MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis

We present MeV+R, an integration of the JAVA MultiExperiment Viewer program with Bioconductor packages. This integration of MultiExperiment Viewer and R is easily extensible to other R packages and provides users with point and click access to traditionally command line driven tools written in R. We demonstrate the ability to use MultiExperiment Viewer as a graphical user interface for Bioconductor applications in microarray data analysis by incorporating three Bioconductor packages, RAMA, BRIDGE and iterativeBMA.     

Unlocking data: Where is the key?

Health‐related data uses and data sharing have been in the spotlight for a while. Since the beginning of the big data era, massive data mining and its inherent possibilities have only increased the debate about what the limits are. Data governance is a relevant aspect addressed in ethics guidelines. In this context, the European project BRIDGE Health (BRidging Information and Data Generation for Evidence‐based Health policy and research) strove to achieve a comprehensive, integrated and sustainable EU health‐information system. One of the aims of the project was to evaluate the requirements to construct a data‐linkage infrastructure for the secure management of health information. In a blueprint provided for this infrastructure, the topics ethics and the intimately related governance occupied a whole section, where the recent ethics guidelines by the Council for International Organizations of Medical Sciences (CIOMS) and the World Medical Association (WMA) were referenced. We explore what has changed in the latest versions of the ethics documents adopted by CIOMS and WMA regarding the management of health data and human tissues, the appropriateness of their application in new forms of research and infrastructures as the proposed in the BRIDGE Health project, and whether society should be so concerned about this topic, in the digital era of social exchange.     

Use of continuous flow microfluorimetry for DNA determinations in Penicillium

BRIDGE, P. D. & HUDSON, L., 1989. Use of continuous flow microfluorimetry for DNA determinations in Penicillium. Continuous flow microfluorimetry has been used to characterize spore suspensions of fasciculate strains of Penicillium. Fluorescent Feulgen staining combined with appropriate filters allows the measurement of conidial DNA content in samples of 10 000 conidia in 30 seconds. The results obtained for apparently closely related strains and single conidium isolates of the same strains showed significant differences which appear to correspond with phenotypic differences. Some implications of, and possible explanations for, this phenomenon are discussed.     

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

The flood of data acquired from the increasing number of publicly available genomes has led to new demands for bioinformatics software. With the growing amount of information resulting from high throughput experiments new questions arise that often focus on the comparison of genes, genomes, and their expression profiles. Inferring new knowledge by combining different kinds of "post-genomics" data obviously necessitates the development of new approaches that allow the integration of variable data sources into a flexible framework. In this paper, we describe our concept for the integration of heterogeneous data into a platform for systems biology. We have implemented a Bioinformatics Resource for the Integration of heterogeneous Data from Genomic Explorations (BRIDGE) and illustrate the usability of our approach as a platform for systems biology for two sample applications.     

Delivering the WISE (Whole Systems Informing Self-Management Engagement) training package in primary care: learning from formative evaluation

Background

Several studies document disparities in access to care and quality of care for depression for African Americans. Research suggests that patient attitudes and clinician communication behaviors may contribute to these disparities. Evidence links patient-centered care to improvements in mental health outcomes; therefore, quality improvement interventions that enhance this dimension of care are promising strategies to improve treatment and outcomes of depression among African Americans. This paper describes the design of the BRIDGE (Blacks Receiving Interventions for Depression and Gaining Empowerment) Study. The goal of the study is to compare the effectiveness of two interventions for African-American patients with depression--a standard quality improvement program and a patient-centered quality improvement program. The main hypothesis is that patients in the patient-centered group will have a greater reduction in their depression symptoms, higher rates of depression remission, and greater improvements in mental health functioning at six, twelve, and eighteen months than patients in the standard group. The study also examines patient ratings of care and receipt of guideline-concordant treatment for depression.

Methods/Design

A total of 36 primary care clinicians and 132 of their African-American patients with major depressive disorder were recruited into a cluster randomized trial. The study uses intent-to-treat analyses to compare the effectiveness of standard quality improvement interventions (academic detailing about depression guidelines for clinicians and disease-oriented care management for their patients) and patient-centered quality improvement interventions (communication skills training to enhance participatory decision-making for clinicians and care management focused on explanatory models, socio-cultural barriers, and treatment preferences for their patients) for improving outcomes over 12 months of follow-up.

