The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update

Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density Basic Protocol 2: Calling peaks for ChIP-seq data Basic Protocol 3: Compare datasets using genomic coordinates Basic Protocol 4: Working with multiple alignments Basic Protocol 5: Single cell RNA-seq.

Fostering accessible online education using Galaxy as an e-learning platform

The COVID-19 pandemic is shifting teaching to an online setting all over the world. The Galaxy framework facilitates the online learning process and makes it accessible by providing a library of high-quality community-curated training materials, enabling easy access to data and tools, and facilitates sharing achievements and progress between students and instructors. By combining Galaxy with robust communication channels, effective instruction can be designed inclusively, regardless of the students' environments.

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Background

The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets.

Results

Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal.

Conclusions

The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.

Pulmonary Lymphangioleiomyomatosis originates in the pleural mesothelial cell population

Lymphangioleiomyomatosis (LAM) is a cystic lung disease mainly affecting women, in which degradation of the lung parenchyma is associated with a cell of unknown provenance, known as a LAM cell. LAM cells carry TSC2 mutations and can be identified in the lung parenchyma by their expression of both smooth muscle actin and antigens characteristic of melanocytes and melanocytic tumors. The nature of the cell-of-origin of LAM is controversial, and despite continued research effort remains elusive. Further, it has not been possible to culture pulmonary LAM cells in vitro, and current research relies on cells and animal models which may not recapitulate all features of the disease. We noted aberrant expression of melanoma antigens in pleural mesothelial cells in lung tissue from LAM patients, indicating that these cells could be the precursors of parenchymal LAM cells. We hypothesise that loss of tuberin function following TSC2 mutation in the mesothelial cell lineage gives rise to the cell-of-origin of pulmonary LAM (P-LAM), and of other associated conditions commonly noted in LAM patients. The unique properties of mesothelial cells provide a straightforward explanation of the diverse presentation of LAM.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Galaxy (https://galaxyproject.org) is a web-based computational workbench used by tens of thousands of scientists across the world to analyze large biomedical datasets. Since 2005, the Galaxy project has fostered a global community focused on achieving accessible, reproducible, and collaborative research. Together, this community develops the Galaxy software framework, integrates analysis tools and visualizations into the framework, runs public servers that make Galaxy available via a web browser, performs and publishes analyses using Galaxy, leads bioinformatics workshops that introduce and use Galaxy, and develops interactive training materials for Galaxy. Over the last two years, all aspects of the Galaxy project have grown: code contributions, tools integrated, users, and training materials. Key advances in Galaxy's user interface include enhancements for analyzing large dataset collections as well as interactive tools for exploratory data analysis. Extensions to Galaxy's framework include support for federated identity and access management and increased ability to distribute analysis jobs to remote resources. New community resources include large public servers in Europe and Australia, an increasing number of regional and local Galaxy communities, and substantial growth in the Galaxy Training Network.

Community-Driven Data Analysis Training for Biology

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.

Gemcitabine enhances the efficacy of reovirus-based oncotherapy through anti-tumour immunological mechanisms

BACKGROUND

Reovirus preferentially infects and kills cancer cells and is currently undergoing clinical trials internationally. While oncolysis is the primary mode of tumour elimination, increasing evidence illustrates that reovirus additionally stimulates anti-tumour immunity with a capacity to target existing and possibly relapsing cancer cells. These virus-induced anti-tumour immune activities largely determine the efficacy of oncotherapy. On the other hand, anti-viral immune responses can negatively affect oncotherapy. Hence, the strategic management of anti-tumour and anti-viral immune responses through complementary therapeutics is crucial to achieve the maximum anti-cancer benefits of oncotherapy.

METHODS

Intra-peritoneal injection of mouse ovarian surface epithelial cells (ID8 cells) into wild-type C57BL/6 mice was treated with a therapeutic regimen of reovirus and/or gemcitabine and then analysed for prolonged survival, disease pathology, and various immunological parameters. Furthermore, in vitro analyses were conducted to assess apoptosis, viral spread, and viral production during reovirus and/or gemcitabine treatment.

RESULTS

We demonstrate that reovirus and gemcitabine combination treatment postpones peritoneal carcinomatosis development and prolongs the survival of cancer-bearing hosts. Importantly, these anti-cancer benefits are generated through various immunological mechanisms, including: (1) inhibition of myeloid-derived suppressor cells recruitment to the tumour microenvironment, (2) downmodulation of pro-MDSC factors, and (3) accelerated development of anti-tumour T-cell responses.

