桃树修剪分枝模式的模拟

在不同修剪手法下,对栽培桃树(Prunuspersica(L.)Batsch)不同母枝上的分枝模式进行了比较研究.从分枝模式来看:修剪后的母枝基本由3个不同的区域组成,基部是不萌发的潜伏芽形成的未分枝区域;中部是延迟分枝和多次分枝组成的分枝区域(主要的枝条类型有短枝、长枝和多次枝);顶部是被剪除的部分.我们通过隐式半马尔可夫模型来模拟这一分枝模式,主要是定量描述1次枝和多次枝在母枝上的数量及其分布状况.在上述模型中,未分枝区、延迟分枝区和多次分枝区称为瞬时态,被剪除的部分称为吸收态.模拟的结果与观察的结果进行对比后发现,两者具有很好的一致性.这说明隐式半马尔可夫模型是模拟植物分枝过程的一种有效方法,尽管隐式半马尔可夫链模型只是一个描述性的模型,但仍能对其所描述的生物现象进行解释,在预测修剪手法对母枝分枝模式影响方面比传统的方法具有明显的优势.本研究结果是建立三维虚拟桃树树冠分枝结构的基础.     

Maintenance mechanisms of the pipe model relationship and Leonardo da Vinci’s rule in the branching architecture of <Emphasis Type="Italic">Acer rufinerve</Emphasis> trees

The pipe model relationship (constancy of branch cross-sectional area/leaf area) and Leonardo da Vinci’s rule (equality of total cross-sectional area of the daughter branches and cross-sectional area of their mother branch) are empirical rules of tree branching. Effects of branch manipulation on the pipe model relationships were examined using five Acer rufinerve trees. Half the branches in each tree were untreated (control branches, CBs), and, for the others (manipulated branches, MBs), either light intensity or leaf area (both relating to photosynthetic source activity), or shoot elongation (source + sink activities), was reduced, and responses of the pipe model relationships were followed for 2 years. The pipe model relationship in MBs changed by suppression of source activity, but not by simultaneous suppression of source + sink activities. The manipulations also affected CBs in the year of manipulation and both branches in the next year. The branch diameter growth was most affected by light, followed by shoot elongation and leaf area, in that order. Because of the decussate phyllotaxis of A. rufinerve, one branching node can potentially have one main and two lateral branches. Analysis of 295 branching nodes from 13 untreated trees revealed that the da Vinci’s rule held in branching nodes having one shed branch but not in the nodes without branch shedding, indicating the necessity of natural shedding of branches for da Vinci’s rule to hold. These analyses highlight the importance of the source–sink balance and branch shedding in maintenance of these empirical rules. This article was contributed at the invitation of the Editorial Committee.     

Patterning parameters associated with the branching of the ureteric bud regulated by epithelial-mesenchymal interactions

The mechanisms by which the branching of epithelial tissue occurs and is regulated to generate different organ structures are not well understood. In this work, image analyses of the organ rudiments demonstrate specific epithelial branching patterns for the early lung and kidney; the lung type typically generating several side branches, whereas kidney branching was mainly dichotomous. Parameters such as the number of epithelial tips, the angle of the first branch, the position index of the first branch (PIFB) in a module, and the percentage of epithelial module type (PMT) were analysed. The branching patterns in the cultured lung and kidney, and in homotypic tissue recombinants recapitulated their early in vivo branching patterns. The parameters were applied to heterotypic tissue recombinants between lung mesenchyme and ureteric bud, and tip number, PIFB and PMT values qualified the change in ureter morphogenesis and the reprogramming of the ureteric bud with lung mesenchyme. All the values for the heterotypic recombinant between ureteric bud and lung mesenchyme were significantly different from those for kidney samples but similar to those of the lung samples. Hence, lung mesenchyme can instruct the ureteric bud to undergo aspects of early lung-type epithelial morphogenesis. Different areas of the lung mesenchyme, except the tracheal region, were sufficient to promote ureteric bud growth and branching. In conclusion, our findings provide morphogenetic parameters for monitoring epithelial development in early embryonic lung and kidney and demonstrate the use of heterotypic tissue recombinants as a model for studying tissue-specific epithelial branching during organogenesis.     

