Thai lotus than in Vietnamese lotus. A Neighbor-Joining tree of five main clusters was constructed using combined EST-SSR and SRAP markers. Cluster I included 17 accessions of Thai lotus; cluster II contained three Thai accessions and 11 accessions from southern Vietnam; and cluster III was constituted by 13 accessions of seed lotus. Consistent with the results from the Neighbor-Joining tree, the genetic structure analysis showed that the genetic background of most Thai and Vietnamese lotus was pure, as artificial breeding has been rare in both countries. Furthermore, these analyses indicate that Thai and Vietnamese lotus germplasms belong to two different gene pools or populations. Most lotus accessions are genetically related to geographical distribution patterns in Thailand or Vietnam. Our findings showed that the origin or genetic relationships of some unidentified lotus sources can be evaluated by comparing morphological characteristics and the data of molecular markers. In addition, these findings provide reliable information for the targeted conservation of tropical lotus and parent selection in breeding novel cultivars of lotus.     

Segmental Kinematic Coupling of the Human Spinal Column during Locomotion

As one of the most important daily motor activities, human locomotion has been investigated intensively in recent decades. The locomotor functions and mechanics of human lower limbs have become relatively well understood. However, so far our understanding of the motions and functional contributions of the human spine during locomotion is still very poor and simultaneous in-vivo limb and spinal column motion data are scarce. The objective of this study is to investigate the delicate in-vivo kinematic coupling between different functional regions of the human spinal column during locomotion as a stepping stone to explore the locomotor function of the human spine complex. A novel infrared reflective marker cluster system was constrncted using stereophotogrammetry techniques to record the 3D in-vivo geometric shape of the spinal column and the segmental position and orientation of each functional spinal region simultaneously. Gait measurements of normal walking were conducted. The preliminary results show that the spinal column shape changes periodically in the frontal plane during locomotion. The segmental motions of different spinal functional regions appear to be strongly coupled, indicating some synergistic strategy may be employed by the human spinal column to facilitate locomotion. In contrast to traditional medical imaging-based methods, the proposed technique can be used to investigate the dynamic characteristics of the spinal column, hence providing more insight into the functional biomechanics of the human spine.     

有关彩色真菌培养基的应用

彩色真菌培养基具有选择性强、分辨率高、易生长、易观察的特点。在真菌培养方面优于其它培养基,其主要作用机理在于应用了化学生物效应促进真菌生长。     

洈水水库鳡鱼(Elopichthys bambusa)生长规律的研究

本文对洈水水库鳡鱼的生长及其利用进行了分析研究,结果表明:1.该种鱼生长快,高速生长时间长,可连续5年每年生长6kg以上;2.雌、雄鱼体长与体重生长分别适合Von.Bertalanffy的生长公式:L=L_∞(1-e-k(t-t·))和W=W_∞(1-e-k(t-t·))~3;3.雌鱼体重生长速度快于雄鱼,体长生长无明显差别;4.建议大中型水体中的鳡鱼与其它鱼类群落体重之比控制在3—5％为宜。     

微杆菌Sneb159杀线虫活性物质的分离与鉴定

【目的】有关Microbacterium maritypicum在植物线虫生物防治方面的研究较少,探究菌株M. maritypicum Sneb159的杀线虫活性,明确菌株发酵液中具有杀线虫活性的物质,为生物农药的开发提供理论依据。【方法】本研究检测了菌株Sneb159发酵液对大豆胞囊线虫二龄幼虫的触杀活性;并以触杀活性为追踪,采用有机溶剂萃取、硅胶柱层析及半制备高效液相色谱等技术对菌株Sneb159发酵滤液中的活性物质进行分离纯化;采用核磁共振波谱对纯化物进行结构鉴定。【结果】菌株Sneb159具有杀线虫活性,在24 h和48 h处理组中线虫的死亡率均显著高于对照组。从菌株Sneb159发酵滤液中分离得到杀线虫活性物质A6,经结构鉴定确定该物质为苯乙酰胺。【结论】首次发现M. maritypicum对大豆胞囊线虫的触杀作用,并且明确活性物质为苯乙酰胺。结果表明菌株M. maritypicum Sneb159和苯乙酰胺在大豆胞囊线虫的生物防治方面具有较好的应用潜力。     

Identification and molecular characterization of two closely related G protein-coupled receptors activated by prokineticins/endocrine gland vascular endothelial growth factor

We previously described two mammalian secreted proteins, prokineticin 1 and prokineticin 2, that potently contract gastrointestinal smooth muscle. Prokineticin 1 has also been shown to promote angiogenesis by stimulating proliferation, migration, and fenestration of endocrine organ-derived endothelial cells. Here we report the cloning and characterization of two closely related G protein-coupled receptors as receptors for prokineticins. Expression of prokineticin receptors in heterologous systems shows that these receptors bind to and are activated by nanomolar concentrations of recombinant prokineticins. Activation of prokineticin receptors leads to mobilization of calcium, stimulation of phosphoinositide turnover, and activation of p44/p42 MAPK signaling pathways that are consistent with the effects of prokineticins on smooth muscle contraction and angiogenesis. mRNA expression analysis reveals that prokineticin receptors are expressed in gastrointestinal organs, endocrine glands, and other tissues.