Modelling protein three-dimensional structure using tritium planigraphy

We propose the use of data on the topography of the label-accessible surface of a protein molecule obtained by the method of tritium planigraphy as a criterion for choosing the optimal intermediate arrangements of alpha-helices in globular proteins so as to model their three-dimensional structures. This approach has been used for modelling the three-dimensional structure of parvalbumin III from pike. The proposed model has been compared with high-resolution X-ray structural data for a related protein, paryvalbumin from carp. The possibilities and limitations of this approach are discussed.     

Discriminating power of localized three-dimensional facial morphology

Many genetic syndromes involve a facial gestalt that suggests a preliminary diagnosis to an experienced clinical geneticist even before a clinical examination and genotyping are undertaken. Previously, using visualization and pattern recognition, we showed that dense surface models (DSMs) of full face shape characterize facial dysmorphology in Noonan and in 22q11 deletion syndromes. In this much larger study of 696 individuals, we extend the use of DSMs of the full face to establish accurate discrimination between controls and individuals with Williams, Smith-Magenis, 22q11 deletion, or Noonan syndromes and between individuals with different syndromes in these groups. However, the full power of the DSM approach is demonstrated by the comparable discriminating abilities of localized facial features, such as periorbital, perinasal, and perioral patches, and the correlation of DSM-based predictions and molecular findings. This study demonstrates the potential of face shape models to assist clinical training through visualization, to support clinical diagnosis of affected individuals through pattern recognition, and to enable the objective comparison of individuals sharing other phenotypic or genotypic properties.     

A three-dimensional topology optimization model for tooth-root morphology

To obtain the root of a lower incisor through structural optimization, we used two methods: optimization with Solid Isotropic Material with Penalization (SIMP) and Soft-Kill Option (SKO). The optimization was carried out in combination with a finite element analysis in Abaqus/Standard. The model geometry was based on cone-beam tomography scans of 10 adult males with healthy bone-tooth interface. Our results demonstrate that the optimization method using SIMP for minimum compliance could not adequately predict the actual root shape. The SKO method, however, provided optimization results that were comparable to the natural root form and is therefore suitable to set up the basic topology of a dental root.     

Modelling flow patterns in conical dendroid graptolites

Life-sized wire models of several different morphologies of conical dendroid graptolites were tested in a flume to observe the flow patterns within the rhabdosome. Testing over a range of unidirectional current speeds from 3 to 15 cm/s showed that upward-directed currents are produced within the cone, and a significant amount of the water that enters the cone through the upstream wall exits the top opening. These upward currents were most evident at speeds of 3–10 cm/s. Shorter cones, wide cones, less porous mesh, and downstream tilting each increased the amount of water exiting the top of the cone, especially at higher speeds. These findings are consistent with a mode of feeding in which conical forms received afferent currents into the sides of the cones, where food particles were captured, and waste efferent currents went out the top opening. This does not support the hypothesis that downward-directed, ciliary feeding currents produced the force necessary to propel the earliest planktic graptolites into the water column in the evolutionary transition from a benthic to a planktic mode of life. The suggestion that differing rhabdosomal morphologies may represent adaptations to differing paleocurrent regimes is supported. Dendroid rhabdosomal morphology may prove to be a useful paleoenvironmental tool, particularly as an indicator of current strengths, especially in fine-grained sediments where other current-indicative structures may be lacking. Graptolite, dendroid, flow, feeding, paleoecology.     

Modelling run-and-tumble chemotaxis in a shear flow

The biased random walk undergone by chemotactic bacteria such as Escherichia coli will be influenced at the microscopic level by flow in the ambient medium. In this paper, we model swimming bacteria being advected and rotated by a simple shear flow. Under certain scaling assumptions, we obtain an advection—diffusion equation for cell density, when the chemotactic response is small, which shows a coupling between the rotation and chemotaxis. We also present an alternative method for calculating the chemotactic flux in an unbounded region which is valid for more general chemotactic responses.     

One-dimensional and three-dimensional models of cerebrovascular flow

The Circle of Willis is a ring-like structure of blood vessels found beneath the hypothalamus at the base of the brain. Its main function is to distribute oxygen-rich arterial blood to the cerebral mass. One-dimensional (1D) and three-dimensional (3D) computational fluid dynamics (CFD) models of the Circle of Willis have been created to provide a simulation tool which can potentially be used to identify at-risk cerebral arterial geometries and conditions and replicate clinical scenarios, such as occlusions in afferent arteries and absent circulus vessels. Both models capture cerebral haemodynamic autoregulation using a proportional-integral (PI) controller to modify efferent artery resistances to maintain optimal efferent flow rates for a given circle geometry and afferent blood pressure. The models can be used to identify at-risk cerebral arterial geometries and conditions prior to surgery or other clinical procedures. The 1D model is particularly relevant in this instance, with its fast solution time suitable for real-time clinical decisions. Results show the excellent correlation between models for the transient efferent flux profile. The assumption of strictly Poiseuille flow in the 1D model allows more flow through the geometrically extreme communicating arteries than the 3D model. This discrepancy was overcome by increasing the resistance to flow in the anterior communicating artery in the 1D model to better match the resistance seen in the 3D results.     

