Proteomic profiling of heat shock proteins: An emerging molecular approach with direct pathophysiological and clinical implications

The HSP family is one of the most ancient and evolutionarily conserved protective protein families found in nature. Originally discovered as inducible molecules capable of maintaining cellular homeostasis against abrupt temperature changes, HSPs were later determined to represent an adaptive physiological response that copes with a variety of different cellular proteotoxic stresses. These physiological molecular chaperones facilitate the synthesis, folding, assembly, trafficking and secretion of specific proteins in various cellular compartments. Most importantly, these proteins guard the whole cell proteome against misfolding and inappropriate aggregation. A series of diversified proteotoxic stresses, including heat, hypoxia/ischemia, free radicals, acidosis, ATP depletion and toxins are capable of inducing a typical cellular stress response characterised by rapid inhibition of overall protein synthesis, with a concomitant dramatic increase in HSP expression. From a pathophysiological point of view, HSP induction has been observed in a wide spectrum of inflammatory and degenerative diseases (from cancer to prion disease by passing to infective and autoimmune diseases) and, intriguingly, overexpression monitoring seems to have potential implications in terms of diagnosis, prognosis and, above all, therapy. Proteomics studies, identifying a series of modification of HSP expression patterns in different diseases, are confirming these promising clinical applications.     

CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

We developed a software package (CAVE) in Fortran language to detect internal cavities in proteins which can be applied also to an arbitrary system of balls. The volume, the surface area and other quantitative characteristics of the cavities can be calculated. The code is based on the recently suggested enveloping triangulation algorithm [J. Buša et al., J. Comp. Chem. 30 (2009) 346] for computing volume and surface area of the cavity by analytical equations. Different standard sets of atomic radii can be used. The PDB compatible file containing the atomic coordinates must be stored on the disk in advance. Testing of the code on different proteins and artificial ball systems showed efficiency and accuracy of the algorithm. The program is fast. It can handle a system of several thousands of balls in the order of seconds on contemporary PC's. The code is open source and free.

Program summary

Program title: CAVECatalogue identifier: AEHC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 8670No. of bytes in distributed program, including test data, etc.: 100 131Distribution format: tar.gzProgramming language: FortranComputer: PC Pentium and CoreOperating system: Linux system and Windows XP systemClassification: 16.1Nature of problem: Molecular structure analysis.Solution method: Analytical method for cavities detection, and numerical algorithm for volume and surface area calculation based on the analytical formulas, after using the stereographic transformation.Running time: Depends on the size of the molecule under consideration. The test example included in the distribution takes about 1 minute to run.     

The anatomy of junior high school science textbooks: An analysis of textual characteristics and a comparison to media reports of science

Abstract

This study compared junior high school science textbooks to media reports of science, on the basis of four textual characteristics: text type, truth status of statements, metalanguage use, and scientific status of statements and their role in scientific reasoning. The text type of both junior high science textbooks and media reports of science was found to be overwhelmingly expository. There was no argumentation in junior high science textbooks, a finding similar for some of the media reports of science, but vastly different for others, which had considerable argumentation. Almost all statements in the junior high science textbooks were presented as being true. In media reports of science, by contrast, only two thirds of the statements were presented as true. The junior high science textbooks reflected a range of metalanguage use largely limited to observational words, words that describe the process of doing research, and relational words, such as ‘cause.’ The frequency of metalanguage use was only one third that found in media reports of science. The majority of both junior high texts and media reports of science was written as statements of fact or conclusion. Implications of these comparisons for the goal of lifelong science learning and scientific literacy are examined.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiring the use of computer programs offering high-resolution analysis and comparison of nucleotide sequence data. The strategy involves the development of a pair of computer programs, called SEQANAL and SEQTALK, designed to operate in tandem. SEQANAL is a large and complex program intended to be used to discover regions of internal repeats and dyad symmetries within one sequence, or regions of homology, complementarity or optimal alignment between two sequences. Three algorithms are supported: those of Staden (1977, 1978); of Korn et al. (1977); Queen and Korn (1980); and the newly-described exhaustive tree-searching algorithm of Burnett et al. (1985, 1986). The SEQTALK program is a small, portable, interactive, front-end program with which the user can specify the instructions to control the SEQANAL program. Together, the SEQANAL and SEQTALK programs permit analyses to be performed at a remote facility on a mainframe computer under the complete control of a distant user equipped with minimal computing facilities, and without needing networking facilities.     

Path-based approach to integrated planning and control for robotic systems: A path-based approach provides an analytical integration of robot planning and control. As a result, the task level control can be achieved, and the system is capable of coping with unexpected or uncertain events

Our newly developed event-based planning and control theory is applied to robotic systems. It Introduces a suitable action or motion reference variable other than time, but directly related to the desired and measurable systems output, called event. Here the event is the length of the path tracked by a robot. It enables the construction of an integrated planning and control system where planning becomes a real-time closed-loop process. The path-based integration planning and control scheme is exemplified by a single-arm tracking problem. Time and energy optimal motion plans combined with nonlinear feedback control are derived in closed form. To the best of our knowledge, this closed-form solution was not obtained before. The equivalence of path-based and time-based representations of nonlinear feedback control is shown, and an overall system stability criterion has also been obtained. The application of event-based integrated planning and control provides the robotic systems the capability to cope with unexpected and uncertain events in real time, without the need for replanning. The theoretical results are illustrated and verified by experiments.