Cobweb: a Java applet for network exploration and visualisation

SUMMARY: Cobweb is a Java applet for real-time network visualization; its strength lies in enabling the interactive exploration of networks. Therefore, it allows new nodes to be interactively added to a network by querying a database on a server. The network constantly rearranges to provide the most meaningful topological view. AVAILABILITY: Cobweb is available under the GPLv3 and may be freely downloaded at http://bioinformatics.charite.de/cobweb.     

jSquid: a Java applet for graphical on-line network exploration

jSquid is a graph visualization tool for exploring graphs from protein-protein interaction or functional coupling networks. The tool was designed for the FunCoup web site, but can be used for any similar network exploring purpose. The program offers various visualization and graph manipulation techniques to increase the utility for the user. AVAILABILITY: jSquid is available for direct usage and download at http://jSquid.sbc.su.se including source code under the GPLv3 license, and input examples. It requires Java version 5 or higher to run properly. CONTACT: erik.sonnhammer@sbc.su.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees

PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided. AVAILABILITY: http://www.pedvizapi.org     

CTRD: a fast applet for computing signed translocation distance between genomes

CTRD is a software for computing translocation distance between genomes. It takes two genomes as its input and tests whether one genome can be transformed into the other. If possible, it computes the translocation distance between two genomes, and gives the translocation operation serial. We adopt the fastest known O(n(2)log n) algorithm. Our contributions include (1) give a necessary and sufficient condition to ensure that one genome can be transformed into the other for translocation operations, and (2) develop a software using the fastest known O(n(2)log n) algorithm.     

DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering

A computer system DIROM for oligonucleotide-directed mutagenesisand artificial gene design has been designed for better experimentalplanning and control. DIROM permits searching for optimal oligonucleotideswith respect to certain important parameters, namely sufficientenergy of oligonucleotide-target hybridization, the secondarystructure of oligonuc-tide and target DNA, the presence of alternatebinding sites in the target DNA and terminal G/C pairs. It canalso be used to plan polymerase chain reaction experiments,for optimal primer selection, in sequencing, etc. DIROM enablesone to search for both existing and potential restriction sites,to perform vector + target sequence construction. The systemconsists of a set of original algorithms that formalize theempirical knowledge of oligonucleotide action as primers.     

The interactive effects of temperature and pH on the isometric contraction of toad sartorius muscle

Summary The main purpose of this study was to examine the interactive effects of pH and temperature on the performance of isolated muscle in order to estimate the effect of temperature in vivo. The development of tetanic tension by the sartorius muscle isolated from toads was tested at either 5 or 25°C. The pH of the physiological solution bathing the muscle was changed from 9.0 to 6.0 stepwise by 0.5 pH units.In order to see if the temperature at which the toads were maintained modified the muscle activity, two groups of toads were used: those acclimated to low temperature (5°C) and those acclimated to high temperature (25°C). Acclimation temperature had no significant effect (Fig. 1, Table 1).Both the amount and rate of tension development increased when test temperature increased (Fig. 1A, B). Maximum tension and rate of tension development were significantly reduced at low pH. The latent period, time to half-maximum tension, and half-relaxation time were longer at low pH (Fig. 1C, D, E). The interactive effects of pH and test temperature were significant for all variables, except the latent period (Table 1). That is, the effects of pH were greater at 5 than at 25°C and the effects of test temperature depend on extracellular pH. We calculated that the in vivo decrease in tetanic tension when the body temperature of a toad decreases from 25 to 5°C is smaller than previously supposed. This is because in previous studies on the effect of test temperature on muscle function, unrealistic pH regimes generally have been employed.This work is supported by an NSERC operating grant to E.D. Stevens     

NMR-based molecular ruler for determining the depth of intercalants within the lipid bilayer Part II. The preparation of a molecular ruler

We have previously shown how the location of an intercalant within the lipid bilayer can be qualitatively determined by using the excellent correlation that exists between the ¹³C NMR chemical shift of a polarizable carbon (e.g., the carbonyl or nitronyl carbon) and the polarity (using the Dimroth-Reichardt's E_T(30) parameter) of the microenvironment in which that carbon resides. In a companion paper, we have determined criteria for reporter molecules that will assist us in converting this qualitative polarity data into quantitative Angstrom values. In the present paper, we report on our initial success in quantitatively mapping of the DMPC bilayer by linking two or more vertical points within a bilayer by both distance (in Angstroms) and E_T(30) polarity. The results correlated well with the values obtained using the “parallax method” of Erwin London.     

