UNIQEM, a microbiological database: Problems and prospects

The UNIQEM database, designed to accumulate general microbiological data, is currently used to store and make available information about microorganisms studied and maintained at the Institute of Microbiology, Russian Academy of Sciences. UNIQEM can accumulate and maintain list-form information on a wide range of microorganisms (a property database) and facilitates collecting, processing, and publishing diverse data having to do with these microorganisms and their properties (a catalogue database). The database supports the retrieval of microorganisms by specifying an arbitrary set of their properties and has the potential for eventually evolving into a computer instrument for unattended identification of microorganisms. UNIQEMAkhlynin, D.S. and Gal’chenko, V.F., 1998.     

Protein identification assisted by the prediction of retention time in liquid chromatography/tandem mass spectrometry

Two-dimensional liquid chromatography (2D-LC) coupled on-line with electrospray ionization tandem mass spectrometry (2D-LC-ESI-MS/MS) is a new platform for analysis and identification of proteome. Peptides are separated by 2D-LC and then performed MS/MS analysis by tandem MS/MS. The MS/MS data are searched against database for protein identification. In one 2D-LC-ESI-MS/MS run, we obtained not only the structural information of peptides directly from MS/MS, but also the retention time of peptides eluted from LC. Information on the chromatographic behavior of peptides can assist protein identification in the new platform for proteomics. The retention time of the matching peptides of the identified protein was predicted by the hydrophobic contribute of each amino acid on reversed-phase liquid chromatography (RPLC). By using this strategy proteins were identified by four types of information: peptide mass fingerprinting (PMF), sequence query, and MS/MS ions searched and the predicted retention time. This additional information obtained from LC could assist protein identification with no extra experimental cost.     

Determination of endogenous peptides in the porcine brain: possible construction of peptidome,a fact database for endogenous peptides

Peptides play crucial roles in many physiological events. However, a database for endogenous peptides has not yet been developed, because the peptides are easily degraded by proteolytic enzymes during extraction and purification. In this study, we demonstrated that the data for endogenous peptides could be collected by minimizing the proteolytic degradation. We separated porcine brain peptides into 5250 fractions by 2-dimensional chromatography (first ion-exchange and second reversed-phase high-performance liquid chromatography), and 75 fractions of average peptide contents were analyzed in detail by mass spectrometers and a protein sequencer. Based on the analysis data obtained in this study, more than 10000 peptides were deduced to be detected, and more than 1000 peptides to be identified starting from 2 g of brain tissue. Thus, we deduce that it is possible to construct a database for endogenous peptides starting from a gram level of tissue by using 2-dimensional high-performance liquid chromatography coupled with a mass spectrometer.     

Separation technologies for glycomics

Progress in genome projects has provided us with fundamentals on genetic information; however, the functions of a large number of genes remain to be elucidated. To understand the in vivo functions of eukaryotic genes, it is essential to grasp the features of their post-translational modifications. Among them, protein glycosylation is a central issue to be discussed, considering the predominant roles of glycoproteins in cell-cell and cell-substratum recognition events in multicellular organisms. In this context, it is necessary to establish a core strategy for analyzing glycosylated proteins under the concept of the "glycome" [Trends Glycosci. Glycotechnol. 12 (2000) 1]. Though the term glycome should be defined, in analogy to the genome and proteome, as "a whole set of glycans produced in a single organism", here we propose a glycome project specifically focusing on glycoproteins. Principal objectives in the project are to identify: (1) which genes encode glycoproteins (i.e. genome information); (2) which sites among potential glycosylation sites are actually glycosylated (i.e. glycosylation site information); (3) what are the structures of glycans (i.e. structural information); and (4) what are the effects (functions) of glycosylation (functional information). For these purposes, two affinity technologies have been introduced. One is named the "glyco-catch method" to identify genes encoding glycoproteins [Proteomics 1 (2001) 295], and the other is the recently reinforced "frontal affinity chromatography" [J. Chromatogr. A 890 (2000) 261]. By the former method, genes that encode glycoproteins as well as glycosylation sites are systematically identified by the efficient combination of conventional lectin-affinity chromatography and contemporary in silico database searching. The following three actions have been devised for rapid and systematic characterization of glycans: (1) mass spectrometry to acquire exact mass information; (2) 2-D/3-D mapping to obtain refined chemical information; and (3) reinforced frontal affinity chromatography to determine affinity constants (K(a)-values) for a set of lectins. Pyridylaminated glycans are used throughout the characterization processes. In this review, the concept and strategy of glycomic approaches are described referring to the on-going glycome project focused on the nematode Caenorhabditis elegans.     

