Use of animation in teaching cell biology

To address the different learning styles of students, and because students can access animation from off-campus computers, the use of digital animation in teaching cell biology has become increasingly popular. Sample processes from cell biology that are more clearly presented in animation than in static illustrations are identified. The value of animation is evaluated on whether the process being taught involves motion, cellular location, or sequential order of numerous events. Computer programs for developing animation and animations associated with cell biology textbooks are reviewed, and links to specific examples of animation are given. Finally, future teaching tools for all fields of biology will increasingly benefit from an expansion of animation to the use of simulation. One purpose of this review is to encourage the widespread use of animations in biology teaching by discussing the nature of digital animation.     

Aldehydo-oligonucleotides for Bioconjugation

Abstract

The synthesis of a new phosphoramidite building block with a masked aldehyde function is described. It was incorporated in an oligodeoxyribonucleotide. Coupling to amino derivatives by reductive animation was performed in high yield after unmasking the aldehyde function.     

Powerpoint2002新增动画功能在教学中的应用

本文通过几个教学实例，介绍了Powerpoint2002新增动画功能，对其中自定义动画中的“进入、强调、退出、动作路径”,都给出了应用。最主要的是给出了动画功能组合应用技巧，使得一些复杂的动画能够得以实现。     

Computer planning for distraction osteogenesis

Distraction osteogenesis of the mandible has found an application in the treatment of patients with a variety of different mandibular deformities. Compared with the relatively simple unidirectional distraction of long bones as described by Ilizarov, the three-dimensional distraction of the mandible is extremely complex. Whereas experience with orthognathic surgery clearly demonstrates that careful presurgical planning is necessary to achieve predictable outcomes, there are few reported methods for the planning of mandibular distraction. The authors have developed a method for planning distraction osteogenesis of the mandible that involves the use of three-dimensional modeling and animation to simulate distraction osteogenesis in virtual reality. The first step in the authors' treatment planning process is to obtain a three-dimensional computerized scan of the facial skeleton. From this scan, a three-dimensional wire-mesh model is built using animation software. With the same software, a virtual distractor is built and installed on the wire-mesh model. The osteotomies and the distraction process are then simulated. Finally, a recipe for sequencing the linear and angular changes of the distractor is calculated. The authors have used this planning process in seven patients (age range, 4 to 10 years): four with unilateral mandibular deformities and three with bilateral. The planning process has yielded predictable and reproducible results.     

Importance of the depressor septi nasi muscle in rhinoplasty: anatomic study and clinical application

An active depressor septi muscle can accentuate a drooping nasal tip and shorten the upper lip on animation. We have found that dissection and transposition of the depressor septi muscle during rhinoplasty can improve the tip-upper lip relationship in appropriately selected patients. Although the anatomy of the depressor septi muscle has been described, the anatomic variations of this muscle have not been previously reported. The goals of this study were two-fold: (1) to define the anatomic variations of the depressor septi muscle using 55 fresh cadaver dissections and (2) to develop a clinically applicable algorithm for modification of this muscle during rhinoplasty in those patients with a short upper lip and/or tip-upper lip imbalance. Fifty-five fresh cadavers were dissected, and the anatomic variations of the depressor septi muscle were recorded. Three variations of the depressor septi muscle were delineated: type I inserted fully into the orbicularis oris (62 percent); type II inserted into the periosteum and incompletely into the orbicularis oris (22 percent); and type III showed no, or rudimentary, depressor septi muscle (16 percent). Sixty-two patients over a 4-year period (from 1995 to 1999) were identified preoperatively with a hyperactive depressor septi diagnosed by a descending nasal tip and shortened upper lip on animation. These patients underwent dissection and transposition (not resection) of the paired depressor septi during rhinoplasty with improvement or correction of the tip-upper lip imbalance in 88 percent of cases. The anatomic study, surgical indications, rationale for the operative technique, and clinical cases are presented. Dissection and transposition of the depressor septi is a valuable adjunct to rhinoplasty in patients with a type I or II muscle variant.     