CONCLUSION

The complementation of reovirus with gemcitabine further potentiates virus-initiated anti-cancer immunity and enhances the efficacy of oncotherapy. In the context of ongoing clinical trials, our findings represent clinically relevant information capable of enhancing cancer outcomes.

CCR3 induced-p42/44 MAPK activation protects against staurosporine induced-DNA fragmentation but not apoptosis in airway smooth muscle cells

BACKGROUND

Chemokine receptors (CCRs) are expressed on airway smooth muscle (ASM) cells. As their ligands are present in the airways in asthma, we hypothesized that ASM CCR activation could promote the increase in ASM mass seen in patients with chronic asthma.

OBJECTIVE

To determine which CCRs are expressed by ASM cells and their potential functional relevance to the chronic airway changes seen in asthma.

METHODS

CCR expression in primary ASM cell cultures and airway biopsies from patients with and without asthma was examined by RT-PCR, fluorescence-activated cell sorting and immunohistochemistry. ASM p42/44 MAPK activity, proliferation, migration and apoptosis were examined by western blotting, thymidine incorporation, transwell assay and TUNEL assay respectively.

RESULTS

CCR3 was the most frequently expressed CCR protein and was present on 79 ± 14% of cells. CX3CR1 and CXCR6 were present on 6% and 11% of cells respectively. CCR3 ligands CCL11 and CCL24 caused rapid activation of p42/44 MAPK but not Akt. CCR3 activation did not affect ASM proliferation, migration or VEGF secretion. DNA fragmentation detected by TUNEL staining could be induced by staurosporine and Fas activation although only Fas activation resulted in caspase 3 cleavage. CCL11 and CCL24 protected ASM cells against DNA fragmentation dependent upon p42/44 MAPK activity only via caspase 3 independent pathways. CCR3 was expressed in the smooth muscle and epithelium in the airways of patients with and without asthma. Smooth muscle cell DNA fragmentation in the airways of patients with stable asthma and controls was very uncommon.

CONCLUSIONS AND CLINICAL RELEVANCE

CCR3 is strongly expressed by ASM cells in vitro and in vivo. Protection against cell death by CCR3 activation is dependent on p42/44 MAPK but does not affect caspase 3 mediated apoptosis.

Using Galaxy to perform large-scale interactive data analyses

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd-party analysis tools.

MetaBase--the wiki-database of biological databases

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.

Rectus abdominis myocutaneous flaps for perineal reconstruction: modifications to the technique based on a large single-centre experience

INTRODUCTION

Perineal wound breakdown with delayed wound healing represents a significant cause of morbidity following surgery and radiotherapy to the perineum. The rectus abdominis myocutaneous (RAM) flap has been used increasingly to reconstruct the perineum with good effect. We describe our six-year experience of reconstruction of the perineum with the RAM flap and share some surgical adjuncts we believe are useful.

METHODS

We conducted a retrospective case note review of all patients who underwent a reconstruction of the perineum using the RAM flap between August 2003 and October 2009. Indications for the flap, complication rates and outcomes were all observed.

RESULTS

We conducted 16 RAM flap procedures, 15 of which (94%) were primary repairs and 1 (6%) a secondary repair. Three (19%) developed donor site hernias, two (12.5%) developed minor perineal wound infections, eight (50%) developed minor perineal wound breakdown and in one (6%) flap failure was observed. No perineal hernias were observed. There were no surgical mortalities.

CONCLUSIONS

The RAM flap has a high success rate and an acceptable morbidity rate and is a useful tool in the reconstruction of complex perineal wounds. Modifications to the standard surgical technique may reduce complications and improve the versatility of this flap.

Short-term outcomes with intrathecal versus epidural analgesia in laparoscopic colorectal surgery

BACKGROUND

Epidural analgesia is the mainstay of perioperative pain management in enhanced recovery programmes. This study compared short-term outcomes following epidural or intrathecal analgesia in patients undergoing elective laparoscopic colorectal surgery.

METHODS

A single-centre observational study was carried out in 175 consecutive patients who had elective laparoscopic colorectal surgery for benign or malignant disease within an enhanced recovery programme. Seventy-six patients received epidural analgesia and 99 had a single injection of intrathecal analgesia to provide perioperative pain control.

RESULTS

Patients who had intrathecal analgesia had a reduced median postoperative pain score compared with those receiving epidural analgesia (0 versus 3.5; P < 0.001), an earlier return to mobility (1 versus 4 days; P < 0.001) and a shorter hospital stay (4 versus 5 days; P < 0.001). Return to normal gut function and postoperative nausea and vomiting were similar in the two groups.

CONCLUSION

Intrathecal analgesia may have advantages over epidural analgesia in patients undergoing laparoscopic colorectal surgery.

