作物分枝的分子调控研究进展

分枝的数量及角度是决定作物株型的重要农艺性状.有效分枝数决定着作物的穗数或荚果数,进而决定着作物的产量;而分枝角度与光合效率、种植密度和抗病性密切相关,不仅影响作物的产量,也会影响作物的品质.由于分枝在作物生产中具有十分重要的作用,吸引了越来越多的研究者的注意,多个与分枝性状相关的关键基因被鉴定,分枝数目调控的分子机制...     

Theoretical models for branch formation in plants

Various branch architectures are observed in living organisms including plants. Branch formation has traditionally been an area of interest in the field of developmental biology, and theoretical approaches are now commonly used to understand the complex mechanisms involved. In this review article, we provide an overview of theoretical approaches including mathematical models and computer simulations for studying plant branch formation. These approaches cover a wide range of topics. In particular, we focus on the importance of positional information in branch formation, which has been especially revealed by theoretical research in plants including computations of developmental processes.

     

代谢组学在乳酸菌研究中的应用

代谢组学是系统生物学的重要分支,因其高效、高通量等特点而广泛应用于食品科学、药物学等研究领域。本文概述了代谢组学的分离和检测技术,综述了代谢组学在乳酸菌鉴定、发酵调控、肠道菌群研究等方面中的应用,对代谢组学在乳酸菌研究中潜在的问题和未来发展趋势进行了讨论,期望为代谢组学在食品工业微生物中的应用提供参考。     

Factors Affecting the Compliance and Sway Properties of Tree Branches Used by the Sumatran Orangutan (Pongo abelii)

The tropical arboreal environment is a mechanically complex and varied habitat. Arboreal inhabitants must adapt to changes in the compliance and stability of supports when moving around trees. Because the orangutan is the largest habitual arboreal inhabitant, it is unusually susceptible to branch compliance and stability and therefore represents a unique animal model to help investigate how animals cope with the mechanical heterogeneity of the tropical canopy. The aim of this study was to investigate how changes in compliance and time of oscillation of branches are related to easily observable traits of arboreal supports. This should help predict how supports react mechanically to the weight and mass of a moving orangutan, and suggest how orangutans themselves predict branch properties. We measured the compliance and time of oscillation of branches from 11 tree species frequented by orangutans in the rainforest of Sumatra. Branches were pulled at several points along their length using a force balance at the end of a stiff rope, and the local diameter of the branch and the distance to its base and tip were measured. Compliance was negatively associated with both local diameter and length to the tip of the branch, and positively, if weakly, associated with length from the trunk. However, branch diameter not only predicted compliance best, but would also be easiest for an orangutan to observe. In contrast, oscillation times of branches were largely unaffected by local diameter, and only significantly increased at diameters below 2 cm. The results of this study validate previous field research, which related locomotory modes to local branch diameter, while suggesting how arboreal animals themselves sense their mechanical environment.     

The zygomaticotemporal branch of the trigeminal nerve: an anatomical study

This study was conducted to determine the site of emergence of the zygomaticotemporal branch of the trigeminal nerve from the temporalis muscle and to identify the number of its accessory branches and their locations. A pilot study, conducted on the same number of patients, concluded that the main zygomaticotemporal branch emerges from the deep temporal fascia at a point on average 17 mm lateral and 6 mm cephalad to the lateral palpebral commissure, commonly referred to as the lateral canthus. These measurements, however, were obtained after dissection of the temporal area, rendering the findings less reliable. The current study included 20 consecutive patients, 19 women and one man, between the ages of 26 and 85 years, with an average age of 47.6 years. Those who had a history of previous trauma or surgery in the temple area were excluded. Before the start of the endoscopic forehead procedure, the likely topographic site of the zygomaticotemporal branch was marked 17 mm lateral and 6 mm cephalad to the lateral orbital commissure on the basis of the information extrapolated from the pilot study. The surface mark was then transferred to the deeper layers using a 25-gauge needle stained with brilliant green. After endoscopic exposure of the marked site, the distance between the main branch of the trigeminal nerve or its accessory branches and the tattoo mark was measured in posterolateral and cephalocaudal directions. In addition, the number and locations of the accessory branches of the trigeminal nerve were recorded. On the left side, the average distance of the emergence site of the main zygomaticotemporal branch of the trigeminal nerve from the palpebral fissure was 16.8 mm (range, 12 to 31 mm) in the posterolateral direction and an average of 6.4 mm (range, 4 to 11 mm) in the cephalad direction. On the right side, the average measurements for the main branch were 17.1 mm (range, 15 to 21 mm) in the lateral direction and 6.65 mm (range, 5 to 11 mm) in the cephalic direction. Three types of accessory branches were found in relation to the main branch: (1) accessory branch cephalad, (2) accessory branch lateral, and (3) accessory branches in the immediate vicinity of the main branch. This anatomical information has proven colossally helpful in injection of botulinum toxin A in the temporalis muscle to eliminate the trigger sites in the parietotemporal region and surgical management of migraine headaches triggered from this zone.     