Branching Morphogenesis: From Cells to Organs and Back

Many animal organs, such as the lung, the kidney, the mammary gland, and the vasculature, consist of branched tubular structures that arise through a process known as “branching morphogenesis” that results from the remodeling of epithelial or endothelial sheaths into multicellular tubular networks. In recent years, the combination of molecular biology, forward and reverse genetic approaches, and their complementation by live imaging has started to unravel rules and mechanisms controlling branching processes in animals. Common patterns of branch formation spanning diverse model systems are beginning to emerge that might reflect unifying principles of tubular organ formation.     

桃树修剪分枝模式的模拟

在不同修剪手法下,对栽培桃树(Prunuspersica(L.)Batsch)不同母枝上的分枝模式进行了比较研究。从分枝模式来看修剪后的母枝基本由3个不同的区域组成,基部是不萌发的潜伏芽形成的未分枝区域;中部是延迟分枝和多次分枝组成的分枝区域(主要的枝条类型有短枝、长枝和多次枝);顶部是被剪除的部分。我们通过隐式半马尔可夫模型来模拟这一分枝模式,主要是定量描述1次枝和多次枝在母枝上的数量及其分布状况。在上述模型中,未分枝区、延迟分枝区和多次分枝区称为瞬时态,被剪除的部分称为吸收态。模拟的结果与观察的结果进行对比后发现,两者具有很好的一致性。这说明隐式半马尔可夫模型是模拟植物分枝过程的一种有效方法,尽管隐式半马尔可夫链模型只是一个描述性的模型,但仍能对其所描述的生物现象进行解释,在预测修剪手法对母枝分枝模式影响方面比传统的方法具有明显的优势。本研究结果是建立三维虚拟桃树树冠分枝结构的基础。     

Branch geometry in Cornus kousa (Cornaceae): computer simulations

Computer simulations similar to actual trees were constructed using simple branching rules. Branch orientation with respect to the direction of gravity was a fundamental consideration. In Cornus kousa BUERG. ex HANCE, several types of branches develop from winter buds, varying from orthotropic shoots to plagiotropic ones. Based on actual observations and measurements of branching structures with a wide range of orientations, we made a flexible geometrical model consisting of five forking branches that varied in outgrowth depending on the direction of the shoot with respect to gravity. Repetition of the branching by computer generated a realistic tree pattern, which was close to the shape of a young C. kousa tree. Reproductive shoots seem to be under a branching rule that was a modification of vegetative branching, although the reproductive branch size was considerably smaller than the vegetative one, and reproductive branching was bifurcated instead of five-forked. We conclude that all branchings in orthotropic and plagiotropic shoots in the vegetative phase and shoots in the reproductive phase are formed under the same branching rule, but each has different parameter values.     

Sox2 is important for two crucial processes in lung development: branching morphogenesis and epithelial cell differentiation

The primary lung bud originates from the foregut and develops into the bronchial tree by repetitive branching and outgrowing of the airway. The Sry related HMG box protein Sox2 is expressed in a cyclic manner during initiation and branching morphogenesis of the lung. It is highly expressed in non-branching regions and absent from branching regions, suggesting that downregulation of Sox2 is mandatory for airway epithelium to respond to branch inducing signals. Therefore, we developed transgenic mice that express a doxycycline inducible Sox2 in the airway epithelium. Continuous expression of Sox2 hampers the branching process resulting in a severe reduction of the number of airways. In addition, the bronchioli transiently go over into enlarged, alveolar-like airspaces, a pathology described as bronchiolization of alveoli. Furthermore, a substantial increase was observed of cGRP positive neuroendocrine cells and ΔNp63 isoform expressing (pre-) basal cells, which are both committed precursor-like cells. Thus, Sox2 prevents airways from branching and prematurely drives cells into committed progenitors, apparently rendering these committed progenitors unresponsive to branch inducing signals. However, Sox2 overexpression does not lead to a complete abrogation of the epithelial differentiation program.     

