The onset repulsion effect

There have been many previous reports of mislocalization associated with moving objects (e.g. flash-lag effect, Frohlich effect, representational momentum). Across four experiments, a new form of mislocalization--the onset repulsion effect (ORE)--is explored in which the error is always back along the observed path of motion. That is, when observers are asked to localize both the initial onset and the final offset positions of a moving object, by far the largest and most systematic error they make is in placing the onset point too early along the correct path of motion. Errors orthogonal to the path of motion and errors in localizing the offset point are minimal by comparison. Errors are also very small when motion is implied rather than continuous. The ORE can be observed with and without fixation, and as with other mislocalization effects, shows some dependence on direction and velocity. As the most obvious prediction in these studies, based on previous reports of mislocalization and the known properties of the visual system, would be for forward rather than backward errors, discussion will focus on the type of mechanism that may have given rise to the observed pattern of results.     

Analysis of metabolic networks using a pathway distance metric through linear programming

The solution of the shortest path problem in biochemical systems constitutes an important step for studies of their evolution. In this paper, a linear programming (LP) algorithm for calculating minimal pathway distances in metabolic networks is studied. Minimal pathway distances are identified as the smallest number of metabolic steps separating two enzymes in metabolic pathways. The algorithm deals effectively with circularity and reaction directionality. The applicability of the algorithm is illustrated by calculating the minimal pathway distances for Escherichia coli small molecule metabolism enzymes, and then considering their correlations with genome distance (distance separating two genes on a chromosome) and enzyme function (as characterised by enzyme commission number). The results illustrate the effectiveness of the LP model. In addition, the data confirm that propinquity of genes on the genome implies similarity in function (as determined by co-involvement in the same region of the metabolic network), but suggest that no correlation exists between pathway distance and enzyme function. These findings offer insight into the probable mechanism of pathway evolution.     

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis

MOTIVATION: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly. RESULTS: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.     

Recurrent mammary hyperplasia: current concepts

LEARNING OBJECTIVES: After studying this article, the participant should be able to: 1. Understand the factors leading to undesirable long-term reduction mammaplasty results. 2. Delineate the differential diagnosis of recurrent hypermastia. 3. Understand the significance of preoperative counseling, particularly with regard to expected postoperative outcome. 4. Understand short-term and long-term expected and undesirable postoperative results. 5. Understand safe and effective surgical planning for revision reduction mammaplasty. A large majority of patients who undergo reduction mammaplasty are satisfied with their aesthetic outcome and resolution of preoperative symptoms. Occasionally, patients present with postoperative concerns; these are usually aesthetic in nature and caused by breast scarring, breast asymmetry, and/or breast shape. Inadequate excision and recurrent hypermastia are more complex concerns, which require careful evaluation and treatment. Analysis of both the presenting deformity and the original surgical approach is critical in determining an operative plan. This article discusses the safe approach to revision reduction mammaplasty. Current concepts are discussed and presented. An algorithm for decision-making is presented and discussed.     

Synchrony in human,mouse and bacterial cell cultures--a comparison

Growth characteristics of synchronous human MOLT-4, human U-937 and mouse L1210 cultures produced with a new minimally-disturbing technology were compared to each other and to synchronous Escherichia coli B/r. Based on measurements of cell concentrations during synchronous growth, synchrony persisted in similar fashion for all cells. Cell size and DNA distributions in the mammalian cultures also progressed synchronously and reproducibly for multiple cell cycles. The results demonstrate that unambiguous multi-cycle synchrony, critical for verifying the absence of significant growth imbalances induced by the synchronization procedure, is feasible with these cell lines, and possibly others.     

Target selection and determination of function in structural genomics

The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.     

Extracellular domain of myelin oligodendrocyte glycoprotein (MOG) exhibits solvent-dependent conformational transitions

The conformation of the non-glycosylated recombinant form of the extracellar domain of rat MOG (rMOG(1-125)) dissolved in different solvent conditions was studied by CD spectroscopy. The results show that rMOG(1-125) exhibits a predominantly beta sheet conformation in aqueous buffer solution at pH 7.5 and that this 'beta-form' is stabilized by zwitterionic phospholipids, DPC and LPCP. The alpha helical content of the protein can increase from 9% to up to 20% when TFE or anionic detergent LPAP and SDS are added.     

An overview of the structures of protein-DNA complexes

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.