Characterization of the Drosophila segment determination morphome

Here we characterize the expression of the full system of genes which control the segmentation morphogenetic field of Drosophila at the protein level in one dimension. The data used for this characterization are quantitative with cellular resolution in space and about 6 min in time. We present the full quantitative profiles of all 14 segmentation genes which act before the onset of gastrulation. The expression patterns of these genes are first characterized in terms of their average or typical behavior. At this level, the expression of all of the genes has been integrated into a single atlas of gene expression in which the expression levels of all genes in each cell are specified. We show that expression domains do not arise synchronously, but rather each domain has its own specific dynamics of formation. Moreover, we show that the expression domains shift position in the direction of the cephalic furrow, such that domains in the anlage of the segmented germ band shift anteriorly while those in the presumptive head shift posteriorly. The expression atlas of integrated data is very close to the expression profiles of individual embryos during the latter part of the blastoderm stage. At earlier times gap gene domains show considerable variation in amplitude, and significant positional variability. Nevertheless, an average early gap domain is close to that of a median individual. In contrast, we show that there is a diversity of developmental trajectories among pair-rule genes at a variety of levels, including the order of domain formation and positional accuracy. We further show that this variation is dynamically reduced, or canalized, over time. As the first quantitatively characterized morphogenetic field, this system and its behavior constitute an extraordinarily rich set of materials for the study of canalization and embryonic regulation at the molecular level.     

Shear stress distribution in arterial tree models, generated by constrained constructive optimization.

Models of arterial trees are generated by the algorithm of Constrained Constructive Optimization (CCO). Straight cylindrical, binary branching tubes are arranged in an optimized fashion so as to convey blood to the terminal sites of the tree, which are distributed over a predefined area, representing the tissue to be perfused. All terminal segments supply equal flows at a unique terminal pressure, and the radii of parent and daughter segments are related via a bifurcation law. The connective structure and geometry of the model are optimized according to a target function such as total intravascular volume. The shear rate between blood and the vessel walls is computed in each segment and a new method is presented for rescaling a given CCO tree to a desired value of shear rate in the root segment. The effect of viscosity varying with shear rate is evaluated and a new method is presented for rescaling a CCO-tree segment by segment to consistent values of radii and variable viscosity. Shear stress is evaluated for its deviation from being proportional to shear rate and then subjected to various types of analyses. Usually both, shear stress and its variability, are found to be larger in the smaller than in the larger segments of the CCO-model trees. However, it is shown how the shear-stress distribution can be reshuffled between small and large segments when rescaling a CCO tree to obey a different bifurcation law, while its whole geometry remains unchanged and all boundary conditions remain fulfilled. The selection of optimization target is found to drastically affect shear-stress variability within bifurcations, which reaches a distinct minimum if the model is optimized according to intravascular volume. Finally, a rank-analysis of shear stress within each bifurcation shows that only two out of six possible rank patterns actually occur: the parent segment always experiences medium shear stress while minimum shear stress resides mostly in the larger, less frequently in the smaller daughter.     

The influence of optimization target selection on the structure of arterial tree models generated by constrained constructive optimization

The computational method of constrained constructive optimization was used to generate complex arterial model trees by optimization with respect to a target function. Changing the target function also changes the tree structure obtained. For a parameterized family of target functions a series of trees was created, showing visually striking differences in structure that can also be quantified by appropriately chosen numerical indexes. Blood transport path length, pressure profile, and an index for relative segment orientation show clear dependencies on the optimization target, and the nature of changes can be explained on theoretical grounds. The main goal was to display, quantify, and explain the structural changes induced by different optimization target functions.     

Assessment of scapular morphology and bone quality with statistical models

The design of total shoulder arthroplasty implants are guided by anatomy. The objective of this study was to develop statistical models to quantify shape and material property variation in the scapula. Material-mapped models were reconstructed from CT scans for a training set of subjects. Statistical shape (SSM) and intensity (SIM) models were created; SSM modes described scaling, changes in the medial border and acromial process, and elongation of the scapular blade. SIM modes captured bone quality changes in the anterior and inferior glenoid. Bone quality was independent of scapular morphology. Variation described by the statistical representations can inform implant design and sizing.     

The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ

Background

Like human infants, songbirds learn their species-specific vocalizations through imitation learning. The birdsong system has emerged as a widely used experimental animal model for understanding the underlying neural mechanisms responsible for vocal production learning. However, how neural impulses are translated into the precise motor behavior of the complex vocal organ (syrinx) to create song is poorly understood. First and foremost, we lack a detailed understanding of syringeal morphology.

