Transduction of cell and matrix geometric cues by the actin cytoskeleton

Engineered culture substrates have proven invaluable for investigating the role of cell and extracellular matrix geometry in governing cell behavior. While the mechanisms relating geometry to phenotype are complex, it is clear that the actin cytoskeleton plays a key role in integrating geometric inputs and transducing these cues into intracellular signals that drive downstream biology. Here, we review recent progress in elucidating the role of the cell and matrix geometry in regulating actin cytoskeletal architecture and mechanics. We address new developments in traditional two-dimensional culture paradigms and discuss efforts to extend these advances to three-dimensional systems, ranging from nanotextured surfaces to microtopographical systems (e.g. channels) to fully three-dimensional matrices.     

Optimization of the catalytic properties of Aspergillus fumigatus phytase based on the three-dimensional structure

Previously, we determined the DNA and amino acid sequences as well as biochemical and biophysical properties of a series of fungal phytases. The amino acid sequences displayed 49-68% identity between species, and the catalytic properties differed widely in terms of specific activity, substrate specificity, and pH optima. With the ultimate goal to combine the most favorable properties of all phytases in a single protein, we attempted, in the present investigation, to increase the specific activity of Aspergillus fumigatus phytase. The crystal structure of Aspergillus niger NRRL 3135 phytase known at 2.5 A resolution served to specify all active site residues. A multiple amino acid sequence alignment was then used to identify nonconserved active site residues that might correlate with a given favorable property of interest. Using this approach, Gln27 of A. fumigatus phytase (amino acid numbering according to A. niger phytase) was identified as likely to be involved in substrate binding and/or release and, possibly, to be responsible for the considerably lower specific activity (26.5 vs. 196 U x [mg protein](-1) at pH 5.0) of A. fumigatus phytase when compared to Aspergillus terreus phytase, which has a Leu at the equivalent position. Site-directed mutagenesis of Gln27 of A. fumigatus phytase to Leu in fact increased the specific activity to 92.1 U x (mg protein)(-1), and this and other mutations at position 27 yielded an interesting array of pH activity profiles and substrate specificities. Analysis of computer models of enzyme-substrate complexes suggested that Gln27 of wild-type A. fumigatus phytase forms a hydrogen bond with the 6-phosphate group of myo-inositol hexakisphosphate, which is weakened or lost with the amino acid substitutions tested. If this hydrogen bond were indeed responsible for the differences in specific activity, this would suggest product release as the rate-limiting step of the A. fumigatus wild-type phytase reaction.     

High resolution electron tomography and segmentation‐by‐modeling interpretation in Bsoft

Bsoft offers many tools for the processing of tomographic tilt series and the interpretation of tomograms. Since I introduced tomography into Bsoft almost two decades ago, the field has advanced significantly, requiring refinement of old algorithms and development of new ones. The current direct detectors allow us to collect data more efficiently and with better quality, progressing towards automation. The goal is then to also automate alignment of tilt series and reconstruction. I added an estimation of the specimen thickness as well as fiducialless alignment, to augment the existing fiducial‐based alignment. High‐resolution work requires correction for the contrast transfer function, in tomography complicated by the tilted specimen. For this, I developed a method to generate a power spectrum using the whole micrograph, compensating for tilting. This is followed by routine determination of the contrast transfer function, and correction for it during reconstruction. The next steps involve interpretation of the tomogram, either by subtomogram averaging where possible, or by segmentation and modeling otherwise. Such interpretation actually constitutes the main time‐consuming part of tomography and is less amenable to automation compared to the initial reconstruction.     