The interactive effects of fatigue and pH on the ionic conductance of frog sartorius muscle fibers

The effects of fatigue on the membrane conductance of frog sartorius muscle at the resting potential and during an action potential were studied. When muscles were exposed to an extracellular pH of 8.0 the membrane conductance at the resting potential increased during fatigue by about 20% and returned to prefatigue level in about 20 min. The membrane conductance of muscle fibers exposed to pH 6.4 was about three times less than that of pH 8.0 and decreased further during fatigue. Furthermore, the recovery of a normal membrane conductance was slow at pH 6.4. Both the inward, depolarizing and the outward, repolarizing currents during the action potential are reduced in fatigue. In each case the effect is greater at pH 6.4 than at 8.0 and recovery towards normal values is slower at pH 6.4. It is concluded that the ionic conductance of the sarcolemmal membrane at the resting potential and during an action potential are modified by fatigue and that these changes are modulated by pHo.     

BAOBAB: a Java editor for large phylogenetic trees

SUMMARY: BAOBAB is a Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees within or between windows; (iii) compressing/ uncompressing subtrees; and (iv) managing sequence files together with tree files. AVAILABILITY: http://www.univ-montp2.fr/~genetix/.     

Endometriosis and physical exercises: a systematic review

Regular physical exercise seems to have protective effects against diseases that involve inflammatory processes since it induces an increase in the systemic levels of cytokines with anti-inflammatory and antioxidant properties and also acts by reducing estrogen levels. Evidence has suggested that the symptoms associated with endometriosis result from a local inflammatory peritoneal reaction caused by ectopic endometrial implants. Thus, the objective of the present review was to assess the relationship between physical exercise and the prevalence and/or improvement of the symptoms associated with endometriosis. To this end, data available in PubMed (1985–2012) were surveyed using the terms “endometriosis and physical exercises”, “endometriosis and life style and physical exercises” in the English language literature. Only 6 of the 935 articles detected were included in the study. These studies tried establish a possible relationship between the practice of physical exercise and the prevalence of endometriosis. The data available are inconclusive regarding the benefits of physical exercise as a risk factor for the disease and no data exist about the potential impact of exercise on the course of the endometriosis. In addition, randomized studies are necessary.     

Influence of permeant acids and bases on net potassium uptake by Chlorella

Salts of membrane-permeant acids and bases strongly influence net K uptake by Chlorella fusca. Na phenylacetate, acetate, isobutyrate, propionate, and butyrate added to buffered algal suspensions containing 0.1–0.2 mM KCl increasingly stimulated net K uptake. In contrast, K release was induced by the chlorides of imidazole, ammonia and methylamine. All these effects were found in the light and, less pronounced, in the dark. The dependence of the net K movements on the concentrations of the salts added and on the pH of the medium suggests that the free acids or bases are the effective agents. Between net uptake of K and uptake of labeled propionate a molar ratio close to 1 was found. It is concluded that the internal pH of the cell is changed by the permeants. Acidification of the cytoplasm stimulates extrusion of protons coupled to uptake of K. Alcalization brings about proton uptake and K extrusion. Apparently K/H exchange serves as a pH-stat of the cell.Abbreviations DA dark/air - DMO 5,5-dimethyloxazolidine-2,4-dione - LA light/air - PIPES piperazine-N-N-bis-2-ethane sulfonic acid     

Changes in intracellular free calcium activity in Xenopus eggs following imposed intracellular pH changes using weak acids and weak bases.

The aim of this work was to determine the potential relationships between rises in intracellular pH (pHi) and intracellular free calcium activity (Cai2+) during cell activation in Xenopus eggs. To do this, we used two weak bases, NH4Cl and procaine, and a weak acid, CO2, and measured Cai2+ variations in response to these imposed pHi variations. NH4Cl and procaine increased Cai2+ in both unactivated and activated eggs. Procaine was found to alkalinize the egg cytoplasm, whereas the other weak base, NH4Cl, acidified the egg cytoplasm. On the other hand, CO2 was found to acidify the cytoplasm and to substantially decrease Cai2+, also in unactivated and activated eggs. In addition, CO2 triggered an increase in the conductance of the plasma membrane to Cl- ions, similarly to what had been found previously with weak bases (Charbonneau, M. (1989) Cell Differ. Develop. 26, 39-52). These Cl- channels, similarly to the sperm-triggered Cl- channels during the fertilization potential, are supposed to be Ca2(+)-sensitive. Therefore, the changes in Ca2+ observed in response to CO2 do not seem to be responsible for the opening of these Cl- channels, which would rather be triggered by an increase in Cai2+ localized near the plasma membrane. We conclude therefore that weak acids and bases represent appropriate tools for studying cytosolic Ca2+ homeostasis, but not for dissecting the complex pathways involved in signal transduction.     