SWEETLEAD: an In Silico Database of Approved Drugs,Regulated Chemicals,and Herbal Isolates for Computer-Aided Drug Discovery

In the face of drastically rising drug discovery costs, strategies promising to reduce development timelines and expenditures are being pursued. Computer-aided virtual screening and repurposing approved drugs are two such strategies that have shown recent success. Herein, we report the creation of a highly-curated in silico database of chemical structures representing approved drugs, chemical isolates from traditional medicinal herbs, and regulated chemicals, termed the SWEETLEAD database. The motivation for SWEETLEAD stems from the observance of conflicting information in publicly available chemical databases and the lack of a highly curated database of chemical structures for the globally approved drugs. A consensus building scheme surveying information from several publicly accessible databases was employed to identify the correct structure for each chemical. Resulting structures are filtered for the active pharmaceutical ingredient, standardized, and differing formulations of the same drug were combined in the final database. The publically available release of SWEETLEAD (https://simtk.org/home/sweetlead) provides an important tool to enable the successful completion of computer-aided repurposing and drug discovery campaigns.     

SaudiVeg ecoinformatics: Aims,current status and perspectives

During the last decade many electronic databases of vegetation plots were established in many countries around the world. These databases contain valuable phytosociological information assisting both governmental and NGO (Non-governmental organizations) agencies to formulate strategies and on-ground plans to manage and protect nature resources. This paper provides an account on aims, current status and perspectives of building of a vegetation database for the Central Region (Najd) of Saudi Arabia – the founding element of the Saudi Vegetation Database (SVD). The data stored by the database are sample plots (vegetation relevés) collected according to the field techniques of the Braun-Blanquet approach (lists of taxa accompanied by semi-quantitative cover assessment), and are accompanied by general vegetation characteristics such as vegetation layering and cover, information on life-form of the recorded species, geographical coordinates, altitude, soil typology, topography and many more. More than 2900 vegetation-plot records (relevés) have so far been collected in the Najd region; of these more than 2000 have already been stored using the Turboveg database platform. These field records cover many habitats such as depressions, wadis (dry river beds), agricultural lands, sand dunes, sabkhas, and ruderal habitats. The ecological information collected in the database is currently the largest set of vegetation data collated into a database in the Middle East. These data are of great importance for biodiversity studies in Saudi Arabia, since the region is recording a loss of biodiversity at a fast rate due to environmental problems such as global warming and land-use changes. We envisage that this database would catalyze further data collection on vegetation of the entire Arabian Peninsula, and shall serve as one of the most important datasets for classification and mapping of the vegetation of the Kingdom of Saudi Arabia.     

Web-accessible proteome databases for microbial research

The analysis of proteomes of biological organisms represents a major challenge of the post-genome era. Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib-berlin.mpg.de/2D-PAGE) for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly". The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.     

Efficient identification of proteins from ovaries and hepatopancreas of the unsequenced edible crab,Cancer pagurus,by mass spectrometry and homology-based,cross-species searching

Proteome maps of hepatopancreas (midgut gland) and ovarian tissues of the crustacean, Cancer pagurus (Decapoda; edible crab) have been produced by 2D-PAGE and identification of proteins, following trypsin proteolysis, by electrospray MS/MS and database searching. Owing to the lack of sequence information on proteins and fully sequenced genomes amongst the decapod crustaceans and given the evolutionary distance to the nearest full genome database (Daphnia), it was necessary to adopt a non-conventional identification approach. Thus, a strategy was developed for effective identification of decapod proteins by sequence similarity, homology-based cross-species database searching, using various algorithms and a combination of NCBI Crustacea and Arthropoda databases, together with the Arthropoda PartiGene database (Blaxter, University of Edinburgh). In both hepatopancreas and ovary tissues, the largest group of proteins identified were a variety of enzymes, followed by a smaller number of storage/transport proteins [including vitellogenin (yolk protein), several subunits of hemocyanin, cryptocyanin, ferritin and calreticulin], with fewer structural proteins (actin, tubulin) and heat-shock proteins, in addition to a number of proteins of miscellaneous functions. Such protein identifications allow the development of tools, such as antibodies and RNA/DNA probes, to investigate the functions of the proteins in specific tissues during development.     