三维几何形态学概述及其在昆虫学中的应用

长期以来二维（two-dimensional, 2D）数据是几何形态学（geometric morphometrics）分析的最主要的数据类型,在推动几何形态学的发展过程中起到了奠基性的作用,并也解决了很多重大的科学问题,展示了几何形态学强大的科学计算能力与问题解决能力。但有些特殊的科学问题或者特殊的形态结构,无法通过二维数据完美解决,亟需大规模、大尺度三维（three-dimensional, 3D）数据的支持,这对几何形态学的三维化发展提出需求。更重要的是,随着三维数据获取成本的日渐降低,大量三维数据涌现出来。因此,三维几何形态学应运而生。本文对三维几何形态学的原理及其应用进行了概述,重点探讨了三维几何形态学与二维几何形态学的异同点,并对前者的两个发展阶段（少量样本的形态模拟与准定量比较及大量样本的定量比较）进行了概述,评价了四维数据和有限元等方法的应用,指出了该方法在昆虫学领域的发展潜力,最后对该方法在样本量增加、硬件提升、数据分辨率提高、新算法的开发、分析结果的呈现及3D打印等方面的发展趋势进行了展望。     

Accuracy of computer-aided geometric 3D reconstruction based on histological serial microgrinding preparation

Purpose: For our research on computer-optimised and automated cochlear implant surgery, we pursue a model-based approach to overcome the limitations of currently available clinical imaging modalities. A serial cross section preparation procedure has been developed and evaluated concerning accuracy to serve for modelling of a digital anatomic atlas to make delicate soft tissue structures available for pre-operative planning.

Methods: A special grinding tool was developed allowing the setting of a specific amount of abrasion as equidistant slice thickness was considered a crucial step. Additionally, each actual abrasion was accurately measured and used during three-dimensional reconstruction of the serial cross-sectional images obtained via digital photo documentation after each microgrinding step. A well-known reference object was prepared using this procedure and evaluated in terms of accuracy.

Results: Reconstruction of the whole sample was achieved with an error less than 0.4%, and the edge lengths in the direction of abrasion could be reconstructed with an average error of 0.6 ± 0.3 mm; both prove the realisation of equidistant abrasion. Using artificial registration fiducials and a custom-made algorithm for image alignment, parallelism and rectangularity could be preserved with average errors less than 0.4° ± 0.3°.

Conclusion: We present a systematic, practicable and reliable method for the geometrically accurate reconstruction of anatomical structures, which is especially suitable for the middle and inner ear anatomy including soft tissue structures. For the first time, the quality of such a reconstruction process has been quantified and successfully proven for its usability.     

Virtual taphonomy: A new method integrating excavation and postprocessing in an archaeological context

The objective of this paper was to integrate excavation and post‐processing of archaeological and osteological contexts and material to enhance the interpretation of these with specific focus on the taphonomical aspects. A method was designed, Virtual Taphonomy, based on the use and integration of image‐based 3D modeling techniques into a 3D GIS platform, and tested on a case study. Merging the 3D models and a database directly in the same virtual environment allowed the authors to fully integrate excavation and post‐processing in a complex spatial analysis reconnecting contexts excavated on different occasions in the field process. The case study further demonstrated that the method enabled a deeper understanding of the taphonomic agents at work and allowed the construction of a more detailed interpretation of the skeletal remains than possible with more traditional methods. The method also proved to add transparency to the entire research process from field to post‐processing and interpretation. Other benefits were the timesaving aspects in documentation, not only in the excavation process but also in post‐processing without creating additional costs in material, as the equipment used is available in most archaeological excavations. The authors conclude that this methodology could be employed on a variety of investigations from archaeological to forensic contexts and add significant value in many different respects (for example, detail, objectivity, complexity, time‐efficiency) compared to methods currently used. Am J Phys Anthropol 157:305–321, 2015. © 2015 Wiley Periodicals, Inc.     

A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

3D Modelling of Biological Systems for Biomimetics

1　IntroductionBasedonthereviewofthepreviousworkof 3Dgeometricalmodellingtechniquesandsystemsdevelopedforindustrial,medicalandanimationapplications,thispaperdiscussestheproblemsassociatedwiththeexist ingtechniquesandsystems ,especiallywhenappliedto3Dmodellingof plants ,insectsandanimalsforbiomimeticsresearchanddevelopment .Then ,paperproposessomeareasofresearchinterestsin 3Dmod ellingofplants ,insectsandanimalsforBiomimetics .Toavoidtherepeating ,inthispaper ,biologicalobjectswillbeusedtorep…     

Functional capabilities of modern and fossil hominid hands: three-dimensional analysis of trapezia