Modelling of multi-phase flow in jet loop reactors

A model for the steady state flow in jet loop reactors with two-phase flow has been developed. The model can be used to predict the critical effect in a reversed flow jet loop fermenter. The calculated critical effect according to the model corresponds well to experimental data.     

The three-dimensional morphology of aggregates of native cotton cellulose microfibrils

The three-dimensional morphology of native bacterial cellulose is confirmed by scanning electron microscopy. In addition, it is shown by scanning electron microscopy, and transmission electron microscopy with positive staining by phosphotungstic acid ions that aggregates of microfibrils of native cotton cellulose have a similar structure. The results are consistent with previous reports on microfibrils of algal cellulose. These observations exclude a simple spinneret process as a mechanism of formation of the microfibrils of these sources of cellulose.     

From three-dimensional morphology to effective diffusivity in filamentous fungal pellets

Filamentous fungi are exploited as cell factories in biotechnology for the production of proteins, organic acids, and natural products. Hereby, fungal macromorphologies adopted during submerged cultivations in bioreactors strongly impact the productivity. In particular, fungal pellets are known to limit the diffusivity of oxygen, substrates, and products. To investigate the spatial distribution of substances inside fungal pellets, the diffusive mass transport must be locally resolved. In this study, we present a new approach to obtain the effective diffusivity in a fungal pellet based on its three-dimensional morphology. Freeze-dried Aspergillus niger pellets were studied by X-ray microcomputed tomography, and the results were reconstructed to obtain three-dimensional images. After processing these images, representative cubes of the pellets were subjected to diffusion computations. The effective diffusion factor and the tortuosity of each cube were calculated using the software GeoDict. Afterwards, the effective diffusion factor was correlated with the amount of hyphal material inside the cubes (hyphal fraction). The obtained correlation between the effective diffusion factor and hyphal fraction shows a large deviation from the correlations reported in the literature so far, giving new and more accurate insights. This knowledge can be used for morphological optimization of filamentous pellets to increase the yield of biotechnological processes.     

Modelling information exchange in worker-queen conflict over sex allocation

We investigate the conflict between queen and worker over sex allocation, specifically the allocation of the queen's eggs between workers and reproductives and the allocation of the reproductive eggs between male and female. In contrast to previous models, we allow workers to observe and use information about the strategy of the queen. We consider three conflict models: simultaneous (no information exchange), sequential (a one-way information exchange) and negotiated (an iterated two-way information exchange). We find that the first model produces sex ratios intermediate between the classic queen (1:1) and worker (1:3) optima. The second model, in which the worker has information about the queen's decisions, produces a different result and one that is somewhat counter-intuitive in that the sex ratios are less female-biased than for the other two models, and in fact are often male-biased. The third model predicts sex ratios intermediate between the first two models. We discuss how these findings may shed new light on observed sex allocation patterns in social insects and we suggest some experimental tests.     

Current flow and potential in a three-dimensional syncytium

Analytical solutions are obtained describing the spread of potential in a continuous syncytium which is the three-dimensional analogue of the “cable” and “thin sheet” models. Two discrete (finite-element) models are also developed and their behaviour shown to agree with that of the continuous model. All three models are able to account for the peculiarities of passive responses to intracellular current injection in tissues such as cardiac and smooth muscle. The time course and spread of junction potentials in electrically coupled tissues is discussed.     

Quantitative analysis of Neanderthal temporal bone morphology using three-dimensional geometric morphometrics

The temporal bone is the location of several traits thought to differentiate Neanderthals from modern humans, including some proposed Neanderthal-derived traits. Most of these, however, are difficult to measure and are usually described qualitatively. This study applied the techniques of geometric morphometrics to the complex morphology of the temporal bone, in order to quantify the differences observed between Neanderthal and modern human anatomy. Two hundred and seventy modern human crania were measured, representing 9 populations of 30 individuals each, and spanning the extremes of the modern human geographical range. Twelve Neanderthal specimens, as well as Reilingen, Kabwe, Skhul 5, Qafzeh 9, and 4 Late Paleolithic European specimens, were included in the fossil sample. The data were collected in the form of three-dimensional (3-D) landmark coordinates, and specimen configurations were superimposed using generalized Procrustes analysis. The fitted coordinates were then analyzed by an array of multivariate statistical methods, including principal components analysis, canonical variates analysis, and Mahalanobis D(2). The temporal bone landmark analysis was very successful in separating Neanderthals from modern humans. Neanderthals were separated from modern humans in both the principal components and canonical variates analyses. They were much further in Mahalanobis distances from all modern human populations than any two modern human groups were from each other. Most of the previously described temporal bone traits contributed to this separation.     

Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images

Experimental and theoretical studies demonstrate that both global dendritic branching topology and fine spine geometry are crucial determinants of neuronal function, its plasticity and pathology. Importantly, simulation studies indicate that the interaction between local and global morphologic properties is pivotal in determining dendritic information processing and the induction of synapse-specific plasticity. The ability to reconstruct and quantify dendritic processes at high resolution is therefore an essential prerequisite to understanding the structural determinants of neuronal function. Existing methods of digitizing 3D neuronal structure use interactive manual computer tracing from 2D microscopy images. This method is time-consuming, subjective and lacks precision. In particular, fine details of dendritic varicosities, continuous dendritic taper, and spine morphology cannot be captured by these systems. We describe a technique for automated reconstruction of 3D neuronal morphology from multiple stacks of tiled confocal and multiphoton laser scanning microscopy (CLSM and MPLSM) images. The system is capable of representing both global and local structural variations, including gross dendritic branching topology, dendritic varicosities, and fine spine morphology with sufficient resolution for accurate 3D morphometric analyses and realistic biophysical compartment modeling. Our system provides a much needed tool for automated digitization and reconstruction of 3D neuronal morphology that reliably captures detail on spatial scales spanning several orders of magnitude, that avoids the subjective errors that arise during manual tracing with existing digitization systems, and that runs on a standard desktop workstation.     

Artificial neural networks and three-dimensional digital morphology: a pilot study

In this pilot study, we used an unsupervised learning algorithm for self-organization and pattern matching to create feature maps that can be applied to morphological problems. We designed a network to analyze 83 first and/or second upper and lower molar sets representing 13 anthropoid primate species, based on three-dimensional measures obtained from laser-digitized, virtual specimens. As shown in a comparison with a principal-component analysis of the virtual specimens, the artificial neural network approach provided more biologically meaningful information than the conventional multivariate analysis approach. The methodology discovered partitions and hierarchical clusters consistent with anthropoid systematics, from the species (or subspecies) level to the highest categories, by sorting and allocating upper and lower molar teeth. As one might expect, measures of upper molars were richer in phenetic information than those of lower molars, even among the anatomically diverse platyrrhines. We also show that reducing taxonomic noise (i.e. biological variation) by limiting the analysis to a monophyletic subset improves discrimination.     

城市三维空间形态的热环境效应研究进展

城市的三维空间形态,通过影响地表能量平衡过程和空气流动,改变城市内部热环境,并可能加剧城市热岛效应。在三维空间上定量解析格局-过程-效应关系对于城市生态安全和可持续发展具有重要意义,可为城市生态规划与景观设计提供重要科学依据。从城市三维形态的热环境效应研究角度,综述了城市三维形态的定量化研究进展;总结了城市三维形态对热环境以及空气流动、太阳辐射等过程的影响;分析了当前城市三维形态的热环境效应研究领域存在的不足。未来的研究应注重建筑与植被三维特征的综合表征,三维形态指标的选择应综合考虑其对设计规划的指导作用,并加强城市三维形态对热环境影响机理及其尺度效应的研究。     

Human osteoblast-like cells in three-dimensional culture with fluid flow

In a previous study, we showed that the combination of appropriately designed three-dimensional (3D) microcarrier scaffolds and fluid flow through and around the scaffolds during high aspect ratio vessel (HARV) rotation enhances the elaboration of mineralized bone matrix by osteoblast-like cells. In this study, we describe the ongoing characterization of our 3D culture system, including the investigation of interior fluid flow within the scaffolds and early stage integrin expression during hydrodynamic culture. Using theoretical and experimental methods, we have estimated that cells cultured on the interior of microcarrier scaffolds experience an interior nutrient flow velocity between 1 x 10(-3) and 1 x 10(-2) cm/s and maximum shear stress of 0.03 N/m(2). Under these conditions, osteoblast-like cells grew extensively in the interior regions of the scaffold and retained their osteoblastic phenotype as measured by alkaline phosphatase. In addition, flow cytometric analysis of the overall cell population showed that cells constitutively expressed integrin alpha3beta1 during 3D hydrodynamic culture.