HPV18 Utilizes Two Alternative Branch Sites for E6~*I Splicing to Produce E7 Protein

Human papillomavirus 18(HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6 E7 pre-mRNA. The E6 ORF region in the bicistronic E6 E7 pre-mRNA contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6~*I RNA for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences(BPS) upstream of its 30 splice site, with an identical heptamer AACUA■C, for E6~*I splicing. One heptamer has a branch site adenosine(underlined) at nt 384 and the other at nt 388. E6~*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6~*I splicing prefers the 30 ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant RNA splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6~*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.     

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn, allows evaluation of its importance in maintaining the structure/function of the protein. When using probabilistic methods for site-specific rate inference, few alternatives are possible. In this study we use simulations to compare the maximum-likelihood and Bayesian paradigms. We study the dependence of inference accuracy on such parameters as number of sequences, branch lengths, the shape of the rate distribution, and sequence length. We also study the possibility of simultaneously estimating branch lengths and site-specific rates. Our results show that a Bayesian approach is superior to maximum-likelihood under a wide range of conditions, indicating that the prior that is incorporated into the Bayesian computation significantly improves performance. We show that when branch lengths are unknown, it is better first to estimate branch lengths and then to estimate site-specific rates. This procedure was found to be superior to estimating both the branch lengths and site-specific rates simultaneously. Finally, we illustrate the difference between maximum-likelihood and Bayesian methods when analyzing site-conservation for the apoptosis regulator protein Bcl-x(L).     

Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure, and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well‐resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly vary depending on phylogenetic tree shape.     

光声光谱技术在生物医学领域的发展与应用

光声光谱（特别是激光光声光谱）技术已成为分子光谱学的一个重要分支,其技术特点为生物医学材料的研究提供了一种灵敏而又无损材料的有效办法,是研究复杂生物体所不缺少的分析工具,本文简述了光声光谱的基本理论及特点,介绍了光声光谱在生物学,医学领域的发展和应用情况。     

植物引种驯化研究概述

植物引种驯化是植物学的一个分支学科,该学科与植物的迁地保护和当地的经济建设紧密相关,属于应用基础研究的范畴。但有关理论和方法的研究至今仍显得比较零碎,不够系统,判断植物引种驯化成功的标准尚不够明确。本文就植物引种驯化的概念和意义、主要理论和方法、影响其成败的因子、途径和程序、判断植物引种驯化成功的标准等进行了综述和探讨,并提出了植物引种驯化的展望。     

Brassinosteroid-stimulated branch elongation in the marubakaido apple rootstock

Brassinosteroids (BRs) comprise a specific class of low-abundance plant steroids now recognized as a new class of phytohormones. In this paper, we demonstrate that a fluoro derivative of 28-homocastasterone (5F-HCTS) stimulates branch elongation in in vitro-grown shoots of Malus prunifolia, the marubakaido apple rootstock. In addition to that, we show that this BR-stimulated branch elongation is paralleled by an increase in ethylene release. However, either the presence of 1-amino-cyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene in higher plants, in the culture medium or an ethylene-enriched atmosphere resulted in inhibition of branch elongation, indicating that the stimulation of branch elongation observed for 5F-HCTS-treated shoots in this study was not, at least directly, related to the BR-induced enhancement in ethylene release rate. Besides its positive effect on the marubakaido shoot growth, i.e. branch elongation, the 5F-HCTS-driven enhancement of branch elongation found in this study is potentially useful to improve micropropagation techniques for other plant species as well, especially woody species, in which branch elongation is typically a constraint for efficient micropropagation.     

基于通识教育理念的合成生物学课程设计与实践

合成生物学作为生物学中新的分支学科,发展迅速,理论研究和应用潜力巨大,在带来了很多新的研究理念和研究方法的同时,给高校教学也带来了新的挑战.目前就合成生物学课程而言,国内可供参考的教学经验不多.文中以浙江大学"博雅技艺"类通识课程—"合成生物学"为例,从课程背景、课程设计、课程实施情况、课程成果与存在问题等方面,全方位...     

Distribution and consensus of branch point signals in eukaryotic genes: a computerized statistical analysis.

An intermediate stage in the process of eukaryotic RNA splicing is the formation of a lariat structure. It is anchored at an adenosine residue in intron between 10 and 50 nucleotides upstream of the 3' splice site. A short conserved sequence (the branch point sequence) functions as the recognition signal for the site of lariat formation. It has been generally assumed that the branch point is recognized mainly by the presence of its unique sequence where the lariat is formed. However, the known branch point consensus sequence is found to be distributed nearly randomly throughout the gene sequence with only a slightly higher frequency in the expected lariat region. Further, the known consensus sequence is found to be clearly inadequate to specify branch points. These observations have implications for understanding the mechanism of branch point recognition in the process of splicing, and the possible evolution of the branch point signal.     