Three-dimensional (3D) trapezium models from Homo sapiens, Gorilla gorilla, Pan troglodytes, Australopithecus afarensis (A.L.333-80), and Homo habilis (O.H.7-NNQ) were acquired through laser digitizing. Least-square planes were generated for each articular surface, and the angles between the planes were compared. Each extant species displays an overall pattern that distinguishes it from the others. The observed angles in G. gorilla and P. troglodytes are more similar to one other than either is to H. sapiens. Our results, obtained from using new 3D modeling and analytical tools, raise interesting questions about the functional capabilities of the fossil trapezia. Multivariate statistical analyses indicate that A.L.333-80 is morphologically more similar to that of modern humans, whereas the O.H.7 trapezium is more similar to that of the gorilla. Significant differences between A.L.333-80 and the extant species occur, but some similarities to humans suggest the ability to form the distinctively human forceful pad-to-side and three-jaw chuck grips. Some key morphological differences from humans highlighted and quantified by our research suggest limitations in the functional capabilities of the O.H.7 trapezium, particularly in those that facilitate pronation at the base of the second metacarpal. If the O.H.7 trapezium represents part of the hand responsible for manufacturing and using the stone tools found at Olduvai, our results suggest that the hand manipulated the stones in a way for which we have no modern analog. Alternative considerations are that the O.H.7 trapezium is not representative of other trapezia from its species (i.e., N=1), or that it represents another primate or hominid species.     

Synchrotron radiation-based microcomputed tomography for three-dimensional growth analysis of Aspergillus niger pellets

Filamentous fungi produce a wide range of relevant biotechnological compounds. The close relationship between fungal morphology and productivity has led to a variety of analytical methods to quantify their macromorphology. Nevertheless, only a µ-computed tomography (µ-CT) based method allows a detailed analysis of the 3D micromorphology of fungal pellets. However, the low sample throughput of a laboratory µ-CT limits the tracking of the micromorphological evolution of a statistically representative number of submerged cultivated fungal pellets over time. To meet this challenge, we applied synchrotron radiation-based X-ray microtomography at the Deutsches Elektronen-Synchrotron [German Electron Synchrotron Research Center], resulting in 19,940 3D analyzed individual fungal pellets that were obtained from 26 sampling points during a 48 h Aspergillus niger submerged batch cultivation. For each of the pellets, we were able to determine micromorphological properties such as number and density of spores, tips, branching points, and hyphae. The computed data allowed us to monitor the growth of submerged cultivated fungal pellets in highly resolved 3D for the first time. The generated morphological database from synchrotron measurements can be used to understand, describe, and model the growth of filamentous fungal cultivations.     

Spatial and functional modeling of carnivore and insectivore molariform teeth

The interaction between the two main competing geometric determinants of teeth (the geometry of function and the geometry of occlusion) were investigated through the construction of three-dimensional spatial models of several mammalian tooth forms (carnassial, insectivore premolar, zalambdodont, dilambdodont, and tribosphenic). These models aim to emulate the shape and function of mammalian teeth. The geometric principles of occlusion relating to single- and double-crested teeth are reviewed. Function was considered using engineering principles that relate tooth shape to function. Substantial similarity between the models and mammalian teeth were achieved. Differences between the two indicate the influence of tooth strength, geometric relations between upper and lower teeth (including the presence of the protocone), and wear on tooth morphology. The concept of "autocclusion" is expanded to include any morphological features that ensure proper alignment of cusps on the same tooth and other teeth in the tooth row. It is concluded that the tooth forms examined are auto-aligning, and do not require additional morphological guides for correct alignment. The model of therian molars constructed by Crompton and Sita-Lumsden ([1970] Nature 227:197-199) is reconstructed in 3D space to show that their hypothesis of crest geometry is erroneous, and that their model is a special case of a more general class of models.     

