Spatial structure of complex cell receptive fields measured with natural images

Neuronal receptive fields (RFs) play crucial roles in visual processing. While the linear RFs of early neurons have been well studied, RFs of cortical complex cells are nonlinear and therefore difficult to characterize, especially in the context of natural stimuli. In this study, we used a nonlinear technique to compute the RFs of complex cells from their responses to natural images. We found that each RF is well described by a small number of subunits, which are oriented, localized, and bandpass. These subunits contribute to neuronal responses in a contrast-dependent, polarity-invariant manner, and they can largely predict the orientation and spatial frequency tuning of the cell. Although the RF structures measured with natural images were similar to those measured with random stimuli, natural images were more effective for driving complex cells, thus facilitating rapid identification of the subunits. The subunit RF model provides a useful basis for understanding cortical processing of natural stimuli.     

Scanning tunneling microscopic images show a laminated structure for glycogen molecules

Scanning tunneling microscopy (STM) has been used to examine glycogen molecules. Individual molecules were approximately ellipsoidal with dimensions in the 20- to 60-nm range. Images of the glycogen molecular surfaces have a laminar appearance. The layered features seen on the surfaces of the molecules suggest that glycogen may grow from one edge as a laminar structure to form an ellipsoid rather than originating at a central point with radial growth of the oligosaccharide chains to form a sphere. The results of these studies indicate that STM can be used to determine details of polysaccharide structures.     

Topological mirror images in protein structure computation: an underestimated problem.

When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.     

Spherical reconstruction: a method for structure determination of membrane proteins from cryo-EM images

We propose a new method for single-particle reconstruction, which should be generally applicable to structure determination for membrane proteins. After reconstitution into a small spherical vesicle, a membrane protein takes a particular orientation relative to the membrane normal, and its position in the projected image of the vesicle directly defines two of its three Euler angles of orientation. The spherical constraint imposed by the vesicle effectively reduces the dimensionality of the alignment search from 5 to 3 and simplifies the detection of the particle. Projection images of particles in vesicles collectively take all possible orientations and therefore cover the whole Fourier space. Analysis of images of vesicles in ice showed that the vesicle density is well described by a simple model for membrane electron scattering density. In fitting this model we found that osmotically swollen vesicles remain nearly spherical through the freezing process. These results satisfy the basic experimental requirements for spherical reconstruction. A computer simulation of particles in vesicles showed that this method provides good estimates of the two Euler angles and thus may improve single-particle reconstruction and extend it to smaller membrane proteins.     

Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination

Several factors, including spatial and temporal coherence of the electron microscope, specimen movement, recording medium, and scanner optics, contribute to the decay of the measured Fourier amplitude in electron image intensities. We approximate the combination of these factors as a single Gaussian envelope function, the width of which is described by a single experimental B-factor. We present an improved method for estimating this B-factor from individual micrographs by combining the use of X-ray solution scattering and numerical fitting to the average power spectrum of particle images. A statistical estimation from over 200 micrographs of herpes simplex virus type-1 capsids was used to estimate the spread in the experimental B-factor of the data set. The B-factor is experimentally shown to be dependent on the objective lens defocus setting of the microscope. The average B-factor, the X-ray scattering intensity of the specimen, and the number of particles required to determine the structure at a lower resolution can be used to estimate the minimum fold increase in the number of particles that would be required to extend a single particle reconstruction to a specified higher resolution. We conclude that microscope and imaging improvements to reduce the experimental B-factor will be critical for obtaining an atomic resolution structure.     

The delineation of nuclear boundaries in microscopic images

A semiautomatic procedure for tracking the boundaries of liver nuclei in digitized microscopic images of normally prepared biopsy material is described. The operator selects the nucleus, and a guided sequential search procedure tracks edge segments, which may subsequently be linked to produce a closed or partially open boundary, which is then accepted, completed or rejected by the user.     

