FlyBase: updates to the Drosophila genes and genomes database

FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

A new experimental evidence-weighted signaling pathway resource in FlyBase

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the comprehensive and systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila.

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).

Comparing the history of signalling pathway research using the research publication record of representative genes

The development and application of genetic techniques in the fruit fly Drosophila melanogaster underlies some major advances in the understanding of metazoan development and biology. To examine whether the publication record for signalling pathway genes can indicate which factors have shaped pathway research, the publication history of selected genes is used to compare differences in research output over time. This is used to discuss how research trends may be shaped by a variety of factors such as advances in technology, ease of study and importance to human health.

A new experimental evidence-weighted signaling pathway resource in FlyBase

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a comprehensive and dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways in Drosophila .

Summary statement

Comprehensive curation of Drosophila signaling pathways and new visual displays of the pathways provides a new FlyBase resource for researchers, and new insights into signaling pathway architecture.

PANGEA: a new gene set enrichment tool for Drosophila and common research organisms

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/ ), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualisations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.

Harmonizing model organism data in the Alliance of Genome Resources

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

FlyBase: a guided tour of highlighted features

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As FlyBase enters our fourth decade of service to the research community, we reflect on our unique aspects and look forward to our continued collaboration with the larger research and model organism communities. In this study, we emphasize the dedicated reports and tools we have constructed to meet the specialized needs of fly researchers but also to facilitate use by other research communities. We also highlight ways that we support the fly community, including an external resources page, help resources, and multiple avenues by which researchers can interact with FlyBase.

FlyPhoneDB: an integrated web-based resource for cell-cell communication prediction in Drosophila

Multicellular organisms rely on cell-cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell-cell communication pathways can be inferred from transcriptomic datasets based on ligand-receptor expression. Recently, data generated from single-cell RNA sequencing have enabled ligand-receptor interaction predictions at an unprecedented resolution. While computational methods are available to infer cell-cell communication in vertebrates such a tool does not yet exist for Drosophila. Here, we generated a high-confidence list of ligand-receptor pairs for the major fly signaling pathways and developed FlyPhoneDB, a quantification algorithm that calculates interaction scores to predict ligand-receptor interactions between cells. At the FlyPhoneDB user interface, results are presented in a variety of tabular and graphical formats to facilitate biological interpretation. To illustrate that FlyPhoneDB can effectively identify active ligands and receptors to uncover cell-cell communication events, we applied FlyPhoneDB to Drosophila single-cell RNA sequencing data sets from adult midgut, abdomen, and blood, and demonstrate that FlyPhoneDB can readily identify previously characterized cell-cell communication pathways. Altogether, FlyPhoneDB is an easy-to-use framework that can be used to predict cell-cell communication between cell types from single-cell RNA sequencing data in Drosophila.

Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases

The role of the blood-brain barrier (BBB) in Alzheimer's and other neurodegenerative diseases is still the subject of many studies. However, those studies using high-throughput methods have been compromised by the lack of Gene Ontology (GO) annotations describing the role of proteins in the normal function of the BBB. The GO Consortium provides a gold-standard bioinformatics resource used for analysis and interpretation of large biomedical data sets. However, the GO is also used by other research communities and, therefore, must meet a variety of demands on the breadth and depth of information that is provided. To meet the needs of the Alzheimer's research community we have focused on the GO annotation of the BBB, with over 100 transport or junctional proteins prioritized for annotation. This project has led to a substantial increase in the number of human proteins associated with BBB-relevant GO terms as well as more comprehensive annotation of these proteins in many other processes. Furthermore, data describing the microRNAs that regulate the expression of these priority proteins have also been curated. Thus, this project has increased both the breadth and depth of annotation for these prioritized BBB proteins. Database URLhttps://www.ebi.ac.uk/QuickGO/.