The development of Archaeopteris: new evolutionary characters from the structural analysis of an Early Famennian trunk from southeast Morocco

A 5 m long trunk of a young Archaeopteris/Callixylon erianum tree from the Late Devonian of Morocco shows new branching patterns for early lignophytes. This progymnosperm tree produces a helical pattern of traces that we infer belonged to reduced, short-lived, primary (apical) branches (type A) as well as two types of adventitious traces (types B and H). We infer that type-B traces supplied branches that initiate close to the site of attachment on the trunk of some, but not all type-A branches in an irregular but nonrandom pattern. Unlike ephemeral type-A branches, those of type B persist and become long-lived, potentially permanent units of the architecture of Archaeopteris trees. Type-H adventitious traces are also short-lived and occur singly or in serial groups, but differ from traces of either type A or B branches by lacking differentiation into a readily identifiable organ category. We interpret type-H traces as supplying latent primordia that could develop into either adventitious roots or shoots depending on extrinsic factors. Our new data suggest that Archaeopteris had a wide range of branch primordium amplitude. Type-B branches compare with axillary lateral branch buds of some Early Carboniferous spermatophytes (Calamopitys) and are a major developmental departure from the strictly apical, pseudomonopodial shoot branching of older aneurophyte progymnosperms. Type-H traces suggest that Archaeopteris trees had some potential for formation of adventitious roots or shoots in response to environmental factors, such as partial burial by overbank sedimentation. Collectively, these novel methods of tree branching may partly explain the extraordinary success and worldwide dominance of Archaeopteris forests on fluvially dominated, Late Devonian floodplains.     

A three-dimensional model of the upper tracheobronchial tree

A new model of the upper tracheobronchial tree is proposed to account for the three-dimensional nature of the airway system. In addition to the tube length, the tube diameter, and the branching angle, the model includes information on the orientation angle of each tube relative to its parent tube. The orientation angle, defined as the angle between two successive bifurcations, is useful for calculating the gravitational inclination of each tube. The information on orientation angle is further used to construct a binary coding system for identifying individual tubes in the airway tree. The proposed model is asymmetrical, but the same principles can be readily used to construct a symmetrical one.     

Quantitation of 3D ureteric branching morphogenesis in cultured embryonic mouse kidney

The growth and branching of the epithelial ureteric tree is critical for development of the permanent kidney (metanephros). Current methods of analysis of ureteric branching are mostly qualitative. We have developed a method for measuring the length of individual branches, and thereby the total length of the ureteric tree in 3 dimensions (3D). The method involves confocal microscopy of whole-mount immunostained metanephroi and computer-based image segmentation, skeletonisation and measurement. The algorithm performs semi-automatic segmentation of a set of confocal images and skeletonisation of the resulting binary object. Length measurements and number of branch points are automatically obtained. The final representation can be reconstructed providing a fully rotating 3D perspective of the skeletonised tree. After 36 h culture of E12 mouse metanephroi, the total length of the ureteric tree was 6103 +/- 291 microm (mean +/- SD), a four-fold increase compared with metanephroi cultured for just 6 h (1522 +/- 149 microm). Ureteric duct length increased at a rate of 153 microm/h over the first 30 h period and was maximal between 18 and 24 h at 325 microm/h. The distribution of branch lengths at the six time points studied was similar, suggesting tight control of ureteric lengthening and branching. This method will be of use in analysing ureteric growth in kidneys cultured in the presence of specific molecules suspected of regulating ureteric growth. The method can also be used to analyse in vivo kidneys and to quantify branching morphogenesis in other developing organs.     

Innervation pattern of the gill arches and gills of the carp (Cyprinus carpio)

The innervation pattern of the respiratory gill arches of the carp (Cyprinus carpio) is described. The gill region is innervated by the branchial branches of the glossopharyngeal and vagal nerves. Each branchial nerve divides at the level of or just distal to the epibranchial ganglion into: 1) a pretrematic branch, 2) a dorsal pharyngeal branch, and 3) a posttrematic branch. The dorsal pharyngeal branch innervates the palatal organ in the roof of the buccal cavity. The pretrematic and posttrematic branches innervate the posterior and anterior halves, respectively, of the gill arches bordering a gill slit. Each branch splits into an internal and an external part. The internal bundle innervates the buccal side of the gill arch, including the gill rakers. The external bundle terminates in the gill filaments. The epibranchial motor branch, a small nerve bundle containing only motor fibers, circumvents the ganglion and anastomoses distally with the posttrematic branch. The detailed course and branching patterns of these branches are described.     