Results

To fill this gap we combined non-invasive (high-field magnetic resonance imaging and micro-computed tomography) and invasive techniques (histology and micro-dissection) to construct the annotated high-resolution three-dimensional dataset, or morphome, of the zebra finch (Taeniopygia guttata) syrinx. We identified and annotated syringeal cartilage, bone and musculature in situ in unprecedented detail. We provide interactive three-dimensional models that greatly improve the communication of complex morphological data and our understanding of syringeal function in general.

Conclusions

Our results show that the syringeal skeleton is optimized for low weight driven by physiological constraints on song production. The present refinement of muscle organization and identity elucidates how apposed muscles actuate different syringeal elements. Our dataset allows for more precise predictions about muscle co-activation and synergies and has important implications for muscle activity and stimulation experiments. We also demonstrate how the syrinx can be stabilized during song to reduce mechanical noise and, as such, enhance repetitive execution of stereotypic motor patterns. In addition, we identify a cartilaginous structure suited to play a crucial role in the uncoupling of sound frequency and amplitude control, which permits a novel explanation of the evolutionary success of songbirds.     

Ontogenetic perspective on mechanical and nonmechanical models of primate circumorbital morphology

Dimensions of the supraorbital torus, postorbital bar, and postorbital septum were collected in an ontogenetic series of Macaca fascicularis and compared with expectations based on models that attribute morphological variation in these features to spatial factors, allometry, anterior dental loading, and neurofacial torsion. Each model was evaluated using correlation, partial correlation, and regression techniques (model I/least squares; model II/reduced major axis) applied to log-transformed and size-corrected data. Results indicate clearly that face or skull size is the primary determinant of variation in circumorbital structures. Strong support is found for the influence of spatial influences on anteroposterior supraorbital torus development (Moss and Young, Am. J. Phys. Anthropol. 18:281-292, 1960). Only minor support is noted for the neurofacial torsion model of Greaves (J. Zool. 207:125-136, 1985), and no support is indicated for the anterior dental loading model. The sexes do not differ significantly in any relevant comparisons of ontogenetic trajectories.     

Interspecific perspective on mechanical and nonmechanical models of primate circumorbital morphology.

Linear dimensions and angular orientations of the browridge, postorbital bar, and postorbital septum were obtained from a representative series of primates and compared with variables associated with several nonmechanical and biomechanical/mechanical models put forward to explain the form and function of the circumorbital region. Analyses of the results indicate that face size is the primary determinant of variation in primate circumorbital morphology. Anteroposterior browridge thickness is correlated with neural-orbital disjunction among anthropoid primates, but not among prosimians. This difference appears related to differences in the construction of the upper face and anterior cranial fossa between prosimians and anthropoids. Little support is demonstrated for the anterior dental loading model of browridge development. Mediolateral postorbital bar width and (to a lesser degree) browridge height are correlated with neurofacial torsion during mastication and variation in masticatory muscle size. These analyses further suggest that since circumorbital structures (especially the browridges) are located the farthest away from the chewing apparatus, they are least affected by masticatory stresses.     

The morphology and phonology of metathesis in Amarasi

I describe and analyse data from Amarasi, a language with morphological consonant-vowel metathesis. Depending on the phonotactic structure of the stem to which it applies, metathesis is associated with a number of other phonological processes including: vowel deletion, consonant deletion and two kinds of vowel assimilation. By proposing that Amarasi has an obligatory CVCVC foot in which C-slots can be empty all these phonological processes can be derived from a single process of metathesis and one associated morphemically conditioned process. I consider analyses other than the rule-based one adopted in this paper and show that they cannot account for all the data in a consistent, plausible way.     

Subject-specific models of the hindfoot reveal a relationship between morphology and passive mechanical properties

The morphology of the bones, articular surfaces and ligaments and the passive mechanical characteristics of the ankle complex were reported to vary greatly among individuals. The goal of this study was to test the hypothesis that the variations observed in the passive mechanical properties of the healthy ankle complex are strongly influenced by morphological variations. To evaluate this hypothesis six numerical models of the ankle joint complex were developed from morphological data obtained from MRI of six cadaveric lower limbs, and from average reported data on the mechanical properties of ligaments and articular cartilage. The passive mechanical behavior of each model, under a variety of loading conditions, was found to closely match the experimental data obtained from each corresponding specimen. Since all models used identical material properties and were subjected to identical loads and boundary conditions, it was concluded that the observed variations in passive mechanical characteristics were due to variations in morphology, thus confirming the hypothesis. In addition, the average and large variations in passive mechanical behavior observed between the models were similar to those observed experimentally between cadaveric specimens. The results suggest that individualized subject-specific treatment procedures for ankle complex disorders are potentially superior to a one-size-fits-all approach.     

