The αβ-tubulin heterodimer, the building block of microtubules, is subject to a large number of post-translational modifications, comparable in diversity to the intensively studied histone modifications. Although these unusual modifications are conserved throughout evolution, their functions have remained almost completely elusive. Recently, however, important advances in the understanding of how tubulin modifications regulate function and organization have been made.

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Post-translational modifications regulate microtubule function

Physically based deformable models have been widely embraced by the Computer Graphics community. Many problems outlined in a previous survey by Gibson and Mirtich [ GM97] have been addressed, thereby making these models interesting and useful for both offline and real-time applications, such as motion pictures and video games. In this paper, we present the most significant contributions of the past decade, which produce such impressive and perceivably realistic animations and simulations: finite element/difference/volume methods, mass-spring systems, meshfree methods, coupled particle systems and reduced deformable models based on modal analysis. For completeness, we also make a connection to the simulation of other continua, such as fluids, gases and melting objects. Since time integration is inherent to all simulated phenomena, the general notion of time discretization is treated separately, while specifics are left to the respective models. Finally, we discuss areas of application, such as elastoplastic deformation and fracture, cloth and hair animation, virtual surgery simulation, interactive entertainment and fluid/smoke animation, and also suggest areas for future research.

/pdf/physically-based-deformable-models-in-computer-graphics-rjirdt191n.pdf

Physically Based Deformable Models in Computer Graphics

Physically Based Deformable Models in Computer Graphics.

Microtubules create diverse arrays with specific cellular functions such as the mitotic spindle, cilia and bundles inside neurons. How microtubules are regulated to enable specific functions is not well understood. Recent work has shown that posttranslational modifications of the tubulin building blocks mark subpopulations of microtubules and selectively affect downstream microtubule-based functions. In this way, the tubulin modifications generate a "code" that can be read by microtubule-associated proteins in a manner analogous to how the histone code directs diverse chromatin functions. Here we review recent progress in understanding how the tubulin code is generated, maintained, and read by microtubule effectors.

The tubulin code.

We present an algorithm for the finite element simulation of elastoplastic solids which is capable of robustly and efficiently handling arbitrarily large deformation. In fact, our model remains valid even when large parts of the mesh are inverted. The algorithm is straightforward to implement and can be used with any material constitutive model, and for both volumetric solids and thin shells such as cloth. We also provide a mechanism for controlling plastic deformation, which allows a deformable object to be guided towards a desired final shape without sacrificing realistic behavior. Finally, we present an improved method for rigid body collision handling in the context of mixed explicit/implicit time-stepping.

/pdf/invertible-finite-elements-for-robust-simulation-of-large-uy1u8f7sae.pdf

Invertible finite elements for robust simulation of large deformation

This paper presents a deformable model that offers control of the isotropy or anisotropy of elastic material, independently of the way the object is tiled into volume elements. The new model is as easy to implement and almost as efficient as mass-spring systems, from which it is derived. In addition to controlled anisotropy, it contrasts with those systems in its ability to model constant volume deformations. We illustrate the new model by animating objects tiled with tetrahedral and hexahedral meshes.

/pdf/controlling-anisotropy-in-mass-spring-systems-3acnh5yirc.pdf

Controlling Anisotropy in Mass-Spring Systems

We present a system for sketching in 3D, which strives to preserve the degree of expression, imagination, and simplicity of use achieved by 2D drawing. Our system directly uses user-drawn strokes to infer the sketches representing the same scene from different viewpoints, rather than attempting to reconstruct a 3D model. This is achieved by interpreting strokes as indications of a local surface silhouette or contour. Strokes thus deform and disappear progressively as we move away from the original viewpoint. They may be occluded by objects indicated by other strokes, or, in contrast, be drawn above such objects. The user draws on a plane which can be positioned explicitly or relative to other objects or strokes in the sketch. Our system is interactive, since we use fast algorithms and graphics hardware for rendering. We present applications to education, design, architecture and fashion, where 3D sketches can be used alone or as an annotation of an existing 3D model.