东湖螅状独缩虫(纤毛门：寡膜纲)的异质性

以螅状独缩虫（Carchesium polypinum Linne,1785）为研究对象,利用RAPD技术对武汉市南湖、沙湖和东湖3个湖区的螅状独缩虫样本进行了DNA多态性比较分析,以确认种群并期望促进微型生物种群生态学研究.结果如下：（1）从120条随机引物中筛选到31条有清晰扩增条带的,其中20条引物扩增出172条条带清晰、多态性高的条带,片段大小为100～1600bp,而其余11个引物扩增出59条相对多态性差的清晰条带,片段大小为100～1500bp;（2）扩增产物经SPSS12.0与RAPDistance 1.04分析显示,东湖世纪钟（Z）、水果湖（H）和南湖（N）3个样点构成一个分支,而东湖风光村样点（F）或独自形成一支,或与沙湖样点（S）构成相对的姊妹分支.东湖3个样点样本被其它湖泊样本所分隔,表明：东湖水体中螅状独缩虫个体集合为多个种群.这一发现不仅将推动同一水体中微型生物种群生态学研究,更有意义的是可启动关于水体微型生物种群间过渡区本质及物种扩散行为的研究,以期为阐明种群分化和物种形成的机制积累基础资料.     

三维几何形态测量方法在石制品分析中的应用

几何形态测量方法是生物学研究中用于形态特征分析和形态比较研究的一种常用方法。其核心思想是利用空间坐标点获取研究对象的形态数据,再通过坐标数据的多元统计分析,定量探讨研究对象的形态特征及影响其形态变异的因素。近年来,随着三维扫描技术的广泛应用以及对于石制品形态特征量化分析要求的提高,基于三维模型的几何形态测量方法开始出现在相关的旧石器考古研究中。本文首先对三维几何形态测量分析方法及其在石制品研究中的应用情况进行介绍,随后具体阐述了该方法的分析流程。为便于国内学者更好地了解这一方法,本文进一步以广西百色盆地南坡山遗址发现的手斧为例,利用三维几何形态测量方法对这些手斧的几何形态特征进行了初步探讨。三维几何形态测量方法为石制品形态研究提供了新思路和新视角,有望成为今后中国旧石器考古研究中一个重要的发展方向。     

Structural crown properties of Norway spruce (Picea abies [L.] Karst.) and European beech (Fagus sylvatica [L.]) in mixed versus pure stands revealed by terrestrial laser scanning

How tree morphology develops in mixed-species stands is essential for understanding and modelling mixed-stand dynamics. However, research so far focused on the morphological variation between tree species and neglected the variation within a species depending on intra- and interspecific competition. Our study, in contrast, addresses crown properties of nine mature Norway spruces (Picea abies [L.] Karst.) of a pure stand and compares them with ten spruces growing in mixture with European beech (Fagus sylvatica [L.]). The same was done with 11 pure stand beeches and 12 beeches growing in mixture with spruce. Through application of a terrestrial laser scanner and a new skeletonization approach, we deal with both species’-specific morphological traits such as branch angle, branch length, branch bending, crown volume and space occupation of branches within the crown, some of which were hardly accessible so far. Special attention is paid to distinct differences between trees growing in mixed and pure stands: for spruce, our study reveals significantly longer branches and greater crown volumes in the mixed stand when compared to the pure stand. In case of European beech, individuals growing in mixture show flatter branch angles, more distinct ramification, greater crown volumes and a lower share of a single branch’s space occupation in the total crown volume. The results show that the presented methods yield detailed information on the morphological traits analyzed in this study and that interspecific competition on its own may have a significant impact on crown structures. Implications for production ecology and stand dynamics of mixed-species forests are discussed.     

Analysis of long branch extraction and long branch shortening

Background

Long branch attraction (LBA) is a problem that afflicts both the parsimony and maximum likelihood phylogenetic analysis techniques. Research has shown that parsimony is particularly vulnerable to inferring the wrong tree in Felsenstein topologies. The long branch extraction method is a procedure to detect a data set suffering from this problem so that Maximum Likelihood could be used instead of Maximum Parsimony.

Results

The long branch extraction method has been well cited and used by many authors in their analysis but no strong validation has been performed as to its accuracy. We performed such an analysis by an extensive search of the branch length search space under two topologies of six taxa, a Felsenstein-like topology and Farris-like topology. We also examine a long branch shortening method.

Conclusions

The long branch extraction method seems to mask the majority of the search space rendering it ineffective as a detection method of LBA. A proposed alternative, the long branch shortening method, is also ineffective in predicting long branch attraction for all tree topologies.

     

Hemodynamic evaluation of the right portal vein in healthy dogs of different body weights

Background  

Doppler ultrasonography is an important tool for evaluating hepatic portal hemodynamics. However, no study in dogs of different body weights, in the range encountered in routine clinical veterinary practice, has been reported. It can be difficult to obtain an ideal insonation angle when evaluating the main portal vein, so evaluation of the right portal vein branch has been described in humans as an alternative. The aim of this study was to analyze, through Doppler ultrasonography, the hemodynamics in the right portal vein branch in dogs of different body weights.