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Insertional mutagenesis and immunochemical analysis of visual arrestin interaction with rhodopsin.

Visual arrestin inactivates the phototransduction cascade by specifically binding to light-activated phosphorylated rhodopsin. This study describes the combined use of insertional mutagenesis and immunochemical approaches to probe the structural determinants of arrestin function. Recombinant arrestins with insertions of a 10-amino acid c-Myc tag (EQKLISEEDL) were expressed in yeast and characterized. When the tag was placed on the C terminus after amino acid 399, between amino acids 99 and 100 or between residues 162 and 163, binding to rhodopsin was found to be very similar to that of wild-type arrestin. Two stable mutants with Myc insertions in the 68-78 loop were also generated. Binding to rhodopsin was markedly decreased for one (72myc73) and completely abolished for the other (77myc78). Limited proteolysis assays using trypsin in the absence or presence of heparin were performed on all mutants and confirmed their overall conformational integrity. Rhodopsin binding to either 162myc163 or 72myc73 arrestins in solution was completely inhibited in the presence of less than a 2-fold molar excess of anti-Myc antibody relative to arrestin. In contrast, the antibody did not block the interaction of the 399myc or 99myc100 arrestins with rhodopsin. These results indicate that an interactive surface for rhodopsin is located on or near the concave region of the N-domain of arrestin.

Amino Acid Sequence↗

Measurement and analysis of visual acuity in multicenter randomized clinical trials in the United States: findings from a survey.

PURPOSE: To describe visual acuity (VA) testing and scoring methods used in multicenter randomized clinical trials in ophthalmology in the United States (USA) sponsored by the National Eye Institute (NEI). METHODS: A survey was conducted among multicenter studies in the US that included one or more randomized clinical trials and were sponsored by the NEI, National Institutes of Health. To be included in the survey, a study had to have VA reported in one or more publications or patient eligibility based on VA, a majority of study subjects 13 years of age or older, and a patient population primarily or exclusively from the US. A standard survey form was completed for each study based on information presented in the study manual of procedures and publications. Findings were summarized and displayed with frequency distributions. RESULTS: The survey included 24 studies, each with enrollment initiated in the period 1972 to 1999. VA was one of the study eligibility criteria for 19 (79%) studies, and VA or change in VA was the primary outcome in 12 (50%) studies. ETDRS charts have been employed in 16 of 19 studies initiated after the charts were published in 1982. All studies but one specified in the documents reviewed that VA testing was performed at multiple VA test distances. For studies that used ETDRS charts, methods of converting VA scores obtained at different test distances to a common scale fell into two categories: 11 studies used a method similar in nature to that first reported in the Macular Photocoagulation Study, and 7 studies used a method similar in nature to that first reported in the Krypton-Argon Regression of Neovascularization Study. conclusion The development of the ETDRS charts and a custom light box has led to more uniformity in VA test charts and chart illumination. However, details of VA measurement protocols vary widely from study to study. To assure comparable data across studies and ocular conditions, it would be useful to have a standard VA testing and scoring protocol with provisions for testing different levels of visual acuity that recommends a single method for converting scores from different test distances to a common scale and standard conversion of "off the chart" VA levels for calculation of means and changes in VA.

Data Collection↗

Peditree: pedigree database analysis and visualization for breeding and science.

At the Wageningen Laboratory of Plant Breeding, a software package has been developed to query a simple structured database with variety pedigree data. The package, called Peditree, creates a tree-shaped representation of pedigree information and has several visualization and lookup options. Estimates of inbreeding coefficient within a pedigree or coefficients of coancestry among pedigrees can be obtained. Furthermore trait data--if available--can be linked, displayed within the pedigree tree, and used to highlight pedigree entries that comply with set criteria.

Animals↗

Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin.