基因组编辑技术在干细胞疾病模型建立和精准医疗中的应用

精准医疗强调针对不同个体定制个性化治疗方案,其推行需要精准疾病模型的建立。人类干细胞因其具有多能性而成为体外不同类型的成体细胞和器官小体的潜在来源,其强增殖能力保证了充足原材料用于科研分析和大规模药物筛选。基因组编辑技术(尤其是CRISPR/Cas9技术)的快速发展使得在人多能干细胞和成体干细胞中进行高效基因组编辑成为可能。两者的有效结合能建立起针对不同遗传致病背景的“个性化”疾病模型,有利于深入解析不同遗传突变的致病机制和开发高针对性的精准医疗方案。本文对基因组编辑技术在人类干细胞中的应用以及利用干细胞疾病模型模拟罕见病和肿瘤发生的研究进行了综述。     

Three-dimensional temporomandibular joint muscle attachment morphometry and its impacts on musculoskeletal modeling

In musculoskeletal models of the human temporomandibular joint (TMJ), muscles are typically represented by force vectors that connect approximate muscle origin and insertion centroids (centroid-to-centroid force vectors). This simplification assumes equivalent moment arms and muscle lengths for all fibers within a muscle even with complex geometry and may result in inaccurate estimations of muscle force and joint loading. The objectives of this study were to quantify the three-dimensional (3D) human TMJ muscle attachment morphometry and examine its impact on TMJ mechanics. 3D muscle attachment surfaces of temporalis, masseter, lateral pterygoid, and medial pterygoid muscles of human cadaveric heads were generated by co-registering measured attachment boundaries with underlying skull models created from cone-beam computerized tomography (CBCT) images. A bounding box technique was used to quantify 3D muscle attachment size, shape, location, and orientation. Musculoskeletal models of the mandible were then developed and validated to assess the impact of 3D muscle attachment morphometry on joint loading during jaw maximal open-close. The 3D morphometry revealed that muscle lengths and moment arms of temporalis and masseter muscles varied substantially among muscle fibers. The values calculated from the centroid-to-centroid model were significantly different from those calculated using the ‘Distributed model’, which considered crucial 3D muscle attachment morphometry. Consequently, joint loading was underestimated by more than 50% in the centroid-to-centroid model. Therefore, it is necessary to consider 3D muscle attachment morphometry, especially for muscles with broad attachments, in TMJ musculoskeletal models to precisely quantify the joint mechanical environment critical for understanding TMJ function and mechanobiology.     

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

The similarity between folding and binding led us to posit the concept that the number of protein-protein interface motifs in nature is limited, and interacting protein pairs can use similar interface architectures repeatedly, even if their global folds completely vary. Thus, known protein-protein interface architectures can be used to model the complexes between two target proteins on the proteome scale, even if their global structures differ. This powerful concept is combined with a flexible refinement and global energy assessment tool. The accuracy of the method is highly dependent on the structural diversity of the interface architectures in the template dataset. Here, we validate this knowledge-based combinatorial method on the Docking Benchmark and show that it efficiently finds high-quality models for benchmark complexes and their binding regions even in the absence of template interfaces having sequence similarity to the targets. Compared to "classical" docking, it is computationally faster; as the number of target proteins increases, the difference becomes more dramatic. Further, it is able to distinguish binders from nonbinders. These features allow performing large-scale network modeling. The results on an independent target set (proteins in the p53 molecular interaction map) show that current method can be used to predict whether a given protein pair interacts. Overall, while constrained by the diversity of the template set, this approach efficiently produces high-quality models of protein-protein complexes. We expect that with the growing number of known interface architectures, this type of knowledge-based methods will be increasingly used by the broad proteomics community.     

Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1

We present an original approach based on full-atom normal mode analysis (NMA) aimed to expand the general framework of homology modeling. Using the rat heme-free oxygenase 1 as a case system, we show how NMA can be used to model different physiologically relevant conformations of the same protein. Starting from a unique heme-bound X-ray structure, and using two structural templates corresponding to a human and an incomplete rat heme-free structures, we generate models of the rat unbound species with open and closed conformations. Less than 100 lowest frequency modes of the target were sufficient to obtain the heme-free conformations, the closest to the templates. The rat HO-1 model built for the open form shows features similar to the open form of the human heme-free oxygenase, and the one built for the closed form was similar to the incompletely resolved X-ray structure of the same protein available in the Protein DataBank. In the latter case, the use of NMA was particularly useful since it allowed to build a complete structure and therefore to discuss on the reason of the structural differences between open and closed forms. This study shows that the amount of main chain flexibility provided by the normal modes can lead to major improvements in homology modeling approaches. Such applications will allow the characterization of alternative conformations of a target protein with respect to the templates and/or the construction of good quality 3D models based on existing templates with unresolved parts in their tertiary structure.     