Discussion

The BRIDGE Study includes clinicians and African-American patients in under-resourced community-based practices who have not been well-represented in clinical trials to improve depression care. The patient-centered and culturally targeted approach to depression care is a relatively new one that has not been tested in most previous studies. The study will provide evidence about whether patient-centered accommodations improve quality of care and outcomes to a greater extent than standard quality improvement strategies for African Americans with depression.

Trial Registration

ClinicalTrials.gov NCT00243425     

BOOK REVIEWS

Book reviewed in this article
BIOLOGICAL STUDIES OF THE ENGLISH LAKES by T. T. Macan
OCEANOGRAPHY AND MARINE BIOLOGY. An annual review. Vol. 7. Edited by Harold Barnes
A SYMPOSIUM ON THE DISEASES OF FISHES AND SHELLFISHES edited by S. F. Snieszko
ADVANCES IN MARINE BIOLOGY Vol. 8 edited by Sir Frederick S. Russel and Sir Maurice Yonge.
MARINE ECOLOGY, Volume 1, ENVIRONMENTAL FACTORS, PART 1 edited by 0. Kinne.
TRAITE DE PISCICULTURE by Marcel Huet
FISH PHYSIOLOGY VOL. Ill REPRODUCTION AND GROWTH, BIOLUMINESCENCE, PIGMENTS AND POISONS edited by W. S. Hoar and D. J. Randall.
A BIBLIOGRAPHY OF PARASITES AND DISEASES OF FISHES OF CANADA: 1879–1969 by L. Margolis.
INFEKTSIONNIE BOLEZNI RIB I BOR'BA S NIMI, [INFECTIOUS DISEASES OF FISHES AND THEIR CONTROL]. Pod redaksiei Prof. Bauera.
CIRCULATION IN FISHES by G. H. Satchell.
BIOETHICS, BRIDGE TO THE FUTURE by Van Rensselaer Potter.     

Studies on the extraction and back-extraction of a recombinant cutinase in a reversed micellar extraction process

This work deals with the extraction and back-extraction of a recombinant cutinase using AOT reversed micelles in isooctane. The effect of pH, ionic strength, AOT concentration and temperature on the extraction and back-extraction of the cutinase was investigated. High extraction (97%) of the cutinase was achieved at pH 7.0 with a 50 mM Tris-HCl buffer solution containing 100 mM KCl, but a low activity was detected in the reversed micellar phase. At pH 9.0, cutinase was extracted (75%) to the reversed micelles with higher activity. Cutinase was recovered (50%) from a reversed micellar phase (100 mM AOT/isooctane) into a 50 mM Tris-HCl buffered solution at pH 9.0 with 100 mM KCl, and 20°C. Protein and cutinase activity global yields of 38 and 45%, respectively, were obtained for the global process, extraction and back-extraction steps, using low ionic strength, pH 9.0, 100 mM AOT and 20°C.Maria das Graças Carneiro da Cunha acknowledges a Ph.D. fellowship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Centro de Pesquisas Aggeu Magalhães, Brasil. This work was partly financed by the BRIDGE Programme (Contract BIOT-CT91-0274(DTEE)).     

Liquid-liquid extraction of a recombinant cutinase from fermentation media with AOT reversed micelles

This work reports the extraction and back-extraction of an intracellular recombinant cutinase from complex biological media using AOT reversed micelles in isooctane. Cutinase was recovered from different complex media namely, fermentation broths and supernatants after cell disruption by osmotic shock and sonication. The application of the AOT reversed micellar system to the extraction of cutinase allowed activity yields and purification factors ranging from about 5% to 50% and 1.2 to 10.2, respectively, depending on the biological medium.Maria das Graças Carneiro da Cunha, from ITEP-Instituto Tecnológico do Estado de Pernambuco, acknowledges a Ph.D fellowship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Centro de Pesquisa Aggeu Magalhães, Recife — PE — Brasil. E. P. Melo thanks Junta Nacional de Investigação Científica, Lisboa, Portugal, for providing a Ph.D. fellowship. The scientific support given by Prof. Sílvia M. B. Costa for the spectroscopic data and further discussions are particularly acknowledged.This work was partly financed by the BRIDGE and BIOTECHNOLOGY Programmes (Contracts BIOT-CT91-0274(DTEE) and BIOT 2 CT-943016).     