/pdf/drawing-for-illustration-and-annotation-in-3d-p0dyt3v86r.pdf

Drawing for Illustration and Annotation in 3D

Tubulins are the major proteins within centriolar and axonemal structures. In all cell types studied so far, numerous alpha- and beta-tubulin isoforms are generated both by expression of a multigenic family and various post-translational modifications. We have developed a primary culture of human nasal epithelial cells where the ciliated cell differentiation process has been observed and quantified. We have used this system to study several properties concerning polyglutamylation and polyglycylation of tubulin. GT335, a monoclonal antibody directed against glutamylated tubulins, stained the centriole/basal bodies and the axonemes of ciliated cells, and the centrioles of non-ciliated cells. By contrast, axonemal but not centriolar tubulins were polyglycylated. Several polyglutamylated and polyglycylated tubulin isotypes were detected by two-dimensional electrophoresis, using GT335 and a specific monoclonal antibody (TAP952) directed against short polyglycyl chains. Immunoelectron microscopy experiments revealed that polyglycylation only affected axonemal tubulin. Using the same technical approach, polyglutamylation was shown to be an early event in the centriole assembly process, as gold particles were detected in fibrogranular material corresponding to the first cytoplasmic structures involved in centriologenesis. In a functional assay, GT335 and TAP952 had a dose-dependent inhibitory effect on ciliary beat frequency. TAP952 had only a weak effect while GT335 treatment led to a total arrest of beating. These results strongly suggest that in human ciliated epithelial cells, tubulin polyglycylation has only a structural role in cilia axonemes, while polyglutamylation may have a function both in centriole assembly and in cilia activity.

Polyglutamylation and polyglycylation of alpha- and beta-tubulins during in vitro ciliated cell differentiation of human respiratory epithelial cells.

This paper presents a modeling system which takes advantage of two-dimensional drawing knowledge to design three-dimensional free-form shapes. A set of mouse or tablet strokes is interpreted by the system as defining both a two-dimensional shape boundary and a displacement map. This information is used for pushing or pulling vertices of existing surfaces, or for creating vertices of new surface patches. To relieve the burden of 3D manipulation from the user, patches are automatically positioned in space. The iterative design process alternates a modeling by drawing sequence and a viewpoint change. To stay as close as possible to the traditional drawing experience, the system imposes the minimum number of constraints on the topology of either the strokes set or the resulting surface.

https://hal.inria.fr/inria-00537463/document

Relief: a modeling by drawing tool

Medicine is a discipline where visualization is an essential component of learning However, the three-dimensional, dynamic structure of the human body poses difficult teaching challenges There is a need for truly interactive computer tools that will enable students to create and manipulate computer models, not just watch them We propose different approaches with that goal in mind We were first interested in interactive physically-based animation of anisotropic elastic materials One possible application scenario is an anatomy course on heart physiology where students can build interactive samples of cardiac muscular tissue To achieve this, our model exhibits two key features The first one is a low computational cost that results in high frame rates; the second one is an intuitive \emph{system image} that ensures easy control by the user Next, we were interested in interaction in three dimensions using two-dimensional input, either for annotating existing models, or for creating new models; taking advantage of the fact that drawing practice is still considered a fundamental learning method by some anatomy teachers in the French medical school curriculum Our 3D drawing system has a stroke representation that enables drawing redisplay when the viewpoint changes Moreover, this representation can be mixed freely with existing polygonal surfaces for annotation purposes In contrast, our modeling by drawing tool uses information from both stroke geometry and the drawn image, to allow three-dimensional modeling without explicit depth specification

https://tel.archives-ouvertes.fr/tel-00528758/document

David Bourguignon

Papers

Controlling Anisotropy in Mass-Spring Systems

Drawing for Illustration and Annotation in 3D

Polyglutamylation and polyglycylation of alpha- and beta-tubulins during in vitro ciliated cell differentiation of human respiratory epithelial cells.

Relief: a modeling by drawing tool

Interactive Animation and Modeling by Drawing -- Pedagogical Applications in Medicine