PTM MarkerFinder,a software tool to detect and validate spectra from peptides carrying post‐translational modifications

Mass spectrometry (MS) analysis of peptides carrying post‐translational modifications is challenging due to the instability of some modifications during MS analysis. However, glycopeptides as well as acetylated, methylated and other modified peptides release specific fragment ions during CID (collision‐induced dissociation) and HCD (higher energy collisional dissociation) fragmentation. These fragment ions can be used to validate the presence of the PTM on the peptide. Here, we present PTM MarkerFinder, a software tool that takes advantage of such marker ions. PTM MarkerFinder screens the MS/MS spectra in the output of a database search (i.e., Mascot) for marker ions specific for selected PTMs. Moreover, it reports and annotates the HCD and the corresponding electron transfer dissociation (ETD) spectrum (when present), and summarizes information on the type, number, and ratios of marker ions found in the data set. In the present work, a sample containing enriched N‐acetylhexosamine (HexNAc) glycopeptides from yeast has been analyzed by liquid chromatography‐mass spectrometry on an LTQ Orbitrap Velos using both HCD and ETD fragmentation techniques. The identification result (Mascot .dat file) was submitted as input to PTM MarkerFinder and screened for HexNAc oxonium ions. The software output has been used for high‐throughput validation of the identification results.     

PACSY, a relational database management system for protein structure and chemical shift analysis

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.     

Laboratory database to manage electrophoresis and chromatography separations and the associated samples

A database was developed to store, organize, and retrieve the data associated with electrophoresis and chromatography separations. It allows laboratories to store extensive data on separation techniques (analytical and preparative). The data for gel electrophoresis includes gel composition, staining methods, electric fields, analysis, and samples loaded. The database stores data on chromatography conditions, the samples used, and the fractions collected. The data structure of this database was designed to maintain the link between samples (including fractions) from chromatography separations and their analysis by gel electrophoresis. The database will allow laboratories to organize and maintain a large amount of separation and sample data in a uniform data environment. It will facilitate the retrieval of the separation history of important samples and the separation conditions used.     

Open source system for analyzing, validating, and storing protein identification data

This paper describes an open-source system for analyzing, storing, and validating proteomics information derived from tandem mass spectrometry. It is based on a combination of data analysis servers, a user interface, and a relational database. The database was designed to store the minimum amount of information necessary to search and retrieve data obtained from the publicly available data analysis servers. Collectively, this system was referred to as the Global Proteome Machine (GPM). The components of the system have been made available as open source development projects. A publicly available system has been established, comprised of a group of data analysis servers and one main database server.     

Data base management system for lymphatic filariasis--a neglected tropical disease

Background

Researchers working in the area of Public Health are being confronted with large volumes of data on various aspects of entomology and epidemiology. To obtain the relevant information out of these data requires particular database management system. In this paper, we have described about the usages of our developed database on lymphatic filariasis.

Methods

This database application is developed using Model View Controller (MVC) architecture, with MySQL as database and a web based interface. We have collected and incorporated the data on filariasis in the database from Karimnagar, Chittoor, East and West Godavari districts of Andhra Pradesh, India.

Conclusion

The importance of this database is to store the collected data, retrieve the information and produce various combinational reports on filarial aspects which in turn will help the public health officials to understand the burden of disease in a particular locality. This information is likely to have an imperative role on decision making for effective control of filarial disease and integrated vector management operations.     

RsGDB, the Rhodobacter sphaeroides Genome Database.

This report provides a summary of the sequencing project of the small chromosome (CII) of Rhodobacter sphaeroides 2.4.1(T),and introduces the first version of the genome database of this bacterium. The database organizes and describes diverse sets of biological information. The main role of the R.sphaeroides genome database (RsGDB) is to provide public access to the collected genomic information for R.sphaeroides via the World-Wide Web at http://utmmg.med.uth.tmc.edu/sphaeroides. The database allows the user access to hundreds of low redundancy R.sphaeroides sequences for further database searching, a summary of our current search results, and other allied information pertaining to this bacterium.     

Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database

Recently, we reported a database (Noncoded Amino acids Database; http://recerca.upc.edu/imem/index.htm) that was built to compile information about the intrinsic conformational preferences of nonproteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, the experimentally established conformational propensities, and applications (Revilla-López et al., J Phys Chem B 2010;114:7413-7422). The database initially contained the information available for α-tetrasubstituted α-amino acids. In this work, we extend NCAD to three families of compounds, which can be used to engineer peptides and proteins incorporating modifications at the--NHCO--peptide bond. Such families are: N-substituted α-amino acids, thio-α-amino acids, and diamines and diacids used to build retropeptides. The conformational preferences of these compounds have been analyzed and described based on the information captured in the database. In addition, we provide an example of the utility of the database and of the compounds it compiles in protein and peptide engineering. Specifically, the symmetry of a sequence engineered to stabilize the 3(10)-helix with respect to the α-helix has been broken without perturbing significantly the secondary structure through targeted replacements using the information contained in the database.     