Management of the asymptomatic primary in the palliative treatment of metastatic colorectal cancer

OBJECTIVE

The management of the asymptomatic primary in stage IV colorectal cancer presents a dilemma. There is an increased morbidity and mortality from surgical resection. Nonresectional management of the primary is associated with the risks of obstruction, perforation or haemorrhage. Our practice in patients with stage IV disease is palliative chemotherapy and symptom control. We reviewed our nonoperatively managed patients with colorectal liver metastases in order to identify the percentage of patients requiring urgent operative interventions for symptoms related to the primary. SUBJECTS/PATIENTS AND METHOD: A retrospective review of all patients treated for stage IV disease at our institution from 2003-2006 was undertaken. Patients were identified from multidisciplinary team (MDT) records. Demographic detail, treatment, and follow-up data were extracted from hospital records. These were analysed with Microsoft Excel.

RESULTS

Thirty-seven patients were identified. 26 Male:11 Female. Median age 63 years (range 38-78). The median survival from diagnosis was 14 months. Three (8%) patients developed obstruction whilst having palliative chemotherapy. Two required a defunctioning stoma, and one was treated by means of a stent. There were no similarities between these three patients in terms of age, sex, site or stage of primary, volume of liver metastases, and alkaline phosphatase (ALP) or carcinoembryonic antigen (CEA) levels.

CONCLUSION

Of 37 patients initially treated palliatively for stage IV colorectal cancer, 92% required no surgical treatment of their primary. Therefore it is the experience of this MDT that it is acceptable to treat such patients in an expectant manner. It is not possible to predict those patients, likely to require surgical intervention.

Application of the BSG guidelines to a colonoscopy waiting list

Abstract Objective Currently priority for colonoscopy is given to diagnostic and therapeutic procedures. Surveillance colonoscopies place a significant demand on the service. These are held on a separate waiting list in our institution, which is currently several years behind. The purpose of this study was to apply the BSG guidelines to this waiting list in our institution in order to ascertain whether patients are appropriately listed. Method This was a retrospective review. The patients on the waiting list whose procedures were due in 2004 and 2005 formed the study group. Information on demographics, previous colonoscopies, and indication was taken from the case notes. Results were analysed using Microsoft Excel. Results A total of 172 patients were overdue their colonoscopies. If the BSG guidelines were strictly adhered to, 49% of these patients were inappropriately listed. If applied less rigidly, 42% of patients should not have been on the list. The reasons for removal from the list were as follows: Thirty-nine patients were older than the upper age limit, 23 had had clear colonoscopies after adenomatous polyp follow up, four were listed for diverticular disease follow up, four for metaplastic polyps, one for constipation and one for per rectum (PR) bleed follow up. Conclusion With strict application of the BSG guidelines to a surveillance colonoscopy waiting list, 49% of the patients on the list do not need the procedure. It is recommended that consultant led education and control of the waiting list be used to reduce unnecessary investigations.

Organization of the pronephric kidney revealed by large-scale gene expression mapping

Gene expression mapping reveals 8 functionally distinct domains in the Xenopus pronephros. Interestingly, no structure equivalent to the mammalian collecting duct is identified.

Background

The pronephros, the simplest form of a vertebrate excretory organ, has recently become an important model of vertebrate kidney organogenesis. Here, we elucidated the nephron organization of the Xenopus pronephros and determined the similarities in segmentation with the metanephros, the adult kidney of mammals.

Results

We performed large-scale gene expression mapping of terminal differentiation markers to identify gene expression patterns that define distinct domains of the pronephric kidney. We analyzed the expression of over 240 genes, which included members of the solute carrier, claudin, and aquaporin gene families, as well as selected ion channels. The obtained expression patterns were deposited in the searchable European Renal Genome Project Xenopus Gene Expression Database. We found that 112 genes exhibited highly regionalized expression patterns that were adequate to define the segmental organization of the pronephric nephron. Eight functionally distinct domains were discovered that shared significant analogies in gene expression with the mammalian metanephric nephron. We therefore propose a new nomenclature, which is in line with the mammalian one. The Xenopus pronephric nephron is composed of four basic domains: proximal tubule, intermediate tubule, distal tubule, and connecting tubule. Each tubule may be further subdivided into distinct segments. Finally, we also provide compelling evidence that the expression of key genes underlying inherited renal diseases in humans has been evolutionarily conserved down to the level of the pronephric kidney.

Conclusion

The present study validates the Xenopus pronephros as a genuine model that may be used to elucidate the molecular basis of nephron segmentation and human renal disease.