FlyBase: updates to the Drosophila melanogaster knowledge base

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

FlyBase 2.0: the next generation

FlyBase (flybase.org) is a knowledge base that supports the community of researchers that use the fruit fly, Drosophila melanogaster, as a model organism. The FlyBase team curates and organizes a diverse array of genetic, molecular, genomic, and developmental information about Drosophila. At the beginning of 2018, ‘FlyBase 2.0’ was released with a significantly improved user interface and new tools. Among these important changes are a new organization of search results into interactive lists or tables (hitlists), enhanced reference lists, and new protein domain graphics. An important new data class called ‘experimental tools’ consolidates information on useful fly strains and other resources related to a specific gene, which significantly enhances the ability of the Drosophila researcher to design and carry out experiments. With the release of FlyBase 2.0, there has also been a restructuring of backend architecture and a continued development of application programming interfaces (APIs) for programmatic access to FlyBase data. In this review, we describe these major new features and functionalities of the FlyBase 2.0 site and how they support the use of Drosophila as a model organism for biological discovery and translational research.

The DNA polymerases of Drosophila melanogaster

DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.

Annotation of gene product function from high-throughput studies using the Gene Ontology

High-throughput studies constitute an essential and valued source of information for researchers. However, high-throughput experimental workflows are often complex, with multiple data sets that may contain large numbers of false positives. The representation of high-throughput data in the Gene Ontology (GO) therefore presents a challenging annotation problem, when the overarching goal of GO curation is to provide the most precise view of a gene's role in biology. To address this, representatives from annotation teams within the GO Consortium reviewed high-throughput data annotation practices. We present an annotation framework for high-throughput studies that will facilitate good standards in GO curation and, through the use of new high-throughput evidence codes, increase the visibility of these annotations to the research community.

Using FlyBase to Find Functionally Related Drosophila Genes

For more than 25 years, FlyBase ( flybase.org ) has served as an online database of biological information on the genus Drosophila, concentrating on the model organism D. melanogaster. Traditionally, FlyBase data have been organized and presented at a gene-by-gene level, which remains a useful perspective when the object of interest is a specific gene or gene product. However, in the modern era of a fully sequenced genome and an increasingly characterized proteome, it is often desirable to compile and analyze lists of genes related by a common function. This may be achieved in FlyBase by searching for genes annotated with relevant Gene Ontology (GO) terms and/or protein domain data. In addition, FlyBase provides preassembled lists of functionally related D. melanogaster genes within "Gene Group" reports. These are compiled manually from the published literature or expert databases and greatly facilitate access to, and analysis of, established gene sets. This chapter describes protocols to produce lists of functionally related genes in FlyBase using GO annotations, protein domain data and the Gene Groups resource, and provides guidance and advice for their further analysis and processing.

Exploring FlyBase Data Using QuickSearch

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2016 by John Wiley & Sons, Inc.

The translation factors of Drosophila melanogaster

Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical ‘translation factors’. Surprisingly, the translation factors of Drosophila melanogaster have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in D. melanogaster, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from Drosophila about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.

FlyBase: establishing a Gene Group resource for Drosophila melanogaster

Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multi-protein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a ‘Gene Group’ resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.

Structural and biochemical characterization of a trapped coenzyme A adduct of Caenorhabditis elegans glucosamine-6-phosphate N-acetyltransferase 1

Glucosamine-6-phosphate N-acetyltransferase is an essential enzyme of the eukaryotic UDP-GlcNAc biosynthetic pathway. A crystal structure at 1.55 Å resolution revealed a highly unusual covalent product complex and biochemical studies investigated the function of a fully conserved active-site cysteine.

Glucosamine-6-phosphate N-acetyltransferase 1 (GNA1) produces GlcNAc-6-phosphate from GlcN-6-phosphate and acetyl coenzyme A. Early mercury-labelling experiments implicated a conserved cysteine in the reaction mechanism, whereas recent structural data appear to support a mechanism in which this cysteine plays no role. Here, two crystal structures of Caenorhabditis elegans GNA1 are reported, revealing an unusual covalent complex between this cysteine and the coenzyme A product. Mass-spectrometric and reduction studies showed that this inactive covalent complex can be reactivated through reduction, yet mutagenesis of the cysteine supports a previously reported bi-bi mechanism. The data unify the apparently contradictory earlier reports on the role of a cysteine in the GNA1 active site.