OligoFaktory: a visual tool for interactive oligonucleotide design

SUMMARY: The OligoFaktory is a set of tools for the design, on an arbitrary number of target sequences, of high-quality long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user-centered interface exists in two flavours: a web portal and a standalone software for Mac OS X Tiger. A unified presentation of results provides overviews with distribution charts and relative location bar graphs, as well as detailed features for each oligonucleotide. Input and output files conform to a common XML interchange file format to allow both automatic generation of input data, archiving, and post-processing of results. The design pipeline can use BLAST servers to evaluate specificity of selected oligonucleotides. AVAILABILITY: The web portal http://ueg.ulb.ac.be/oligofaktory/; the software for Macintosh: http://www.oligofaktory.org/     

Growth of the developing mouse heart: an interactive qualitative and quantitative 3D atlas

Analysis of experiments aimed at understanding the genetic mechanisms of differentiation and growth of the heart, calls for detailed insights into cardiac growth and proliferation rate of myocytes and their precursors. Such insights in mouse heart development are currently lacking. We quantitatively assessed the 3D patterns of proliferation in the forming mouse heart and in the adjacent splanchnic mesoderm, from the onset of heart formation till the developed heart at late gestation. These results are presented in an interactive portable document format (Suppl. PDF) to facilitate communication and understanding. We show that the mouse splanchnic mesoderm is highly proliferative, and that the proliferation rate drops upon recruitment of cells into the cardiac lineage. Concomitantly, the proliferation rate locally increases at the sites of chamber formation, generating a regionalized proliferation pattern. Quantitative analysis shows a gradual decrease in proliferation rate of the ventricular walls with progression of development, and a base-to-top decline in proliferation rate in the trabecules. Our data offers clear insights into the growth and morphogenesis of the mouse heart and shows that in early development the phases of tube formation and chamber formation overlap. The resulting interactive quantitative 3D atlas of cardiac growth and morphogenesis provides a resource for interpretation of mechanistic studies.     

CLANS: a Java application for visualizing protein families based on pairwise similarity

SUMMARY: The main source of hypotheses on the structure and function of new proteins is their homology to proteins with known properties. Homologous relationships are typically established through sequence similarity searches, multiple alignments and phylogenetic reconstruction. In cases where the number of potential relationships is large, for example in P-loop NTPases with many thousands of members, alignments and phylogenies become computationally demanding, accumulate errors and lose resolution. In search of a better way to analyze relationships in large sequence datasets we have developed a Java application, CLANS (CLuster ANalysis of Sequences), which uses a version of the Fruchterman-Reingold graph layout algorithm to visualize pairwise sequence similarities in either two-dimensional or three-dimensional space. AVAILABILITY: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download.     

Influence of permeant acids and bases on active Na+ extrusion by Chlorella

Chlorella cells were enriched with Na⁺ by incubation in 3.5 mM ²²Na labelled NaOH for 2–3 h. The active Na⁺ extrusion from these cells into media containing 6.5 × 10⁻⁴ M salts of permeant acids (sodium acetate, phenylacetate, propionate, isobutyrate) or bases (ammonium and methylammonium chloride) was studied under illumination and aeration at pH 6.0 and and 7.8. The carboxylates depressed and the hydrochlorides stimulated Na⁺ efflux efflux. The effect of the carboxylates could be attributed to acidification of the cell interior due to penetration of the undissociated acids. The strong effect of the hydrochlorides could only partially be explained by penetration of the free bases. When the external medium contained only low concentrations of K⁺, Na⁺ export was increasingly inhibited with time. This effect was attibuted to acidification of the cell interior by Na⁺/H⁺ exchange. The results can be explained either by secondary active Na⁺/H⁺ antiport or by competition between Na⁺ and H⁺ at the inner site of a primary active extrusion pump, some observations favouring the latter assumption.     

JSBML: a flexible Java library for working with SBML

SUMMARY: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. AVAILABILITY: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.