A high-resolution anatomical ontology of the developing murine genitourinary tract

Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided.

Effective teamwork in healthcare: research and reality

Issues affecting health workplaces range from serious concerns that could affect the immediate physical safety of workers to those that would improve productivity and efficiency, or make an organization a preferred employer. Employers and workers might consider effective teamwork an asset, but for patients it is a prerequisite. This paper reviews the evidence for effective teamwork, primarily that gathered by a research team funded by the Canadian Health Services Research Foundation (CHSRF). We also review the expert opinion provided by a group of 25 researchers and decision makers convened by CHSRF in late 2005 at a forum for discussion about issues related to effective teamwork. Included in the retreat were representatives from professional organizations and occupations as well as areas such as legal liability. Taken together, the research and expert opinion provide a comprehensive overview of the benefits of effective teamwork and the conditions needed for its implementation. In addition, we review policy and management perspectives on the most significant challenges to the implementation of effective teamwork in the Canadian context, and potential opportunities to overcome these obstacles.

The Zebrafish Information Network: the zebrafish model organism database

The Zebrafish Information Network (ZFIN; ) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information. Recent enhancements to ZFIN include (i) comprehensive curation of gene expression data from the literature and from directly submitted data, (ii) increased support and annotation of the genome sequence, (iii) expanded use of ontologies to support curation and query forms, (iv) curation of morpholino data from the literature, and (v) increased versatility of gene pages, with new data types, links and analysis tools.

The Zebrafish Information Network (ZFIN): the zebrafish model organism database

The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data. ZFIN is publicly accessible at http://zfin.org. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data. Recent enhancements to ZFIN include: (i) an anatomical dictionary that provides a controlled vocabulary of anatomical terms, grouped by developmental stages, that may be used to annotate and query gene expression data; (ii) gene expression data; (iii) expanded support for genome sequence; (iv) gene annotation using the standardized vocabulary of Gene Ontology (GO) terms that can be used to elucidate relationships between gene products in zebrafish and other organisms; and (v) collaborations with other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnections based on shared curation.

Determining the spatial distribution of viable and nonviable bacteria in hydrated microcosm dental plaques by viability profiling

AIMS

The aim of this study was to use confocal laser scanning microscopy (CLSM) to examine the spatial distribution of both viable and nonviable bacteria within microcosm dental plaques grown in vitro. Previous in vivo studies have reported upon the distribution of viable bacteria only.

METHODS AND RESULTS

Oral biofilms were grown on hydroxyapatite (HA) discs in a constant-depth film fermenter (CDFF) from a saliva inoculum. The biofilms were stained with the BacLight LIVE/DEAD system and examined by CLSM. Fluorescence intensity profiles through the depth of the biofilm showed an offset between the maximum viable intensity and the maximum nonviable intensity. Topographical differences between the surface properties of the viable and nonviable biofilm virtual surfaces were also measured.

CONCLUSIONS

The profile of fluorescence intensity from viable and nonviable staining suggested that the upper layers of the biofilm contain proportionally more viable bacteria than the lower regions of the biofilm.

SIGNIFICANCE AND IMPACT OF STUDY

Viability profiling records the transition from predominantly viable to nonviable bacteria through biofilms suggesting that this technique may be of use for quantifying the effects of antimicrobial compounds upon biofilms. The distribution of viable bacteria was similar to that found in dental plaque in vivo suggesting that the CDFF produces in vitro biofilms which are comparable to their in vivo counterparts in terms of the spatial distribution of viable bacteria.

Delayed post-traumatic osteonecrosis of a vertebral body (Kummell's disease)

Kummell's disease is a rare spinal disorder characterized as avascular necrosis of a vertebral body occurring in a delayed fashion after minor trauma. The disease derives its name from the German surgeon Hermann Kummell, who described a series of patients with the disorder in 1895. Kummell's disease is distinguished from typical osteoporotic compression fractures, by virtue of the fact that patients with Kummell's disease develop symptoms in delayed fashion. In addition, Kummell's disease exhibits different signal characteristics on magnetic resonance imaging when compared to osteoporotic compression fractures. In this review we discuss the pathophysiology, histopathology and treatment of this interesting disorder.

Initiation and early patterning of the endoderm

We review the early stages of endoderm formation in the major animal models. In Amphibia maternal molecules are important in initiating endoderm formation. This is followed by successive signaling events that establish and then pattern the endoderm. In other organisms there are differences in endodermal development, particularly in the initial, prephylotypic stages. Later many of the same key families of transcription factors and signaling cassettes are used in all animals, but more work will be needed to establish exact evolutionary homologies.