DNA-templated protein arrays for single-molecule imaging

Single-particle electron cryomicroscopy permits structural characterization of noncrystalline protein samples, but throughput is limited by problems associated with sample preparation and image processing. Three-dimensional density maps are reconstructed from high resolution but noisy images of individual molecules. We show that self-assembled DNA nanoaffinity templates can create dense, nonoverlapping arrays of protein molecules, greatly facilitating data collection. We demonstrate this technique using a G-protein-coupled membrane receptor, a soluble G-protein, and a signaling complex of both molecules.

Constitutive dimerization of the G-protein coupled receptor, neurotensin receptor 1, reconstituted into phospholipid bilayers

Neurotensin receptor 1 (NTS1), a Family A G-protein coupled receptor (GPCR), was expressed in Escherichia coli as a fusion with the fluorescent proteins eCFP or eYFP. A fluorophore-tagged receptor was used to study the multimerization of NTS1 in detergent solution and in brain polar lipid bilayers, using fluorescence resonance energy transfer (FRET). A detergent-solubilized receptor was unable to form FRET-competent complexes at concentrations of up to 200 nM, suggesting that the receptor is monomeric in this environment. When reconstituted into a model membrane system at low receptor density, the observed FRET was independent of agonist binding, suggesting constitutive multimer formation. In competition studies, decreased FRET in the presence of untagged NTS1 excludes the possibility of fluorescent protein-induced interactions. A simulation of the experimental data indicates that NTS1 exists predominantly as a homodimer, rather than as higher-order multimers. These observations suggest that, in common with several other Family A GPCRs, NTS1 forms a constitutive dimer in lipid bilayers, stabilized through receptor-receptor interactions in the absence of other cellular signaling components. Therefore, this work demonstrates that well-characterized model membrane systems are useful tools for the study of GPCR multimerization, allowing fine control over system composition and complexity, provided that rigorous control experiments are performed.

Improved design of nasogastric feeding tubes

Disappointed with the overall performance of weighted and unweighted nasogastric feeding tubes, a design programme was initiated which resulted in the development of two new nasogastric tubes, one weighted and one unweighted. The tubes were manufactured with polyurethane rather than polyvinylchloride (PVC) which permitted an increase in diameter of the internal lumen which in turn was coated with water activated lubricant to ease removal of the introducer wire. A specially modelled outflow port was incorporated into the tips of both tubes. The performance of the two new polyurethane nasogastric feeding tubes was assessed under controlled trial condition using as a reference a widely used PVC unweighted open ended tube. While intubation times were similar in patients without concurrent endotracheal intubation, it took a significantly shorter time to intubate patients with concurrent endotracheal intubation with the new weighted tube. Following tube intubation, it was possible to aspirate gastric contents significantly more often through the new polyurethane tubes (p < 0.001) than through the PVC tube, and the unweighted polyurethane tube stayed in situ longer (p < 0.05) than the PVC tube. The newly designed polyurethane nasogastric feeding tubes are the first tubes that have been shown to have advantages over the simpler type of open ended, unweighted PVC nasogastric feeding tubes.

Do fibre containing enteral diets have advantages over existing low residue diets?

This study investigated the influence of fibre on the pattern of absorption of protein and carbohydrate following administration of polymeric enteral diet and also the effect of added fibre on frequency of bowel action, stool weight and gastrointestinal side effects during enteral nutrition. No difference was seen in frequency of bowel action, stool weight or gastrointestinal side effects in five patients fed with either a fibre free polymeric diet or with the same diet augmented with 24 g fibre/24 h. Addition of fibre did not significantly alter breath hydrogen excretion. In an oral tolerance test on six normal subjects, the post prandial rises in blood glucose and levels of 17 amino acids were similar on ingestion of a fibre containing or fibre free test meal.

Limitations and drawbacks of 'fine bore' nasogastric feeding tubes

The clinical use of unweighted nasogastric feeding tubes (n = 491) was compared with that of weighted nasogastric feeding tubes. No advantage was found in the use of the weighted tubes.