Sequence, packing and nanometer scale structure in STM images of nucleic acids under water

Scanning tunneling microscope (STM) images of random-sequence nucleic acid polymers under water show internal structure which depends strongly on the packing density of the polymer. Images of dense aggregates have a semicrystalline order with the individual polymers adopting simple periodic structures. Loose aggregates (or isolated molecules) show structural variability with considerable local bending and curving on a nanometer scale. It is not clear to what extent this structure is induced by the operation of the microscope. In order to investigate the possibility that the structure is sequence directed, we have imaged various DNA and RNA polymers at low packing densities. We present results here for random sequence DNA, poly(dAT).poly(dAT), poly(dA).poly(dT), poly(dCG).poly(dCG) and for random sequence RNA and poly(U). In contrast to loose aggregates of the random sequence material, the homopolymers show few sharp bends. Furthermore, the homopolymers appear to yield characteristic backbone patterns, usually at resolutions in excess of that obtained with random sequence polymers. The random sequence polymers show much more evidence of image distortion due to tip-molecule interactions, suggesting that they are, on average, mechanically less stable in the STM tunnel-gap than the homopolymers. Thus, while some of the structure observed in STM images is a consequence of tip-molecule interactions, it is related to sequence-directed properties of the polymer.     

The digital processing of the images in x-ray microanalysis

Image analysis of X-ray microanalytical maps of sodium, potassium, phosphorus, chloride and calcium was carried out on the IBAS image analysis system (OPTON, FRG). In the present work, algorithms were developed for getting a new semiquantitative information from the binary images of maps: the element profile on the chosen line, the isoconcentration mapping and the multiple elemental mapping. It is possible to get as many as eight different elemental maps on the same image (with 8-bit resolution of pixel) and to extract the pixels with element overlappings.     

GUI programs for processing individual images in early stages of helical image reconstruction--for high-resolution structure analysis

A set of programs equipped with graphical user interface has been developed for processing individual images in early stages of the three-dimensional helical image reconstruction procedure. These programs can be used for initial screening of suitable image area, straightening the object image, determination of box parameters including the repeat distance, determination of the out-of-plane tilt and initial editing of the layer-line data. These tasks are difficult to automate and therefore very time-consuming. The programs, developed by adopting the concept of the layer-line indexing [Ultramicroscopy 84 (2000) 1-14], are effective for processing many images of filamentous molecular assemblies and especially tubular crystals having various helical classes. Using these programs, higher-resolution signals can be extracted more reliably and quickly, and the time required for processing each image can be reduced to 1/2-1/10. Here also presented is an overview on helical image reconstruction for high-resolution structure analysis.     

The resolution and discrimination of images in the visual system

We analysed the conformity of optic and retinal cones anatomy factors by the two-point test. Obtained by F. Campbell and R. W. Gubish, the point spread function has a width of about 1 arc min. Cones sizes are equal to 0.5 arc min in the fovea. Functional pixel consists of 3-5 cones under the point spread function. Such an organisation in very useful in decreasing the samping noise of receptors. We carried out psychophysical investigations to show a consensus among the optic, receptors', and neuronal levels. In experiments we studied changes of the two-point pattern perception in respect to the points separation, measured the orientation threshold of small size stimuli. Data were compared with optical point-spread function, the hexagonal mosaic of cones, and line spread function of spatial elements, which form spatial frequency channels at the cortical level.     

The structure of prekeratin

The subunit of epidermal prekeratin has been shown to consist of three polypeptide chains. One of these has a molecular weight of 72,000 and two have molecular weights of 60,000, giving a total subunit molecular weight of 192,000. The prekeratin molecule, examined by ultracentrifugation, appears monodisperse and has a molecular weight of about 375,000 which is twice the subunit weight. It is concluded that prekeratin consists of a pair of three-stranded subunits and that this dimer is most probably of physiological significance, being a building block of epidermal filaments (“α-keratin”).