Facial animation in children with Möbius syndrome after segmental gracilis muscle transplant

M?bius syndrome is a complex congenital anomaly involving multiple cranial nerves, including the abducens (VI) and facial (II) nerves, and often associated with limb anomalies. Muscle transplantation has been used to address the lack of facial animation, lack of lower lip support, and speech difficulties these patients experience. The purpose of this study was to investigate the results of bilateral, segmental gracilis muscle transplantation to the face using the facial vessels for revascularization and the motor nerve to the masseter for reinnervation. The outcome of the two-stage procedure was assessed in 10 consecutive children with M?bius syndrome by direct interview, speech assessment, and oral commissure movement. Preoperative data were collected from direct questioning, viewing of preoperative videotapes, notes from prior medical evaluations, and rehabilitation medicine and speech pathology assessments. All of the patients developed reinnervation and muscle movement. The children who described self-esteem to be an issue preoperatively reported a significant posttransplant improvement. The muscle transplants produced a smile with an average commissure excursion of 1.37 cm. The frequency and severity of drooling and drinking difficulties decreased postoperatively in the seven symptomatic children. Speech difficulties improved in all children. Specifically, of the six children with bilabial incompetence, three received complete correction and three had significant improvement. Despite the length and complexity of these procedures, complications were minimal. Muscle transplantation had positive effects in all problematic areas, with a high degree of patient satisfaction and improvement in drooling, drinking, speech, and facial animation. The surgical technique is described in detail and the advantages over regional muscle transfers are outlined. Segmental gracilis muscle transplantation innervated by the motor nerve to the masseter is an effective method of treating patients with M?bius syndrome.     

Animation: a useful tool for protein molecular dynamicists,applied to hydrogen bonds in the active site of elastase

Massive amounts of coordinate data result from molecular dynamics calculations. The animation program MDKINO is a simple but powerful tool for previewing or reviewing the results. In recent simulations of elastase, we have examined hydrogen bonding patterns, conformational changes involving shifts in ring positions and rotations of amino acid side chains, electric fields in interatomic space, and electric forces acting on chosen nuclei. Animation is also useful for checking on the stability of calculations in progress. Simple programming techniques achieve acceptable levels of animation with readily available hardware (PS330 or PS390 display with a serial interface to a laboratory VAX). In about half an hour, it is possible to make and watch a color stereo “movie” of a selected subsystem of a simulation (up to 1 000 frames of about 100 atoms each).     

A CAL program to teach the basic principles of genetic engineering—a change from the traditional approach

An interactive computer-assisted learning program written for the BBC microcomputer to teach the basic principles of genetic engineering is described. The pro-gram makes extensive use of colour, graphics, and animation and is aimed at A-level students of biology. Students select, from a menu, to investigate one of a number of identified processes involved in the overall production of a protein, each of which is treated as a self-contained unit. An assessment of how much of the factual information the student has learned is provided in the form of a computer 'adventure game' which is not only challenging but fun to play. Briefly, the student is led into an imaginary laboratory and must choose from shelves those essential items (e.g. reagents, starting materials, techniques) to progress through several stages culminating in the production of genetically engineered bacteria capable of producing a specific protein.     

A 3D visualization and simulation of the individual human jaw

A new biomechanical three-dimensional (3D) model for the human mandible based on computer-generated virtual model is proposed. Using maps obtained from the special kinds of photos of the face of the real subject, it is possible to attribute personality to the virtual character, while computer animation offers movements and characteristics within the confines of space and time of the virtual world. A simple two-dimensional model of the jaw cannot explain the biomechanics, where the muscular forces through occlusion and condylar surfaces are in the state of 3D equilibrium. In the model all forces are resolved into components according to a selected coordinate system. The muscular forces act on the jaw, along with the necessary force level for chewing as some kind of mandible balance, preventing dislocation and loading of nonarticular tissues. In the work is used new approach to computer-generated animation of virtual 3D characters (called "Body SABA"), using in one object package of minimal costs and easy for operation.     

Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations

Based on previous molecular dynamics simulation results for acetylcholinesterase dimer, we calculate and analyse the electrostatic field fluctuations around the enzyme. The results show that dynamic features of the electrostatic field favor attraction of the positively-charged substrate. An Internet link to an animation of the results is also provided.     

Workshop on molecular animation

From February 25 to 26, 2010, in San Francisco, the Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for producing high-quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories.     

Molecular movies... coming to a lecture near you

Scientific visualizations are powerful tools for communicating the intricacies of cellular and molecular structures and dynamics. There is a disconnect, however, between the research data sets we seek to represent and the kinds of animation that allow us to visualize and communicate them. Scientists are increasingly turning to 3D animation software borrowed from the entertainment industry to import, animate, and even create simulations of their data.     

Molecular conformational space analysis using computer graphics: Going beyond FRODO

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.     

Design considerations and techniques for constructing video stimuli

Techniques for constructing video playback stimuli fall into five categories. The first three involve manipulating video sequences: (1) edited video is a temporal rearrangement of raw footage, (2) processed video applies global filtering algorithms to edited video, and (3) frame-manipulated video involves manually altering individual frames. The last two, (4) exemplar-based animation and (5) parameter-based animation, are synthetic models derived from visual parameters based on a single exemplar and sample data, respectively. Image-based approaches are straightforward to apply and preserve fine spatiotemporal detail. Synthetic stimuli are desirable when a large number of manipulations are called for and to ensure individual stimuli reflect population characteristics. Received: 13 December 1999 / Received in revised form: 25 February 2000 / Accepted: 1 March 2000     

Computer-generated animal model stimuli

Communication between animals is diverse and complex. Animals may communicate using auditory, seismic, chemosensory, electrical, or visual signals. In particular, understanding the constraints on visual signal design for communication has been of great interest. Traditional methods for investigating animal interactions have used basic observational techniques, staged encounters, or physical manipulation of morphology. Less intrusive methods have tried to simulate conspecifics using crude playback tools, such as mirrors, still images, or models. As technology has become more advanced, video playback has emerged as another tool in which to examine visual communication (Rosenthal, 2000). However, to move one step further, the application of computer-animation now allows researchers to specifically isolate critical components necessary to elicit social responses from conspecifics, and manipulate these features to control interactions. Here, I provide detail on how to create an animation using the Jacky dragon as a model, but this process may be adaptable for other species. In building the animation, I elected to use Lightwave 3D to alter object morphology, add texture, install bones, and provide comparable weight shading that prevents exaggerated movement. The animation is then matched to select motor patterns to replicate critical movement features. Finally, the sequence must rendered into an individual clip for presentation. Although there are other adaptable techniques, this particular method had been demonstrated to be effective in eliciting both conspicuous and social responses in staged interactions.     

Anisotropic network model: systematic evaluation and a new web interface

MOTIVATION: The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage. RESULTS: ANM has been evaluated on a large set of proteins to establish the optimal model parameters that achieve the highest correlation with experimental data and its limits of accuracy and applicability. Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones. Significant improvement in agreement with experiments is observed with increase in the resolution of the examined structure. A new server for ANM calculations is presented, which offers flexible options for controlling model parameters and output formats, interactive animation of collective modes and advanced graphical features. AVAILABILITY: ANM server (http://www.ccbb.pitt.edu/anm)     

Dephosphorylation of cell cycle-regulated proteins correlates with anoxia-induced suspended animation in Caenorhabditis elegans