The roles of lactose and Clostridium difficile in the pathogenesis of enteral feeding associated diarrhoea

This study investigated the influence of the disaccharide lactose on the incidence of clinically significant enteral feeding associated diarrhoea. In this double blind study both groups each of 25 patients were randomised to receive either a lactose containing diet Clinifeed 400 in 25 patients or a lactose free diet Ensure in 25 patients. Diarrhoea occurred with equal frequency in both treatment groups, even in those patients with symptomatic and biochemical evidence of impaired lactose handling. Although the onset of diarrhoea was significantly associated with antibiotic administration (p<0.01), Cl. difficile was not isolated from the stools of any patient with diarrhoea.

Neurotensin receptor type 1: Escherichia coli expression, purification, characterization and biophysical study

NT (neurotensin) is an endogenous tridecapeptide neurotransmitter found in the central nervous system and gastrointestinal tract. One receptor for NT, NTS1, belongs to the GPCR (G-protein-coupled receptor) superfamily, has seven putative transmembrane domains, and is being studied by a range of single-molecule, functional and structural approaches. To enable biophysical characterization, sufficient quantities of the receptor need to be expressed and purified in an active form. To this end, rat NTS1 has been expressed in Escherichia coli in an active ligand-binding form at the cell membrane and purified in sufficient amounts for structural biology studies either with or without fluorescent protein [YFP (yellow fluorescent protein) and CFP (cyan fluorescent protein)] fusions. Ligand binding has been demonstrated in a novel SPR (surface plasmon resonance) approach, as well as by conventional radioligand binding measurements. These improvements in production of NTS1 now open up the possibility of direct structural studies, such as solid-state NMR to interrogate the NT-binding site, EM (electron microscopy), and X-ray crystallography and NMR.

Negative regulation of leucocyte functions by CD33-related siglecs

The siglecs (sialic acid-binding Ig-like lectins) are a family of transmembrane receptors expressed in the haemopoietic, immune and nervous systems. The CD33-related siglecs are a distinct subset mostly expressed in the innate immune system where they can function as inhibitory receptors by suppressing the signalling mediated by receptors coupled with ITAMs (immunoreceptor tyrosine-based activation motifs). CD33-related siglecs contain ITIMs (immunoreceptor tyrosine-based inhibitory motifs) that recruit and activate SHP-1 [SH2 (Src homology 2) domain-containing phosphatase-1] and SHP-2. In addition, the ITIMs of CD33-related siglecs can suppress siglec-dependent adhesion of sialylated ligands and mediate endocytosis. Siglec-H is a recently characterized murine CD33-related endocytic receptor that lacks intrinsic tyrosine-based signalling motifs and is expressed selectively on PDCs (plasmacytoid dendritic cells). Siglec-H depends on DAP12 (DNAX-activating protein of 12 kDa) for surface expression and cross-linking with anti-siglec-H antibodies can selectively inhibit interferon-alpha production by PDCs following TLR9 (Toll-like receptor 9) ligation. Thus CD33-related siglecs are able to mediate diverse inhibitory functions of leucocytes in the innate immune system via both ITIM-dependent and -independent pathways.

Siglec-7 undergoes a major conformational change when complexed with the alpha(2,8)-disialylganglioside GT1b

The siglecs are a group of mammalian sialic acid binding receptors expressed predominantly in the immune system. The CD33-related siglecs show complex recognition patterns for sialylated glycans. Siglec-7 shows a preference for alpha(2,8)-disialylated ligands and provides a structural template for studying the key interactions that drive this selectivity. We have co-crystallized Siglec-7 with a synthetic oligosaccharide corresponding to the alpha(2,8)-disialylated ganglioside GT1b. The crystal structure of the complex offers a first glimpse into how this important family of lectins binds the structurally diverse gangliosides. The structure reveals that the C-C' loop, a region implicated in previous studies as driving siglec specificity, undergoes a dramatic conformational shift, allowing it to interact with the underlying neutral glycan core of the ganglioside. The structural data in combination with mutagenesis studies show that binding of the ganglioside is driven by extensive hydrophobic contacts together with key polar interactions and that the binding site structure is complementary to preferred solution conformations of GT1b.