The cognitive neuroscience of constructive memory: remembering the past and imagining the future

Episodic memory is widely conceived as a fundamentally constructive, rather than reproductive, process that is prone to various kinds of errors and illusions. With a view towards examining the functions served by a constructive episodic memory system, we consider recent neuropsychological and neuroimaging studies indicating that some types of memory distortions reflect the operation of adaptive processes. An important function of a constructive episodic memory is to allow individuals to simulate or imagine future episodes, happenings and scenarios. Since the future is not an exact repetition of the past, simulation of future episodes requires a system that can draw on the past in a manner that flexibly extracts and recombines elements of previous experiences. Consistent with this constructive episodic simulation hypothesis, we consider cognitive, neuropsychological and neuroimaging evidence showing that there is considerable overlap in the psychological and neural processes involved in remembering the past and imagining the future.     

The morphology of apoptosis

The concept of apoptotic cell death as an essential part of the development and life of complex organisms has been devised in different situations and tested from various angles. This review article discusses the morphological changes during death by apoptosis. In cells undergoing apoptosis, an intracellular signalling pathway operates cell autonomously to implement the death and disposal of the cell. The similarity of the biochemical events during apoptosis in different situations is reflected by a high uniformity of morphological changes in many situations of naturally occurring or experimentally induced cell death. The unifying concept of apoptosis has been derived from the observation of this morphological consistency of dying cells almost 30 years ago. Since then, we have learned much about the intracellular signalling in the apoptotic process and the molecular background has been delineated which guides the initiation of the morphological changes. Here, an attempt is made to present the current knowledge about the molecular events in the development of these morphological alterations and to place these changes in the context of apoptotic cell death.     

Simulation modelling of ecological hierarchies in constructive dynamical systems

Organized complexity is a characteristic feature of ecological systems with heterogeneous components interacting at several spatio-temporal scales. The hierarchy theory is a powerful epistemological framework to describe such systems by decomposing them vertically into levels and horizontally into holons. It was at first developed in a temporal and functional perspective and then, in the context of landscape ecology, extended to a spatial and structural approach. So far, most ecological applications of this theory were restricted to observational purposes, using multi-scale analysis to describe hierarchies. In spite of an increasing attention to dynamics of hierarchically structured ecological systems, current simulation models are still very limited in their representation of self-organization in complex adaptive systems. An ontological conceptualization of the hierarchy theory is outlined, focusing on key concepts, such as levels of organization and the compound and component faces of the holons. Various existing formalisms are currently used in simulation modelling, such as system dynamics, discrete event and agent based paradigms. Their ability to express the hierarchical organization of dynamical ecological systems is discussed. It turns out that a multi-modelling approach linking all these formalisms and oriented toward the specification of a constructive dynamical system would be able to express the dynamical structure of the hierarchy (creation, destruction and change of holons) and the functional and structural links between levels of organization.     

气候变化条件下东北森林主要建群种的空间分布

全球气候模型HADCM2SUL和CC-CM1分别预测100a后全球年均温增加3．7℃和5．2℃,年降水增加30．7％和25．1％。为了研究东北森林对这两种预测方案的反应,使用logistic回归模型分析了东北森林8个建群种与11种环境因子之间的相关关系。结果表明,除了山杨和蒙古栎之外,年均温是决定其它树种存在与否的重要因子。采用模型结果预测现行气候条件下8个树种的分布并与其现实分布比较,发现针叶树种的总正确率、敏感度、指定度和错误肯定率均比阔叶树种的要高,而错误否定率比后者低,说明模型对针叶树种的拟合程度要优于对阔叶树种的拟合程度。在此基础上,预测了8个树种在两种气候变化方案下100a后的分布图。结果表明,在HADCM2SUL方案下,兴安落叶松、白桦、冷杉和云杉的覆盖率分别下降91．2％、67．4％、11．9％、10％;长白落叶松、红松和蒙古栎的覆盖率分别增长87．8％、54．6％、31．3％;在CGCM1方案下,兴安落叶松、白桦、云杉、冷杉和红松的覆盖率分别下降99．2％、89．9％、85．9％、83．2％、4．9％;长白落叶松、蒙古栎的覆盖率分别增长93．3％、27．5％;山杨在这两种方案下数量不变。