The effect of three-dimensional glottal geometry on intraglottal quasi-steady flow distributions and their relationship with phonation

Vocal fold geometry plays an important role in human phonation. The intraglottal quasi-steady pressure and velocity distributions depend upon the shape, size, and diameter of the glottis. This study reports the effects of the variation of glottal shapes on intraglottal pressures and velocities using a Plexiglas model with a glottis having nine symmetric glottal angles (uniform, as well as convergent and divergent 5°, 10°, 20° and 40°), while the minimal glottal diameter was held constant at 0.06 cm. The empirical data were supported by penalty finite element computational results. The results suggest that larger convergent glottal angles correspond to increased pressures and decreased velocities in the glottis upstream of the minimum glottal location, with a reversal of this pattern at the minimal glottal diameter location. The pressure dip near the glottal entrance for divergent glottal angles was greatest for the 10° divergence angle condition, and was sequentially less for 5°, 20°, and 40°. Flow resistance was greater for a convergent angle than a divergent angle of the same value, and least for the 10° divergent condition. Pressure recovery in the glottis suggested that the optimal glottal diffuser angle was near 10°. Results suggest that the glottal geometry has a critical relationship with phonation (especially for vocal efficiency), and therefore important significance to understanding artistic voice and clinical voice management.     

米根霉富马酸酶三维结构的同源建模与分析

利用Modeller7v7软件对米根霉（Rhizopus oryzoe）富马酸酶（fumarase）进行了三级结构的同源建模并对结果的空间和能量上的合理性进行了验证,进一步对酶的结构域和催化活性位点进行了研究。结果表明：富马酸酶由三个结构域组成,中心区域为一个由五个几乎平行的α螺旋组成的独特的束型结构,其催化活性位点是由三个亚基上的氨基酸相互靠近共同组成的。为以后有针对性的进行富马酸酶的定点突变提高富马酸产量提供分子水平上的理论指导。     

The effect of three-dimensional glottal geometry on intraglottal quasi-steady flow distributions and their relationship with phonation

In order to model laryngeal aerodynamics from a quasi-steady point of view[1], both the dynamic distri-bution of intraglottal air pressures that act upon the vocal folds and the tissue properties of the vocal folds are required[2]. Concerning the first po…     

Tinkerbell—A Tool for Interactive Segmentation of 3D Data

A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed.     

Comparative analysis of protein aggregates by blue native electrophoresis and subsequent sodium dodecyl sulfate-polyacrylamide gel electrophoresis in a three-dimensional geometry gel

We describe the comparative analysis of protein aggregates by combining blue native electrophoresis and subsequent sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using a 3-D geometry gel for simultaneous processing of many samples. The first native electrophoresis step, separating the aggregates, is carried out for a series of samples in parallel lanes within a slab gel. This gel is then placed on the top surface of a cylindrical, 3-D geometry gel for the second denaturing electrophoresis step, separating the proteins composing the aggregates. The samples migrate parallel to the vertical axis of the gel cylinder. Data are acquired online by photodetection of laser-induced fluorescence during electrophoresis. For this purpose, the samples are fluorescently labeled within the slab gel after the first separation step. A 3-D geometry gel separates the equivalent of many conventional SDS slab gels represented by vertical layers in the 3-D gel body. In this way, many samples are analyzed in the same gel under identical conditions, improving comparability and resolution and making the process considerably more efficient. This novel technique allowed the identification of several aggregate classes of recombinant proteins expressed in bacteria. We observed that proteins preferentially bind to homolog polypeptides, but also seem to form a trapping mesh co-aggregating with other proteins. The aggregation pattern revealed by this technique supplements data obtained from standard two-dimensional gel electrophoresis analysis. We expect interesting applications, for instance in aggregate monitoring of clinical samples. It should be feasible to quickly gain a diagnostic picture during amyloid-related neurodegenerative disease development or to observe drug effects on protein aggregation.