The structure of siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design

Siglecs (sialic acid binding Ig-like lectins) are transmembrane receptors for sialylated glycoconjugates that modulate cellular interactions and signalling events in the haematopoietic, immune and nervous systems. Siglec-7 is a structural prototype for the recently described family of immune inhibitory CD33-related siglecs and is predominantly expressed on natural killer cells and monocytes, as well as subsets of CD8 T-cells. Siglec-specific inhibitors are desired for the detection of masked and unmasked forms of siglecs, to aid in dissection of signalling pathways and as tools to investigate siglecs as potential therapeutic targets. As a first step towards this end, we present the crystal structure of siglec-7 in complex with a sialylated ligand, the ganglioside analogue DSLc4 [alpha(2,3)/alpha(2,6) disialyl lactotetraosyl 2-(trimethylsilyl)ethyl], which allows for a detailed description of the binding site, required for structure-guided inhibitor design. Mutagenesis and binding assays were used to demonstrate a key structural role for Lys131, a residue that changes conformation upon sialic acid binding. Differences between the binding sites of siglec family members were then exploited using alpha-methyl Neu5Ac (N-acetylneuraminic acid) as a basic scaffold. A co-crystal of siglec-7 in complex with the sialoside inhibitor, oxamido-Neu5Ac [methyl alpha-9-(amino-oxalyl-amino)-9-deoxy-Neu5Ac] and inhibition data for the sialosides gives clear leads for future inhibitor design.

Siglec-5 (CD170) Can Mediate Inhibitory Signaling in the Absence of Immunoreceptor Tyrosine-based Inhibitory Motif Phosphorylation

Siglec-5 (CD170) is a member of the recently described human CD33-related siglec subgroup of sialic acid binding Ig-like lectins and is expressed on myeloid cells of the hemopoietic system. Similar to other CD33-related siglecs, Siglec-5 contains two tyrosine-based motifs in its cytoplasmic tail implicated in signaling functions. To investigate the role of these motifs in Siglec-5-dependent signaling, we used transfected rat basophil leukemia cells as a model system. Tyrosine phosphorylation of Siglec-5 led to recruitment of the tyrosine phosphatases SHP-1 and SHP-2, as seen in both pull-down assays and microscopy. Siglec-5 could efficiently inhibit FcepsilonRI-mediated calcium fluxing and serotonin release after co-cross-linking. Surprisingly, a double tyrosine to alanine mutant of Siglec-5 could still mediate strong inhibition of serotonin release in the absence of detectable tyrosine phosphorylation, whereas a double tyrosine to phenylalanine mutant lost all inhibitory activity. In comparison, suppression of Siglec-5-dependent adhesion to red blood cells was reversed by either tyrosine to alanine or tyrosine to phenylalanine mutations of the membrane proximal tyrosine-based motif. Using an in vitro phosphatase assay with synthetic and recombinant forms of the cytoplasmic tail, it was shown that a double alanine mutant of Siglec-5 had weak, but significant SHP-1 activating properties similar to those of wild type, non-phosphorylated cytoplasmic tail, whereas a double phenylalanine mutant was inactive. These findings establish that Siglec-5 can be classified as an inhibitory receptor with the potential to mediate SHP-1 and/or SHP-2-dependent signaling in the absence of tyrosine phosphorylation.

High resolution crystal structures of Siglec-7. Insights into ligand specificity in the Siglec family

Sialic acid-binding immunoglobulin-like lectins (Siglecs) recognize sialylated glycoconjugates and play a role in cell-cell recognition. Siglec-7 is expressed on natural killer cells and displays unique ligand binding properties different from other members of the Siglec family. Here we describe the high resolution structures of the N-terminal V-set Ig-like domain of Siglec-7 in two crystal forms, at 1.75 and 1.9 A. The latter crystal form reveals the full structure of this domain and allows us to speculate on the differential ligand binding properties displayed by members of the Siglec family. A fully ordered N-linked glycan is observed, tethered by tight interactions with symmetry-related protein molecules in the crystal. Comparison of the structure with that of sialoadhesin and a model of Siglec-9 shows that the unique preference of Siglec-7 for alpha(2,8)-linked disialic acid is likely to reside in the C-C' loop, which is variable in the Siglec family. In the Siglec-7 structure, the ligand-binding pocket is occupied by a loop of a symmetry-related molecule, mimicking the interactions with sialic acid.