四川大头茶的分枝率和顶芽动态

以四川大头茶植株的枝和顶芽为基本构件单元,对不同年龄级成熟植株的分枝率和枯芽数动态进行了研究。结果表明：四川大头茶成株任一种分枝率在种群内不同龄级植析间以及在同一植株内不同发育位置的主枝间无显著变化;而同一主枝内各类型分枝率并非按相同的几何及数增减,即枝内各类分枝率间具显著的差异。     

Interdependent regional lung emptying during forced expiration: a transistor model

We recognized similarities between isovolume pressure-flow curves of the lung and emitter-collector voltage-current characteristics of bipolar transistors, and used this analogy to model expiratory flow limitation in a two-generation branching network with parallel nonhomogeneity. In this model, each of two bronchi empty parenchymal compliances through a common trachea, and each branch includes resistances upstream and downstream of a flow-limiting site. Properties of each airway are specified independently, allowing simulation of differences between the tracheal and bronchial generations and between the parallel bronchial paths. Simulations of four types of parallel asymmetry were performed: unilateral peripheral bronchoconstriction; unilateral central bronchoconstriction; asymmetric redistribution of parenchymal compliance; and unilateral alteration of the bronchial area-transmural pressure characteristic. Our results indicate that multiple axial choke points can exist simultaneously in a symmetric lung when large airway opening-pleural pressure gradients exist; despite severe nonhomogeneity of regional lung emptying, flow interdependence among parallel branches tends to maintain a near normal configuration of the overall maximal expiratory flow-volume (MEFV) curve throughout a large fraction of the vital capacity; and sudden changes of slope of the MEFV curve ("knees" or "bumps") may reflect choking in one branch in a nonuniform lung, but need not be obvious even when severe heterogeneity of lung emptying exists.     

Human coronary arteries. II. Branching anatomical pattern and arterial wall microarchitecture

A study on 22 pairs, including subjects of similar age, sex and cause of death but with different branching anatomical patterns, shows, that the amount and structural organization of elastic and muscular tissue of the thickened intima are strongly influenced by (a) the size, length, mode of ramification of the parent vessels of the coronary tree; (b) the number of branch orifices in a given arterial segment, and (c) the collateral or terminal character of certain daughter branches.     

Redistribution of water via layering branches between connected parent and daughter trees in Norway spruce clonal groups

Key message

We measured sap flow and shoot water potentials in clonally connected parent and daughter trees. We found bidirectional flow patterns in branches mediating the connection between parent and daughter trees.

Abstract

Layering is an important mode of vegetative reproduction at treeline, in which clonal daughter trees are formed by the rooting of lower (“layering”) branches of the parent tree. These branches mediate the connection between parent (PT) and daughter tree (DT). Here, we measured quantity and direction of sap flow in layering branches as well as PT and DT, and measured shoot water potentials in the crowns of a connected PT and DT. We found bidirectional sap flow pattern in layering branches, with the bidirectionality of the flow resulting from water potential dynamics of the parent and daughter trees varying diurnally. We found that 4.3 % of the total water transpired by the DT was supplied by the PT root system, with up to 25 % of the instantaneous daughter tree sap flow coming from the parent tree. In contrast, water provided by the daughter’s root system to the parent tree comprised only a negligible amount, less than 1 % of the parent’s entire sap flow. Additionally, after experimental excavation of part of the DT roots, layering branch flow towards the DT increased, while flows in the opposite direction almost vanished. This study showed that aboveground clonal connections can facilitate a new type of hydraulic redistribution where water is transported bidirectionally through branches. This transfer of water and nutrients is vital especially in the first years of the daughter tree but supplies considerable amounts of water even several years after the establishment of a new clonal tree.

     

Evaluating a non-destructive method for calibrating tree biomass equations derived from tree branching architecture

Key message

Functional branch analysis (FBA) is a promising non-destructive method that can produce accurate tree biomass equations when applied to trees which exhibit fractal branching architecture.

Abstract

Functional branch analysis (FBA) is a promising non-destructive alternative to the standard destructive method of tree biomass equation development. In FBA, a theoretical model of tree branching architecture is calibrated with measurements of tree stems and branches to estimate the coefficients of the biomass equation. In this study, species-specific and mixed-species tree biomass equations were derived from destructive sampling of trees in Western Kenya and compared to tree biomass equations derived non-destructively from FBA. The results indicated that the non-destructive FBA method can produce biomass equations that are similar to, but less accurate than, those derived from standard methods. FBA biomass prediction bias was attributed to the fact that real trees diverged from fractal branching architecture due to highly variable length–diameter relationships of stems and branches and inaccurate scaling relationships for the lengths of tree crowns and trunks assumed under the FBA model.     