Identification of an essential histidine residue at the active site of the tonoplast malate carrier in Catharanthus roseus cells

Summary The involvement of a histidyl residue in the binding or translocation step was investigated in the malate carrier at the tonoplast of Catharanthus roseus cells. The transport rate was strongly stimulated when the pH of the incubation medium was decreased from pH 7.0 to 5.0. The histidine-specific reagent diethylpyrocarbonate (DEPC) efficiently inhibited the activity of the malate carrier. Inhibition developed rapidly and was completed after 5 min at a concentration of 2 mM DEPC. The original substrate, malate, partially protected the carrier from inactivation by DEPC. Other organic acids (citrate, quinate) which are known to affect the malate transport of isolated vacuoles or tonoplast vesicles also showed protective properties. Inhibition of malate transport on tonoplast vesicles can also be achieved by photooxidation in the presence of the dye Rose Bengal. Malate also proved to protect against inactivation.The results strongly support the notion that a histidyl residue(s) is involved either in the binding or translocation of malate and that the protonation of the histidyl residue is essential to provide a high rate of malate transport.This research was supported by the Centre National de la Recherche Scientifique and by a grant from the European Community (BRIDGE program). K.-J. Dietz acknowledges support by the Jubiläumsstiftung der Julius-Maximilians-Universität Würzburg, which made the stay in Toulouse possible, and the Sonderforschungsbereich 176.     

The most abundant soluble basic protein of the stylar transmitting tract in potato (Solanum tuberosum L.) is an endochitinase

An abundant, pistil-specific basic protein has been purified and characterized from potato (Solanum tuberosum L.). A polymerase chain reaction (PCR) probe was generated for the corresponding gene using oligonucleotides based on internal peptide sequences of the protein, and the PCR probe was further employed to isolate cDNA and genomic clones. The sequence of the gene exhibits up to 70% similarity to previously described endochitinase class 1a protein sequences, and the purified protein possesses chitinase {poly[1, 4-(N-acetyl--D-glucosaminide)] glucanohydrolase, EC 3.2.1.14} activity. The protein, termed SK2, has been located by immunocytochemistry to the intercellular matrix of the stylar transmitting tract. Immunoblot analysis has shown SK2 to be distinct from the wound-induced chitinases of potato. The SK2-class of chitinase is restricted in its distribution within the Solanaceae to the sub-family Solanoidae, which includes cultivated tomato and potato species. It was absent from the Cestroidae species tested (Petunia hybrida, Nicotiana tabacum). A role for SK2 endochitinase in protecting the ovary against pollen-tubemediated pathogen ingress is proposed.Abbreviations FPLC fast protein liquid chromatography - IEF isoelectric focussing - PCR polymerase chain reaction We are indebted to Drs. E. Kombrink, J. Logemann, J. Schmidt and Mr. G. Jach (MPI für Züchtungsforschung, Köln, Germany) for advice on chitinase assays. The technical assistance of Ms. U. Seul and Mrs. B. Piegeler is gratefully acknowledged. Electron microscopy was carried out under the supervision of Drs. Brian Wells and Keith Roberts, (John Innes Centre for Plant Science Research, Norwich, UK). This research was supported by the Deutsche Forschungsgemeinschaft SPP Mechanisms of Hybrid Breeding, and the EC BRIDGE programme.     

Nucleotide sequence of the gene encoding the serotype-specific antigen of human (Wa) rotavirus: comparison with the homologous genes from simian SA11 and UK bovine rotaviruses

The nucleotide sequence of human (Wa) rotavirus genome segment 9, which encodes the serotype-specific antigen VP7, has been determined. Comparison of the deduced amino acid sequence of Wa VP7 protein to the sequences of simian SA11 and UK bovine VP7 proteins shows that the majority of the amino acid differences are clustered between amino acid residues 37 through 49, 65 through 75, 87 through 105, 122 through 126, 146 through 149, 178 through 181, and 208 through 242. A hydrophilicity profile of the three proteins reveals correlations between hydrophilic peaks, potentially antigenic determinants, and certain clusters of amino acid changes.     

Differences in the temporal dynamics of phenotypic selection among fitness components in the wild

The balance of selection acting through different fitness components (e.g. fecundity, mating success, survival) determines the potential tempo and trajectory of adaptive evolution. Yet the extent to which the temporal dynamics of phenotypic selection may vary among fitness components is poorly understood. Here, we compiled a database of 3978 linear selection coefficients from temporally replicated studies of selection in wild populations to address this question. Across studies, we find that multi-year selection through mating success and fecundity is stronger than selection through survival, but varies less in direction. We also report that selection through mating success varies more in long-term average strength than selection through either survival or fecundity. The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival. Similar patterns were apparent for the subset of studies that evaluated the temporal dynamics of selection on traits simultaneously using several different fitness components, but few such studies exist. Taken together, these results reveal key differences in the temporal dynamics of selection acting through different fitness components, but they also reveal important limitations in our understanding of how selection drives adaptive evolution.     