Clinical efficacy and design changes of "fine bore" nasogastric feeding tubes: a seven-year experience involving 809 intubations in 403 patients

We report here our clinical experiences of "fine bore" nasogastric feeding tubes. Data have been collated over a 7-year period (1978-1985). A total of 403 patients were intubated on 809 occasions. In the first retrospective study, the clinical use of 491 unweighted tubes was compared with that of fifty 3.5-g weighted tubes. No advantage was found in the use of the weighted tubes. In the second prospective controlled clinical trial, these results were confirmed. Forty-six patients were intubated on 76 occasions with an 85-cm open-ended, unweighted nasogastric feeding tube (Prima, Portex UK), and 57 patients were intubated on 79 occasions with a 91-cm 3.0-g weighted tube (Entriflex, Biosearch, Raritan, NJ). Mean duration of placement was similar in each case, and 62% of both types of tubes were inadvertently removed. Without exception, all the tubes remained in the stomach throughout. Disappointed with the similar and overall performance of both types of tubes, we initiated a design program which resulted in the development of two new nasogastric tubes, one weighted and one unweighted. The tubes were manufactured with polyurethane, rather than polyvinylchloride (PVC), which permitted an increase in diameter of the internal lumen which, in turn, was coated with water-activated lubricant to ease removal of the introducer wire. A specially modeled outflow port was incorporated into the tips of both tubes. The performance of the two new polyurethane nasogastric feeding tubes was assessed under controlled trial conditions; as a reference, a widely used PVC unweighted open-ended tube was used.(ABSTRACT TRUNCATED AT 250 WORDS)

Elemental diet administered nasogastrically without starter regimens to patients with inflammatory bowel disease

The present study questions the concept of routinely using 'starter regimens' at the outset of enteral feeding with chemically defined elemental diets. A hypertonic elemental diet with an osmolality of 630 mOsm/kg was administered by 24-hr nasogastric infusion to 12 patients with exacerbations of inflammatory bowel disease and to two patients with short bowel syndrome. Starter regimens were not used. Upper gastrointestinal symptoms of nausea, abdominal bloating, and colicky pain occurred transiently in only five of 14 patients. Stool frequency did not increase during full-strength feeding, and daily stool weights decreased significantly (p less than 0.01). These findings show that it is safe to administer undiluted hypertonic elemental diets by constant nasogastric infusion to patients with inflammatory bowel disease. Avoiding starter regimens leads to increased nutrient intake and improved nitrogen balance.

Relation between osmolality of diet and gastrointestinal side effects in enteral nutrition

One hundred and eighteen patients with normal gastrointestinal function were randomly allocated to one of three feeding regimens in a double blind study to determine the relation between the tonicity of the diet and gastrointestinal side effects related to the diet and to evaluate the efficacy of "starter" regimens in reducing gastrointestinal side effects during enteral nutrition. Patients received a hypertonic diet with an osmolality of 430 mmol (mosmol)/kg (group 1), the same diet but with the osmolality increasing from 145 to 430 mmol/kg over the first four days (group 2), or an isotonic diet (300 mmol/kg) (group 3). All diets were prepared aseptically and administered by 24 hour nasogastric infusion. The mean daily nitrogen intake in group 1 was significantly greater (p less than 0.05) than that in both groups 2 and 3, and the mean overall daily nitrogen balance was significantly better (p less than 0.05) in group 1 than groups 2 and 3. The incidence of side effects related to the diet was similar in all three groups, but diarrhoea was significantly (p less than 0.001) associated with concurrent treatment with antibiotics. These findings show that undiluted hypertonic diet results in significantly better nitrogen intake and balance, that starter regimens reduce nutrient intake but not symptoms, and that diarrhoea is significantly related to treatment with antibiotics and not to administration of an undiluted hypertonic polymeric diet.