We have characterized the structure of transcriptionally active nucleosome subunits using electron spectroscopic imaging. Individual nucleosomes were analyzed in terms of total mass, DNA and protein content, while the ensemble of images of active nucleosomes was used to calculate a three-dimensional reconstruction. Transcriptionally active nucleosomes were separated from inactive nucleosomes by mercury-affinity chromatography thus making it possible to compare their structures. The chromatographic results combined with electron spectroscopic imaging confirm that active nucleosomes unfold to form extended U-shaped particles. Phosphorus mapping indicated that the nucleosomal DNA also underwent a conformational change consistent with particle unfolding. The three-dimensional structure of the Hg-affinity purified nucleosomes determined using quaternion-assisted angular reconstitution methods unites and resolves the different electron microscopic views of the particle and is concordant with a sulphydryl-exposing disruption of the H3-H4 tetramer.

Chromatin↗

MolMovDB: analysis and visualization of conformational change and structural flexibility.

The Database of Macromolecular Movements (http://MolMovDB.org) is a collection of data and software pertaining to flexibility in protein and RNA structures. The database is organized into two parts. Firstly, a collection of 'morphs' of solved structures representing different states of a molecule provides quantitative data for flexibility and a number of graphical representations. Secondly, a classification of known motions according to type of conformational change (e.g. 'hinged domain' or 'allosteric') incorporates textual annotation and information from the literature relating to the motion, linking together many of the morphs. A variety of subsets of the morphs are being developed for use in statistical analyses. In particular, for each subset it is possible to derive distributions of various motional quantities (e.g. maximum rotation) that can be used to place a specific motion in context as being typical or atypical for a given population. Over the past year, the database has been greatly expanded and enhanced to incorporate new structures and to improve the quality of data. The 'morph server', which enables users of the database to add new morphs either from their own research or the PDB, has also been enhanced to handle nucleic acid structures and multi-chain complexes.

Computer Graphics↗

Quantitative analysis of visual acuity through amber discolored lenses.

Discoloration of hydrogel contact lenses is frequently encountered in clinical practice and often precipitates lens replacement. This investigation sought to determine if lens discoloration was associated with a compromise in low or high contrast, high illumination visual acuity. This association would lead to a more scientific rationale for lens replacement. Amber lens discoloration was achieved using human-worn 55% water hydrophilic contact lenses (Methafilcon-A) heated in a 1% potassium sorbate, low pH saline solution. A spectrum of 6 discolored lenses was obtained with a peak absorbance at 320 nm. Fifteen subjects, between the ages of 22 and 38 years, were tested wearing each of the discolored lenses. None of the differences in high or low contrast acuity between our discolored and nondiscolored lenses were found to be statistically significant using a paired t-test at the 99% significance level.

Adult↗

The functions of the proprioceptors of the eye muscles.