Vessel network extraction and analysis of mouse pulmonary vasculature via X-ray micro-computed tomographic imaging

In this work, non-invasive high-spatial resolution three-dimensional (3D) X-ray micro-computed tomography (μCT) of healthy mouse lung vasculature is performed. Methodologies are presented for filtering, segmenting, and skeletonizing the collected 3D images. Novel methods for the removal of spurious branch artefacts from the skeletonized 3D image are introduced, and these novel methods involve a combination of distance transform gradients, diameter-length ratios, and the fast marching method (FMM). These new techniques of spurious branch removal result in the consistent removal of spurious branches without compromising the connectivity of the pulmonary circuit. Analysis of the filtered, skeletonized, and segmented 3D images is performed using a newly developed Vessel Network Extraction algorithm to fully characterize the morphology of the mouse pulmonary circuit. The removal of spurious branches from the skeletonized image results in an accurate representation of the pulmonary circuit with significantly less variability in vessel diameter and vessel length in each generation. The branching morphology of a full pulmonary circuit is characterized by the mean diameter per generation and number of vessels per generation. The methods presented in this paper lead to a significant improvement in the characterization of 3D vasculature imaging, allow for automatic separation of arteries and veins, and for the characterization of generations containing capillaries and intrapulmonary arteriovenous anastomoses (IPAVA).     

Finding the optimal lengths for three branches at a junction

This paper presents an exact analytical solution to the problem of locating the junction point between three branches so that the sum of the total costs of the branches is minimized. When the cost per unit length of each branch is known the angles between each pair of branches can be deduced following reasoning first introduced to biology by Murray. Assuming the outer ends of each branch are fixed, the location of the junction and the length of each branch are then deduced using plane geometry and trigonometry. The model has applications in determining the optimal cost of a branch or branches at a junction. Comparing the optimal to the actual cost of a junction is a new way to compare cost models for goodness of fit to actual junction geometry. It is an unambiguous measure and is superior to comparing observed and optimal angles between each daughter and the parent branch. We present data for 199 junctions in the pulmonary arteries of two human lungs. For the branches at each junction we calculated the best fitting value of x from the relationship that flow ∞ (radius)^x. We found that the value of x determined whether a junction was best fitted by a surface, volume, drag or power minimization model. While economy of explanation casts doubt that four models operate simultaneously, we found that optimality may still operate, since the angle to the major daughter is less than the angle to the minor daughter. Perhaps optimality combined with a space filling branching pattern governs the branching geometry of the pulmonary artery.     

Distribution of airway narrowing responses across generations and at branching points,assessed in vitro by anatomical optical coherence tomography

Background

Previous histological and imaging studies have shown the presence of variability in the degree of bronchoconstriction of airways sampled at different locations in the lung (i.e., heterogeneity). Heterogeneity can occur at different airway generations and at branching points in the bronchial tree. Whilst heterogeneity has been detected by previous experimental approaches, its spatial relationship either within or between airways is unknown.

Methods

In this study, distribution of airway narrowing responses across a portion of the porcine bronchial tree was determined in vitro. The portion comprised contiguous airways spanning bronchial generations (#3-11), including the associated side branches. We used a recent optical imaging technique, anatomical optical coherence tomography, to image the bronchial tree in three dimensions. Bronchoconstriction was produced by carbachol administered to either the adventitial or luminal surface of the airway. Luminal cross sectional area was measured before and at different time points after constriction to carbachol and airway narrowing calculated from the percent decrease in luminal cross sectional area.

Results

When administered to the adventitial surface, the degree of airway narrowing was progressively increased from proximal to distal generations (r = 0.80 to 0.98, P < 0.05 to 0.001). This ''serial heterogeneity'' was also apparent when carbachol was administered via the lumen, though it was less pronounced. In contrast, airway narrowing was not different at side branches, and was uniform both in the parent and daughter airways.

Conclusions

Our findings demonstrate that the bronchial tree expresses intrinsic serial heterogeneity, such that narrowing increases from proximal to distal airways, a relationship that is influenced by the route of drug administration but not by structural variations accompanying branching sites.