Effect of catheter tunnelling and a nutrition nurse on catheter sepsis during parenteral nutrition. A controlled trial

In a three-year controlled trial of subcutaneous catheter tunnelling as a method of reducing total parenteral nutrition (TPN) catheter sepsis 99 silicone catheters (52 tunnelled, 47 untunnelled) were inserted into the subclavian (94%) or jugular (6%) veins under aseptic conditions. The influence of a nutrition nurse, who joined the nutrition team after 18 months, on catheter sepsis rate was also documented. Catheter sepsis was confirmed in 13 of 47 (28%) untunnelled catheters and only 6 of 52 (11.5%) tunnelled catheters (p less than 0.05). A nutrition nurse reduced sepsis rate from 33% (tunnelled 6, untunnelled 11) to 4% (0 tunnelled; 2 untunnelled) (p less than 0.001). There was no significant difference between tunnelled and untunnelled catheters in sepsis rates after the arrival of the nutrition nurse. Although 85% patients had concurrent internal sepsis, the pathogens implicated in catheter sepsis came from superficial sites in 16 of 19 cases (p less than 0.01). Rigorous aseptic nursing care is thus the most significant factor in the reduction of TPN catheter sepsis, but tunnelling can reduce sepsis rate when nursing care is suboptimum.

Enteral nutrition in malnourished patients with hepatic cirrhosis and acute encephalopathy

Ten patients with histologically proven cirrhosis, admitted in grade I to II acute hepatic coma, received in addition to a standard dietary protein free "anticoma" regime, a continuous nasogastric infusion of a branched-chain amino acid enriched chemically defined enteral diet (Hepaticaid) containing an equivalent of 70 g protein/day for a mean of 7.3 days (range 3-23). No complications of therapy were observed and, specifically, the use of fine bore tubes did not provoke variceal hemorrhage. Overall positive nitrogen balance (4.3 +/- 1.7 g N/day) was observed in patients fed 7 or more days. Improvement to coma grade 0 was seen in all patients save one, who died from hepatorenal failure. While serum ammonia levels remained elevated during the study period, there was a significant increase in the branched-chain/aromatic ratio (p less than 0.01) as plasma branched-chain amino acids rose (p less than 0.05) and tyrosine levels fell (p less than 0.05).

A controlled trial of aseptic enteral diet preparation — Significant effects on bacterial contamination and nitrogen balance

This study was performed to evaluate the clinical effectiveness of the 'standard' and aseptic enteral diet preparation techniques and to investigate the relationship between bacterial contamination of diets and symptoms during enteral nutrition. In this controlled study patients were prescribed isonitrogenous polymeric diets prepared using either 'standard' or aseptic techniques, administered by 24 nasogastric infusion. 'Standard' diet preparation resulted in significant bacterial contamination (p<0.01), but this did not increase incidence of diet related symptoms. Use of sterile techniques permitted safe use of large volumes (1.5-2 litre) containers, and this resulted in significantly better nitrogen intake (p<0.05) and balance (p<0.05).

Clinical indications for weighted enteral feeding tubes

Simple unweighted fine bore feeding tubes have been used by our Nutritional Support Team for routine nasogastric feeding with success in large numbers of patients. Three clinical situations where mercury or tungsten weighted tubes offer advantages over fine bore tubes have been defined. Significant advantages in patients with concurrent endotracheal intubation, gastric atony and severe oesophageal stricturing are described.

Endoscopic placement of fine bore nasogastric and nasoenteric feeding tubes

In a small proportion of patients requiring enteral nutrition it may not be possible to site nasogastric or nasoenteric feeding tubes using standard intubation techniques. We describe an endoscopic method of tube placement applicable not only for positioning nasogastric feeding tubes in patients with coexisting oesophageal pathology, but also for placement of nasoenteric feeding tubes when disordered gastric emptying is present.