This article sets out to present a fairly comprehensive review of our knowledge about the functions of the receptors that have been found in the extraocular muscles--the six muscles that move each eye of vertebrates in its orbit--of all the animals in which they have been sought, including Man. Since their discovery at the beginning of the 20th century these receptors have, at various times, been credited with important roles in the control of eye movement and the construction of extrapersonal space and have also been denied any function whatsoever. Experiments intended to study the actions of eye muscle receptors and, even more so, opinions (and indeed polemic) derived from these observations have been influenced by the changing fashions and beliefs about the more general question of how limb position and movement is detected by the brain and which signals contribute to those aspects of this that are perceived (kinaesthesis). But the conclusions drawn from studies on the eye have also influenced beliefs about the mechanisms of kinaesthesis and, arguably, this influence has been even larger than that in the converse direction. Experimental evidence accumulated over rather more than a century is set out and discussed. It supports the view that, at the beginning of the 21st century, there are excellent grounds for believing that the receptors in the extraocular muscles are indeed proprioceptors, that is to say that the signals that they send into the brain are used to provide information about the position and movement of the eye in the orbit. It seems that this information is important in the control of eye movements of at least some types, and in the determination by the brain of the direction of gaze and the relationship of the organism to its environment. In addition, signals from these receptors in the eye muscles are seen to be necessary for the development of normal mechanisms of visual analysis in the mammalian visual cortex and for both the development and maintenance of normal visuomotor behaviour. Man is among those vertebrates to whose brains eye muscle proprioceptive signals provide information apparently used in normal sensorimotor functions; these include various aspects of perception, and of the control of eye movement. It is possible that abnormalities of the eye muscle proprioceptors and their signals may play a part in the genesis of some types of human squint (strabismus); conversely studies of patients with squint in the course of their surgical or pharmacological treatment have yielded much interesting evidence about the central actions of the proprioceptive signals from the extraocular muscles. The results of experiments on the eye have played a large part in the historical controversy, now in at least its third century, about the origin of signals that inform the brain about movement of parts of the body. Some of these results, and more of the interpretations of them, now need to be critically re-examined. The re-examination in the light of recent experiments that is presented here does not support many of the conclusions confidently drawn in the past and leads to both new insights and fresh questions about the roles of information from motor signals flowing out of the brain and that from signals from the peripheral receptors flowing into it. There remain many lacunae in our knowledge and filling some of these will, it is contended, be essential to advance our understanding further. It is argued that such understanding of eye muscle proprioception is a necessary part of the understanding of the physiology and pathophysiology of eye movement control and that it is also essential to an account of how organisms, including Man, build and maintain knowledge of their relationship to the external visual world. The eye would seem to provide a uniquely favourable system in which to study the way in which information derived within the brain about motor actions may interact with signals flowing in from peripheral receptors. The review is constructed in relatively independent sections that deal with particular topics. It ends with a fairly brief piece in which the author sets out some personal views about what has been achieved recently and what most immediately needs to be done. It also suggests some lines of study that appear to the author to be important for the future.

Afferent Pathways↗

A neural circuit analysis of visual recognition memory: role of perirhinal, medial, and lateral entorhinal cortex.

Using a continuous recognition memory procedure for visual object information, we sequentially presented rats with eight novel objects and four repeated objects (chosen from the 8). These were selected from 120 different three-dimensional objects of varying sizes, shapes, textures, and degree of brightness. Repeated objects had lags ranging from 0 to 4 (from 0 to 4 different objects between the first and repeated presentation). An object was presented on one side of a long table divided in half by an opaque Plexiglas guillotine door, and the latency between opening the door and the rat moving the object was measured. The first presentation of an object resulted in reinforcement, but repeated presentations did not result in a reinforcement. After completion of acquisition training (significantly longer latencies for repeated presentation compared with the first presentation of an object), rats received lesions of the perirhinal, medial, or lateral entorhinal cortex or served as sham operated controls. On the basis of postsurgery testing and additional tests, the results indicated that rats with perirhinal cortex lesions had a sustained impairment in performing the task. There were no sustained deficits with medial or lateral entorhinal cortex lesions. The data suggest that recognition memory for visual object information is mediated primarily by the perirhinal cortex but not by the medial or lateral entorhinal cortex.

Animals↗

Analysis and visualization of multiply oriented lattice structures by a two-dimensional continuous wavelet transform.

The phase-field-crystal model [K. R. Elder and M. Grant, Phys. Rev. E 70, 051605 (2004)] produces multigrain structures on atomistic length scale but on diffusive time scales. Since individual atoms are resolved but are treated identically it is difficult to distinguish the exact position of grain boundaries and defects within grains. In order to analyze and visualize the whole grains a two-dimensional wavelet transform has been developed, which is capable of extracting grain boundaries and the lattice orientation of a grain relative to a laboratory frame of reference. This transformation makes it possible not only to easily visualize the multigrain structure, but also to perform exact measurements on low- and high-angle boundaries, grain size distributions and boundary-angle distributions, which can then be compared to experimental data. The presented wavelet transform can also be applied to results of other atomistic simulations, e.g., molecular dynamics or granular materials.

Journal Article↗