A novel metabolic form of the 32 kDa-D1 protein in the grana-localized reaction center of photosystem II

Two forms of the 32 kDa-D1 reaction center protein of photosystem II (PSII), having slightly different mobilities on denaturing polyacrylamide gels, have been resolved in Spirodela oligorrhiza, Glycine max L., Gossypium hirsutum L., Triticum aestivum L., and Zea mays L. The protein band with faster mobility is identified as the 32 kDa-D1 protein, and the less mobile band as a novel form, designated 32*. The two forms are structurally similar based on immunological and partial proteolytic tests. 32* is associated exclusively with the grana and is present in the PSII reaction center. Temporally, 32* appears several hours after the translocation of newly synthesized and processed 32 kDa-D1 protein from the stroma lamellae to the grana. Formation of the 32* is strictly light-dependent under physiological light intensities and correlates with a reciprocal loss of the 32-kDa form. Light induced formation of 32* is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea but is not coupled to linear electron transport.     

Electron microscopic analysis of the modulation of lymphocyte receptor mobility

The topographic distribution of ferritin-labelled concanavalin A (FT-ConA) bound to the surface membrane of mouse lymphocytes has been analysed by examining ultrathin sections and ghost membranes in the electron microscope. Binding of FT-ConA to lymphocytes at 37 °C did not induce redistribution of ConA receptors at any dose of the labelled lectin. In contrast, in cells treated with colchicine, FT-ConA induced both patch and cap formation. These findings suggest that the modulation of receptor mobility by colchicine occurs at the level of individual receptors. Ultrastructural observations revealed both microtubules and microfilaments in lymphocytes consistent with the suggestion that these cellular structures may be involved in the control of receptor mobility. Analyses using freeze-fracture methods indicated that the distribution of intramembranous particles is not correlated with either the movement of surface receptors or the modulation events. An hypothesis on the modulation of surface receptors by cytoplasmic structures is proposed on the basis of these and previous observations.     

Class similarity and viewpoint invariance in the recognition of 3D objects

 In human vision, the processes and the representations involved in identifying specific individuals are frequently assumed to be different from those used for basic level classification, because classification is largely viewpoint-invariant, but identification is not. This assumption was tested in psychophysical experiments, in which objective similarity between stimuli (and, consequently, the level of their distinction) varied in a controlled fashion. Subjects were trained to discriminate between two classes of computer-generated three-dimensional objects, one resembling monkeys and the other, dogs. Both classes were defined by the same set of 56 parameters, which encoded sizes, shapes, and placement of the limbs, ears, snout, etc. Interpolation between parameter vectors of the class prototypes yielded shapes that changed smoothly between monkey and dog. Within-class variation was induced in each trial by randomly perturbing all the parameters. After the subjects reached 90% correct performance on a fixed canonical view of each object, discrimination performance was tested for novel views that differed by up to 60° from the training view. In experiment 1 (in which the distribution of parameters in each class was unimodal) and in experiment 2 (bimodal classes), the stimuli differed only parametrically and consisted of the same geons (parts), yet were recognized virtually independently of viewpoint in the low-similarity condition. In experiment 3, the prototypes differed in their arrangement of geons, yet the subjects’ performance depended significantly on viewpoint in the high-similarity condition. In all three experiments, higher interstimulus similarity was associated with an increase in the mean error rate and, for misorientation of up to 45°, with an increase in the degree of viewpoint dependence. These results suggest that a geon-level difference between stimuli is neither strictly necessary nor always sufficient for viewpoint-invariant performance. Thus, basic and subordinate-level processes in visual recognition may be more closely related than previously thought. Received: 15 November 1993/Accepted in revised form: 14 July 1994     

A probabilistic methodology for integrating knowledge and experiments on biological networks.

Biological systems are traditionally studied by focusing on a specific subsystem, building an intuitive model for it, and refining the model using results from carefully designed experiments. Modern experimental techniques provide massive data on the global behavior of biological systems, and systematically using these large datasets for refining existing knowledge is a major challenge. Here we introduce an extended computational framework that combines formalization of existing qualitative models, probabilistic modeling, and integration of high-throughput experimental data. Using our methods, it is possible to interpret genomewide measurements in the context of prior knowledge on the system, to assign statistical meaning to the accuracy of such knowledge, and to learn refined models with improved fit to the experiments. Our model is represented as a probabilistic factor graph, and the framework accommodates partial measurements of diverse biological elements. We study the performance of several probabilistic inference algorithms and show that hidden model variables can be reliably inferred even in the presence of feedback loops and complex logic. We show how to refine prior knowledge on combinatorial regulatory relations using hypothesis testing and derive p-values for learned model features. We test our methodology and algorithms on a simulated model and on two real yeast models. In particular, we use our method to explore uncharacterized relations among regulators in the yeast response to hyper-osmotic shock and in the yeast lysine biosynthesis system. Our integrative approach to the analysis of biological regulation is demonstrated to synergistically combine qualitative and quantitative evidence into concrete biological predictions.