Synthesising the trait information of European Chironomidae (Insecta: Diptera): Towards a new database

Chironomidae are among the most conspicuous and ecological diverse group of freshwater invertebrates. They may dominate unimpacted communities in abundance and biomass, accounting for more than 50% of macroinvertebrate species in standing and flowing waters. In deep zones of eutrophic lakes and highly human-impacted streams, they are often the only family of aquatic insects remaining. In bioassessment programmes, Chironomids are often identified at the family and subfamily levels, due to difficulties in the taxonomic identification of larvae resulting from a high intrinsic morphological similarity. This may potentially result in bias as, similarly to Ephemeroptera, Trichoptera or Plecoptera, Chironomidae species, which are replaced along natural and human-impacted gradients due to differences in their ecological requirements. Recently, multiple trait-based approaches have been proposed to complement taxonomic-based assessment of streams and rivers using macroinvertebrates. However, the lack of specific trait information for Chironomidae prevents their use in the functional assessment of communities. Therefore, here, we aimed to: (1) develop a trait database for European Chironomidae genera that can be used in future bioassessment and ecological studies; (2) evaluate, by multivariate analyses, whether our new database provides additional information on Chironomidae compared to the trait information provided in the commonly used European trait database (Tachet et al., 2010); and (3) determine whether the new information on Eltonian traits (proxy to biological traits) translates the most accepted phylogenetic relationships among Chironomidae subfamilies. We gathered information on 744 species and 178 genera, for 37 traits covering 186 trait categories, and found substantial differences between our database and the commonly used European trait database. In addition, available information on traits was not always in agreement with phylogenetic relationships among subfamilies. Orthocladiinae and Chironominae which are considered sister groups in evolutionary terms actually showed confident trait relatedness based on Eltonian traits tree while the remaining relationships between subfamilies are questionable. In addition, different traits can occur in closely related taxa depending on the environmental drivers operating on their habitats. Our study reveals that the usually accepted redundancy within the Chironomidae family and subfamilies must be a product of averaging the information from finer taxonomic resolution added to the substantial lack of information for this insect group.     

Gramene,a tool for grass genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.     

Identification and characterization of an intracellular lectin, calnexin, from Aspergillus oryzae using N-glycan-conjugated beads

Recently, asparagine-linked oligosaccharides (N-glycans) have been found to play a pivotal role in glycoprotein quality control in the endoplasmic reticulum (ER). In order to screen proteins interacting with N-glycans, we developed affinity chromatography by conjugating synthetic N-glycans on sepharose beads. Using the affinity beads with the dodecasaccharide Glc(1)Man(9)GlcNAc(2), one structure of the N-glycans, a 75-kDa protein, was isolated from the membranous fraction including the ER in Aspergillus oryzae. By LC-MS/MS analysis using the A. oryzae genome database, the protein was identified as one (AO090009000313) sharing similarities with calnexin. Further affinity chromatographic experiments suggested that the protein specifically bound to Glc(1)Man(9)GlcNAc(2), similarly to mammalian calnexins. We designated the gene AoclxA and expressed it as a fusion gene with egfp, revealing the ER localization of the AoClxA protein. Our results suggest that our affinity chromatography with synthetic N-glycans might help in biological analysis of glycoprotein quality control in the ER.     

TGB: the tobacco genetics and breeding database

The germplasm of the genus Nicotiana contains more than 5,000 accessions and plays an important role in modern biological research. Tobacco can be used as a model system to develop methodologies for plant transformation and for investigating gene function. In order to develop the study of Nicotiana, a large quantity of data on germplasm, sequences, molecular markers and genetically modified tobacco was required for in-depth and systematic collation and research. It became necessary to establish a special database for tobacco genetics and breeding. The tobacco genetics and breeding (TGB, http://yancao.sdau.edu.cn/tgb) database was developed with the aim of bringing together tobacco genetics and breeding. The database has three main features: (1) a materials database with information on 1,472 Nicotiana germplasm accessions, as well as updated genomic and expressed sequence tag (EST) data available from the public database; (2) a molecular markers database containing a total of 12,388 potential intron polymorphisms 10,551 EST-simple sequence repeat (EST-SSR) and 66,297 genomic-SSR markers; and (3) an applications database with genetic maps and some genetically modified studies in tobacco. The TGB database also makes Basic Local Alignment Search Tool and primer designing tools publicly available. As far as can be ascertained, the TGB database is the first tobacco genetics and breeding database to be created, and all this comprehensive information will aid basic research into Nicotiana and other related plants. It will serve as an excellent resource for the online tobacco research community.