Some metazoans have evolved the capacity to survive severe oxygen deprivation. The nematode, Caenorhabditis elegans, exposed to anoxia (0 kPa, 0% O(2)) enters into a recoverable state of suspended animation during all stages of the life cycle. That is, all microscopically observable movement ceases including cell division, developmental progression, feeding, and motility. To understand suspended animation, we compared oxygen-deprived embryos to nontreated embryos in both wild-type and hif-1 mutants. We found that hif-1 mutants survive anoxia, suggesting that the mechanisms for anoxia survival are different from those required for hypoxia. Examination of wild-type embryos exposed to anoxia show that blastomeres arrest in interphase, prophase, metaphase, and telophase but not anaphase. Analysis of the energetic state of anoxic embryos indicated a reversible depression in the ATP to ADP ratio. Given that a decrease in ATP concentrations likely affects a variety of cellular processes, including signal transduction, we compared the phosphorylation state of several proteins in anoxic embryos and normoxic embryos. We found that the phosphorylation state of histone H3 and cell cycle-regulated proteins recognized by the MPM-2 antibody were not detectable in anoxic embryos. Thus, dephosphorylation of specific proteins correlate with the establishment and/or maintenance of a state of anoxia-induced suspended animation.     

SMILE-shaded molecular imaging on low-cost equipment

The SMILE program runs under MS-DOS on IBM PC AT-compatible computers equipped with the SM640 or the PG640 Matrox graphic board. The program allows real-time three-dimensional (3D) animation and modeling of several isolated molecules that can be built from scratch, manipulated interactively and compared by superimposition.SMILE enables users to compute atomic partial charges, molecular surface area, molecular volume, electrostatic and nonbonded potential energies. PLUTO, ORTEP, and MMP2 input files are set up automatically. The program also provides simple access to crystal packing by real-time animation of the unit cell contents, interactive inspection of the relevant stereochemical parameters and fragment manipulation within the unit cell. SMILE animates stereo views and produces beautiful shaded 3D images (8 colors, 32 shades each) of molecules in many different styles—stick, ball-and-stick, CPK (space filling), and transparent CPK with backbone.     

Design and validation of a machine for reproducible precision insertion of femoral hip prostheses for preclinical testing

Preclinical testing of orthopaedic implants is becoming increasingly important to eliminate inferior designs before animal experiments or clinical trials are begun. Preclinical tests can include both laboratory bench tests and computational modeling. One problem with bench tests is that variability in prosthesis insertion can significantly influence the failure rate; this makes comparison of prostheses more difficult. To solve this problem an insertion method is required that is both accurate and reproducible. In this work, a general approach to the insertion of hip prostheses into femoral bones is proposed based on physically replicating an insertion path determined using computer animation. As a first step, the seated prosthesis position is determined from templates and femur radiographs. Three-dimensional images of the prosthesis and bone are then imported into computer animation software and an insertion path in the coronal plane is determined. The insertion path is used to determine the profile of a cam. By attaching the prosthesis to a carriage, which is pneumatically moved along this cam, the required insertion motion of the prosthesis in the coronal plane can be achieved. This paper describes the design and validation of the insertion machine. For the validation study, a nonsymmetric hip prosthesis design (Lubinus SPII, Waldemar Link, Germany) is used. It is shown that the insertion machine has sufficient accuracy and reproducibility for preclinical mechanical testing.     

Animated life cycles of fungi and plants with spores for teaching

The conveyance of knowledge of the life cycles performed by fungi and plants with spores is a challenge for teaching in university education. The life cycles of fungi, in particular, can be very complex and difficult to understand. This paper presents the development and implementation of a German and English educational software program, including seven animated life cycles of fungi, two animated developments of fungal meiosporangia, and two examples each for ferns, mosses, and algae (cryptogams). We could show that the use of the software supported the study of fungi and spore-producing plants. It was possible to identify attributes of usability that contributed to a high quality of the educational material in concrete teaching situations. Notably, an easy handling of the software and an appropriate amount of information per animation step are crucial. In addition to the didactic insights, the conversations between the animation designers and the mycologist on correct details of developmental processes in the animations lead to interesting questions concerning cell biology. Some of the resulting open questions are at the edge of currently available knowledge, e.g. concerning the transformation of a plasmodium into a high number of small fruiting bodies in myxomycetes or the dikaryotisation of monokaryotic hyphae after spermatisation in rust fungi.