The Dynamic Cell: A New Concept for Teaching Molecular Cell Biology.

The Dynamic Cell is a CD-ROM program intended as a resource for students and instructors of molecular and cellular biology. The content of the program is oriented exclusively toward basic science and includes no clinical correlations. It approaches the level, though not the scope of, the textbooks, Molecular Biology of the Cell and Molecular Cell Biology [1, 2]. The latter text, incidentally, comes with a CD-ROM of animations, video clips, quiz questions, and other resources.

The content of Dynamic Cell is organized into five main topic areas (deep cytosol, apical membrane, basal membrane, nucleus, and extracellular matrix), provided as animated three-dimensional (3-D) scenes. For each of the five main scenes, a stripping function allows the user to remove successive layers and gain access to underlying structures. As the cursor is moved over structures in a scene, identifying labels appear. Clicking on a structure opens a menu of relevant topics, each of which opens a pop-up window. There are 130 pop-up windows in total. Each includes an illustration and scrollable text as well as buttons that turn figure labels and captions on or off (default is off), a back button that allows retracing of one's steps, and a print button.

The illustrations in the pop-up windows are of cells, cellular components, and cellular processes. They include transmission and scanning electron micrographs, fluorescently labeled light micrographs, and line drawings. Most of the animations are line drawings; some are 3-D drawings; and some are of real cells labeled fluorescently. Animations come with a scroll bar that allows regulation of the speed and direction of viewing. The scrollable text to the right of each illustration discusses the illustrated topic and provides color-coded hyperlinks that connect to a glossary or to a molecular structure (which can be viewed in different forms and rotated using built-in Rasmol software) or that cross-reference to other pop-up windows.

The user can navigate material in the program via the 3-D scenes and pop-up window hyperlinks or by using an index of terms available from the main menu bar and organized both alphabetically and hierarchically in tree form according to the five main topics. The back button in pop-up windows allows the user to return window by window to the first pop-up window of a series, though not to the starting point in the 3-D scene. A help function is available from the main menu bar to provide assistance with running the program. There are search functions for accessing the glossary and help sections of the program but none that access the main content of the program, namely, the text in the pop-up windows. There is no quiz function.

The program contains many good descriptions and animated illustrations of a wide variety of cellular processes including transcription, gene regulation, translation, DNA repair, traffic through nuclear pores, synthesis of membrane proteins, glycosylation, protein retention in rough endoplasmic reticulum (ER), receptor-mediated endocytosis, ATP synthesis in mitochondria, microtubule-based movement of vesicles, receptor-mediated endocytosis, membrane channel function, and active transport. The accompanying pop-up window text is rich with hyperlinks to glossary items, molecular structures, other topics, and other animations that encourage exploration of the depth and interrelatedness of the topics covered.

There are a few bugs and other problems. Some of the hyperlinks do not work (e.g., “intracellular degradation of macromolecules” in the lysosome window, “divides the cell” in the mitosis window, “lipofuscin granule” in the autophagy window). The back button sometimes skips a window in a sequence. There are typographical errors in some of the figure labels and captions.

Two aspects of the program may cause confusion especially for the novice. The first is that some concepts are not well illustrated. An example of this is in a set of three animations that relate to collagen synthesis. The first begins with a view of a cell showing nucleus, rough ER, smooth ER, and plasma membrane (no Golgi apparatus), then zooms into the rough ER, which looks like a cisterna with membrane outpouchings rather than ribosomes. Three procollagen helices appear in the lumen, assemble into a triple helix, and transfer to the Golgi apparatus (what was smooth ER is now labeled Golgi apparatus). Procollagen is secreted; propeptides are cleaved; and collagen fibrils assemble extracellularly. In the second animation, the rough ER does have ribosomes, and there is a Golgi apparatus from the start, but the Golgi apparatus and trans Golgi network are shown on opposite sides of the rough ER, and the procollagen triple helix goes directly from the rough ER to the trans Golgi network. The third animation focuses on assembly and does not show any cellular components. It shows formation of the procollagen triple helix (incorrectly labeled as an alpha helix) and further assembly into collagen fibrils without illustrating propeptides and their cleavage. Thus, in these three animations, there is a combination of redundancy, inaccuracy, and inconsistency that together are likely to frustrate and confuse anyone not already familiar with the details being illustrated.

The second confusing aspect of the program has to do with the great variability in the relevance of pop-up menu items and hyperlinks. For example, the choices in the basal lamina menu are collagen overview, fibronectin, cell-cell junctions, and glycosaminoglycans. The collagen overview focuses on Type I collagen, which is not a component of the basal lamina, and the cell-cell junctions item leads to an illustration of an epithelial cell lateral junctional complex and a discussion that focuses on lateral junctions. Similarly, the choices in the nuclear envelope menu are nuclear envelope, membrane overview, lipid bilayer simulation, membrane processes, and nuclear envelope assembly and disassembly. Of these, two are directly relevant to nuclear envelope, and three take the user pretty far afield. These leaps of context are inherent in the nature of a program designed with extensive cross-referencing capability and indeed can be part of its strength. They are also very disorienting, however, especially for users unfamiliar with the material and therefore unable to judge relevance. It would be helpful if the menu choices came with some indication of whether an item is directly or peripherally relevant to the structure being explored. It would also be helpful if the back function in pop-up windows took the user all the way back to the original pop-up menu rather than just to the first pop-up window of a series.

Overall, the program provides a novel and stimulating approach to the study of basic concepts in molecular and cell biology. Because of the potential for confusion of novices, the program is probably not suitable for use by medical students. It can serve, however, as a useful resource for instructors of medical students looking for interesting ways to illustrate lectures. It may also be useful for molecular and cell biology majors and their instructors as a tool for exploring the field.