EUROCarbDB: An open-access platform for glycoinformatics.

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

Information management for proteomics: a perspective.

Proteomics is a data-rich discipline that makes extensive use of separation tools, mass spectrometry and bioinformatics to analyze and interpret the features and dynamics of the proteome. A major challenge for the field is how proteomics data can be stored and managed, such that data become permanent and can be mined with current and future tools. This article details our experience in the development of a commercial proteomic information management system. We identify the challenges faced in data acquisition, workflow management, data permanence, security, data interpretation and analysis, as well as the solutions implemented to address these issues. We finally provide a perspective on data management in proteomics and the implications for academic and industry-based researchers working in this field.

Does an isolated history of loss of consciousness or amnesia predict brain injuries in children after blunt head trauma?

BACKGROUND: A history of loss of consciousness (LOC) is frequently used as an indication for cranial computed tomography (CT) in the emergency department (ED) evaluation of children with blunt head trauma. OBJECTIVE: We sought to determine whether an isolated LOC and/or amnesia is predictive of traumatic brain injury (TBI) in children with blunt head trauma. METHODS: We prospectively enrolled children <18 years old presenting to a level I trauma center ED between July 1998 and September 2001 with blunt head trauma. We evaluated the association of LOC and/or amnesia with 1) TBI identified on CT and 2) TBI requiring acute intervention. We defined the latter by a neurosurgical procedure, antiepileptic medication for >1 week, persistent neurologic deficits, or hospitalization for > or =2 nights. We then investigated the association of LOC and/or amnesia with TBI in those patients without other symptoms or signs of TBI ("isolated" LOC and/or amnesia). RESULTS: Of eligible children, 2043 (77%) were enrolled, 1271 (62%) of whom underwent CT; 1159 (91%) of these 1271 had their LOC and/or amnesia status known. A total of 801 (39%) of the 2043 enrolled children had a documented history of LOC and/or amnesia. Of the 745 with documented LOC and/or amnesia who underwent CT, 70 (9.4%; 95% confidence interval [CI]: 7.4%, 11.7%) had TBI identified on CT versus 11 of 414 (2.7%; 95% CI: 1.3%, 4.7%) without LOC and/or amnesia (difference: 6.7%; 95% CI: 4.1%, 9.3%). Of the 801 children known to have had LOC and/or amnesia (regardless of whether they underwent CT), 77 (9.6%; 95% CI: 7.7%, 11.9%) had TBI requiring acute intervention versus 11 of 1115 (1%; 95% CI: 0.5%, 1.8%) of those without LOC and/or amnesia (difference: 8.6%; 95% CI: 6.5%, 10.7%). For those with an isolated LOC and/or amnesia without other signs or symptoms of TBI, however, 0 of 142 (95% CI: 0%, 2.1%) had TBI identified on CT, and 0 of 164 (95% CI: 0%,1.8%) had TBI requiring acute intervention. CONCLUSIONS: Isolated LOC and/or amnesia, defined by the absence of other clinical findings suggestive of TBI, are not predictive of either TBI on CT or TBI requiring acute intervention. Elimination of an isolated LOC and/or amnesia as an indication for CT may decrease unnecessary CT use in those patients without an appreciable risk of TBI.

Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data.

The bioinformatic tool GlycosidIQ was developed for computerized interpretation of oligosaccharide mass spectrometric fragmentation based on matching experimental data with theoretically fragmented oligosaccharides generated from the database GlycoSuiteDB. This use of the software for glycofragment mass fingerprinting obviates a large part of the manual, labor intensive, and technically challenging interpretation of oligosaccharide fragmentation. Using 130 negative ion electrospray ionization-tandem mass spectrometry fragment spectra from identified oligosaccharide structures, it was shown that the GlycosidIQ scoring algorithms were able to correctly identify oligosaccharides in the great majority of cases (correct structure top ranked in 78% of the cases and an additional 17% were ranked second highest in the sample set).

A decision rule for identifying children at low risk for brain injuries after blunt head trauma.

STUDY OBJECTIVE: Computed tomography (CT) is frequently used in evaluating children with blunt head trauma. Routine use of CT, however, has disadvantages. Therefore, we sought to derive a decision rule for identifying children at low risk for traumatic brain injuries. METHODS: We enrolled children with blunt head trauma at a pediatric trauma center in an observational cohort study between July 1998 and September 2001. We evaluated clinical predictors of traumatic brain injury on CT scan and traumatic brain injury requiring acute intervention, defined by a neurosurgical procedure, antiepileptic medications for more than 1 week, persistent neurologic deficits, or hospitalization for at least 2 nights. We performed recursive partitioning to create clinical decision rules. RESULTS: Two thousand forty-three children were enrolled, 1,271 (62%) underwent CT, 98 (7.7%; 95% confidence interval [CI] 6.3% to 9.3%) had traumatic brain injuries on CT scan, and 105 (5.1%; 95% CI 4.2% to 6.2%) had traumatic brain injuries requiring acute intervention. Abnormal mental status, clinical signs of skull fracture, history of vomiting, scalp hematoma (in children < or =2 years of age), or headache identified 97/98 (99%; 95% CI 94% to 100%) of those with traumatic brain injuries on CT scan and 105/105 (100%; 95% CI 97% to 100%) of those with traumatic brain injuries requiring acute intervention. Of the 304 (24%) children undergoing CT who had none of these predictors, only 1 (0.3%; 95% CI 0% to 1.8%) had traumatic brain injury on CT, and that patient was discharged from the ED without complications. CONCLUSION: Important factors for identifying children at low risk for traumatic brain injuries after blunt head trauma included the absence of: abnormal mental status, clinical signs of skull fracture, a history of vomiting, scalp hematoma (in children < or =2 years of age), and headache.

GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update.

GlycoSuiteDB is an annotated and curated relational database of glycan structures reported in the literature. It contains information on the glycan type, core type, linkages and anomeric configurations, mass, composition and the analytical methods used by the researchers to determine the glycan structure. Native and recombinant sources are detailed, including species, tissue and/or cell type, cell line, strain, life stage, disease, and if known the protein to which the glycan structures are attached. There are links to SWISS-PROT/TrEMBL and PubMed where applicable. Recent developments include the implementation of searching by 2D structure and substructure, disease and reference. The database is updated twice a year, and now contains over 7650 entries. Access to GlycoSuiteDB is available at http://www.glycosuite.com.

Glycosylation of acetylxylan esterase from Trichoderma reesei.

The nature of the N- and O- linked glycosylation of acetylxylan esterase (AXE) of the Trichoderma reesei strain Rut-C30 has been characterized using different enzymatic, chromatographic, and mass spectrometric techniques. The combined data showed that the AXE N-glycan is phosphorylated and highly mannosylated. The predominant N-glycans on the single glycosylation site on AXE can be represented as GlcNAc(2)Man((1-6))P. The linker-substrate binding domain peptide separated from the core by papain digestion is heavily O-glycosylated and consists of mannose, galactose, and possibly glucose as monosaccharide and disaccharide substituents. In addition to glycosylation, sulfation was observed in the linker region. Both N- and O- linked glycans show remarkable heterogeneity. Three isoforms of AXE, separated by 2D SDS-PAGE, are described with pI values of 5.0, 5.3, and 5.9. The three isoforms can be explained by posttranslational modification of the enzyme by glycans, phosphate, and sulfate. Advancing the knowledge on the nature of the glycans produced by T. reesei is elementary for its use as a host for the expression of heterologous glycoproteins of industrial and pharmaceutical importance.