The influence of red cell mechanical properties on flow through single capillary-sized pores

The resistive pulse technique was used to study the influence of specific mechanical properties of the red cell on its ability to enter and flow through single capillary-sized pores with diameters of 3.6, 5.0 and 6.3 micron and lengths of 11 micron. A two-fold increase in membrane shear elasticity resulted in a 40 percent increase in the cell's transit time through a 3.6 micron pore but produced no change in transit time through a 6.3 micron pore. A two-fold increase in membrane shear viscosity produced a 40 percent increase in transit time through the 3.6 micron pore and small but significant increases in transit times through the larger pores. Osmotically dehydrated cells showed no increase in transit time through a 6.3 micron pore, but showed increases in transit times of 50 to 70 percent through 5.0 and 3.6 micron pores. Dense red cells showed increased transit times through both 5.0 micron and 6.0 micron pores. These results indicate that for cells with normal geometric properties, the membrane's shear viscosity and elasticity only influence the cell's transit through pores of 5 micron or less in diameter. However, alterations in the cell's geometric properties can extend the influence of membrane shear properties to larger diameter pores.     

DNA内电子传递特性的研究进展

评述了近年来对DNA的电子传递特性的研究进展,并介绍了关于DNA电子传递机制及理论的研究结果。同时,结合从无序体系的角度研究DNA内电子传递特性的工作,对围绕DNA内电子传递问题的争论要点以及尚存在的问题进行了探讨。     

Passage of Treponema pallidum Through Membrane Filters of Various Pore Sizes

The passage of Treponema pallidum through commercially available Millipore membrane filters of various pore sizes was examined. No microscopically detectable organisms passed through a filter with a pore diameter of 0.22 mum. As pore size was increased, progressively more organisms passed through. Motile organisms passed through filters to a greater extent than nonmotile ones; however, 22% of the motile and 50% of the nonmotile T. pallidum organisms did not pass through the largest pore diameter tested (14.0 mum). Filtration of T. pallidum suspensions through membrane filters may offer a way of separating the organisms from larger particles of debris which accompany their extraction from rabbit testicular syphilomas.     

经支气管镜气管插管与常规气管插管救治呼吸衰竭对比分析

目的：回顾性分析呼吸机辅助呼吸救治危重呼吸衰竭患者气管插管方式对于救治成功率的影响。方法：我科收治的各种呼吸衰竭患者94例,回顾分析插管方式对于救治成功率、引发心跳骤停及其对心肺复苏效果的影响。结果：经纤维支气管镜经口气管插管（35例）与经直接喉镜经口（59例）引发心跳骤停有明显统计学差异（X^2=11．5,v=1,t〈0．001）。经直接喉镜经口气管插管在术前用药与否对引发心跳骤停并无统计学意义,但是对于引发心跳骤停后心肺复苏成功率确有明显统计学意义。结论：经纤维支气管镜气管插管具有较高的安全性,在经直接喉镜气管插管是选择镇静药或浅麻醉药物应慎重,尽力避免心跳骤停和心肺复苏失败。     

Flux through glycine cleavage system in isolated hepatocytes: effects of glucagon, cAMP, and calcium

The hepatic glycine cleavage system (GCS) is the principal route for the metabolism of glycine in mammals. Flux through the GCS in isolated rat hepatocytes was stimulated by about 100% by glucagon (10(-7) M), forskolin (10(-4) M), and dibutyryl cAMP (10(-4) M). The stimulation of flux through the GCS by these agents was accompanied by marked elevation of cellular cAMP levels. A significant correlation was observed between increased cellular cAMP levels induced by glucagon and stimulation of flux through the GCS by glucagon. Exclusion of calcium from the incubation medium reduced the basal flux by 38%, but did not affect the degree of stimulation of flux through the GCS by glucagon. A single intraperitoneal injection of glucagon to rats prior to isolation of hepatocytes resulted in a 76% stimulation of flux through the GCS. These hepatocytes with stimulated flux through the GCS showed reduced sensitivity for further stimulation by glucagon. Half-maximal stimulation of flux through the GCS occurred at 3.8 +/- 1.1 and 8.5 +/- 1.4 nM glucagon in hepatocytes isolated from control and glucagon-injected rats, respectively. We conclude that cAMP is involved in the regulation of flux through the GCS by glucagon.