Changes in embryonic cell fate produced by expression of an endodermal transcription factor, Xsox17

Many molecules induce the ectopic expression of tissue-specific genes in Xenopus embryos. Conversely, interfering with their activity disrupts patterns of gene expression, implicating them in normal development. Does this mean that they control cell fate (i.e. position, as well as differentiation)? Xsox17alpha and beta can induce ectopic expression of endodermal markers; inhibiting their function suppresses expression of endodermal marker genes in the developing gut (Cell 91 (1997) 397). Here we show the effect of these manipulations on cell lineage. Expressing Xsox17 in a cells normally fated to become ectoderm causes their descendants either to relocate into the embryonic gut or to die at a late developmental stage. Conversely, disrupting Xsox17 activity in cells normally fated to be endodermal causes them to enter mesodermal and ectodermal lineages.

Interference of antibody production to hepatitis B surface antigen in a combination hepatitis A/hepatitis B vaccine

A randomized trial comparing 3 manufacturing consistency lots of a combination hepatitis A/hepatitis B vaccine to each other and to hepatitis A vaccine and hepatitis B vaccine given separately and concurrently was done to evaluate safety, tolerability, and immunogenicity. Healthy volunteers >/=11 years of age were divided into 4 groups. Each of 3 groups received a separate consistency lot of the combination vaccine, and 1 group received separate but concurrent injections of hepatitis A and hepatitis B vaccines. Injections were given at weeks 0 and 24. The combination vaccine was generally well tolerated. The hepatitis A portion of the combination vaccine produced clinically acceptable high seropositivity rates 4 and 52 weeks after the first injection. The hepatitis B portion of the vaccine did not produce clinically acceptable seropositivity rates 4 weeks after the second injection. Lack of antibody production may be attributed, at least in part, to immunologic interference.

Mode of action of VegT in mesoderm and endoderm formation

mRNA encoding the T-box transcription factor VegT is located throughout the vegetal pole of the Xenopus egg and is believed to play an important part in endoderm and mesoderm formation. We find that VegT generates endoderm both by cell-autonomous action and by generating TGF-beta family signals, the latter being entirely responsible for its mesoderm-inducing activity. Signalling molecules induced cell-autonomously by VegT include derriere, Xnr4 and activin B. Xnr1 and Xnr2 are also induced, but primarily in a non-autonomous manner. All of these signalling molecules are found in the blastula and gastrula vegetal pole and induce both endoderm and mesoderm in the animal cap assay, and hence are good candidates both for the endogenous zygotic mesoderm-inducing signal and for reinforcing the vegetal expression of endoderm markers.

Biomarkers of oxidative stress are significantly elevated in Down syndrome

There is convincing epidemiological and in vitro evidence of chronic oxidative stress in individuals with Down syndrome (DS). These individuals develop Alzheimer like changes in the brain in their 30s and 40s. The incidence of autoimmune diseases and cataracts is significantly increased, and the overall ageing process is accelerated. In vitro studies show that impaired viability of DS neurons may be amended by simple chemical antioxidants, such as vitamin E, BHT and propyl gallate, clearly indicative of oxyl radical involvement. However, because of the lack of in vivo experiments, the role of oxidative stress in DS remains controversial. We report here on the results of the chemical analyses of urine samples of 166 individuals, where DS subjects were matched by their siblings. The levels of 8-hydroxy-2'-deoxyguanosine (2.35 +/- 1.69 in DS vs. 1.35 +/- 1.04 in controls, P = 0.00011), a biomarker of oxidative damage to DNA, and malondialdehyde (0.255 +/- 0.158 in DS vs. 0.204 +/- 0.128 in controls, P = 0.033), a biomarker of lipid peroxidation, are significantly elevated in individuals with DS. Dietary influences failed to show any significant correlation with the oxidative stress biomarkers. These results provide direct evidence for increased oxidative stress in individuals with DS.

Xsox17alpha and -beta mediate endoderm formation in Xenopus

We have isolated two Xenopus relatives of murine Sox17 expressed in gastrula presumptive endoderm. Xsox17alpha and -beta expression can be induced in animal caps by activin, but not by FGF. Ectopic expression of these genes in animal caps induces the expression of endoderm markers; this induction is blocked by overexpression of a fusion of the Xsox17beta HMG domain to the Drosophila Engrailed repressor domain, as is induction of endoderm markers by activin and the expression of endodermal markers in whole embryos and isolated vegetal poles. These experiments, as well as the effects of the mRNAs on embryo phenotypes, suggest that the Xsox17 genes mediate an activin-induced endoderm differentiation pathway in animal caps and are involved in normal endoderm differentiation in embryos.