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At least 1,297 records · Page 72Linked to original sources

PubMed2004

Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism.

A genomics analysis on sulphur metabolism has been conducted at the level of transcriptomics and metabolomics. The analysis of these data after applying bioinformatic tools is to reveal novel findings. The findings are discussed and the knowledge obtained from comparable analyses on sulphur metabolism and other plant nutrient genomic studies is reviewed. The analysis of the response of the transcriptome and metabolome to sulphur deprivation in the growth medium provides a tool set for the analysis of comparable genomics studies of other nutrients. The goal of this 'sulphobolomics' (i.e. sulphur genomics and metabolome analysis) approach, and of other investigations, is to describe in a holistic way the biochemical, molecular, and physiological response of a plant to nutrient starvation, here sulphate, or, more generally, to alterations and imbalances in nutrient availability. Eventually, this analysis will provide a case study for a systems biology approach.

Arabidopsis↗

PubMed2006

The LIFEdb database in 2006.

LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an updated user interface with enhanced query capabilities, (ii) a configurable output table and the option to download search results in XML, (iii) the integration of data from cell-based screening assays addressing the influence of protein-overexpression on cell proliferation and (iv) the display of the relative expression ('Electronic Northern') of the genes under investigation using curated gene expression ontology information. LIFEdb enables researchers to systematically select and characterize genes and proteins of interest, and presents data and information via its user-friendly web-based interface.

Cell Proliferation↗

PubMed2005

Integrating probe-level expression changes across generations of Affymetrix arrays.

There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene expression levels within or between different platforms, we propose a novel meta-analytic method that takes into account the vast amount of available probe-level information to combine the expression changes across different studies. We first show that the comparability of relative expression changes and the consistency of differentially expressed genes between different Affymetrix array generations can be considerably improved by determining the expression changes at the probe-level and by considering the latest information on probe-level sequence matching instead of the probe annotations provided by the manufacturer. With the improved probe-level expression change estimates, data from different generations of Affymetrix arrays can be combined more effectively. This will allow for the full exploitation of existing results when designing and analyzing new experiments.

Animals↗

PubMed2006

Immunoproteomics of Actinobacillus actinomycetemcomitans outer-membrane proteins reveal a highly immunoreactive peptidoglycan-associated lipoprotein.

In a search for novel bioactive cell surface structures of periodontal pathogens, it was found that sera from two patients with Actinobacillus actinomycetemcomitans-associated infections reacted strongly at 17 kDa on immunoblots of A. actinomycetemcomitans outer-membrane protein (OMP) preparations. The 17 kDa antigen was also recognized by anti-CsgA (Escherichia coli curli major subunit) antibody. The 17 kDa A. actinomycetemcomitans protein was identified as peptidoglycan-associated lipoprotein (PAL; AaPAL) by two-dimensional immunoblotting and subsequent sequence analysis by mass spectrometry and bioinformatics tools. AaPAL was an OMP and a lipoprotein, and it had an OmpA-like domain. In a group of middle-aged subjects (n = 26), serum reactivity to AaPAL was associated with the presence of periodontitis but not with the oral detection of A. actinomycetemcomitans. Both human sera and rabbit antisera against three different types of antigens, the gel-purified AaPAL, A. actinomycetemcomitans whole-cell antigens, and CsgA, recognized putative PALs of oral haemophili in addition to AaPAL. The results demonstrated that the novel AaPAL is a conserved bacterial lipoprotein. It is expressed in vivo and is strongly immunoreactive. The antigenic cross-reactivity found between AaPAL and oral haemophili may enhance local and systemic immuno-inflammatory reactions in periodontitis.

Actinobacillus Infections↗

PubMed2006

Molecular refinement of gibbon genome rearrangements.

The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to approximately 5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome.

Animals↗

PubMed1998

BioViews: Java-based tools for genomic data visualization.

Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a language designed for distributed programming over the Web, the technology now exists to build a genomic data visualization tool that meets these requirements. Using Java we have developed a prototype genome browser applet (BioViews) that incorporates a three-level graphical view of genomic data: a physical map, an annotated sequence map, and a DNA sequence display. Annotated biological features are displayed on the physical and sequence-based maps, and the different views are interconnected. The applet is linked to several databases and can retrieve features and display hyperlinked textual data on selected features. In addition to browsing genomic data, different types of analyses can be performed interactively and the results of these analyses visualized alongside prior annotations. Our genome browser is built on top of extensible, reusable graphic components specifically designed for bioinformatics. Other groups can (and do) reuse this work in various ways. Genome centers can reuse large parts of the genome browser with minor modifications, bioinformatics groups working on sequence analysis can reuse components to build front ends for analysis programs, and biology laboratories can reuse components to publish results as dynamic Web documents.

Animals↗

PubMed2005

Deleted in polyposis 1-like 1 gene (Dp1l1): a novel gene richly expressed in retinal ganglion cells.

PURPOSE: To characterize a novel gene, deleted in polyposis 1-like 1 (Dp1l1), which is expressed in the retina. METHODS: A systematic screening by subtraction hybridization of the cDNAs from mouse retina and mouse brain was performed to obtain novel genes expressed in the retina. In situ hybridization, immunohistochemistry, and intracellular localization analyses were performed to investigate the expression patterns of Dp1l1. The chromosomal location of Dp1l1 was determined by radiation hybrid mapping. Bioinformatics was used for homology analysis. RESULTS: A novel gene, Dp1l1, was expressed abundantly in the retina. It encodes a 201-amino-acid protein, and the encoded protein is designated mouse TB2-like 1. It is highly homologous to the mouse TB2, which is encoded by deleted in polyposis 1 (Dp1). In situ hybridization and immunohistochemical analyses showed that Dp1l1 mRNA and the TB2-like 1 were localized richly in retinal ganglion cells (RGCs). TB2-like 1 was present in the cytoplasm in a punctate pattern. Dp1l1 was mapped to mouse chromosome 10 by radiation hybrid mapping. CONCLUSIONS: TB2-like 1 is a membrane protein that belongs to the YOP1/TB2/DP1/HVA22 family, and it probably plays an important role in intracellular membrane trafficking in RGCs, based on the properties of other homologous proteins.

Amino Acid Sequence↗

PubMed2005

A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

BACKGROUND: Chronic Fatigue Syndrome (CFS), Persian Gulf War Illness (PGI), and fibromyalgia are overlapping symptom complexes without objective markers or known pathophysiology. Neurological dysfunction is common. We assessed cerebrospinal fluid to find proteins that were differentially expressed in this CFS-spectrum of illnesses compared to control subjects. METHODS: Cerebrospinal fluid specimens from 10 CFS, 10 PGI, and 10 control subjects (50 mul/subject) were pooled into one sample per group (cohort 1). Cohort 2 of 12 control and 9 CFS subjects had their fluids (200 mul/subject) assessed individually. After trypsin digestion, peptides were analyzed by capillary chromatography, quadrupole-time-of-flight mass spectrometry, peptide sequencing, bioinformatic protein identification, and statistical analysis. RESULTS: Pooled CFS and PGI samples shared 20 proteins that were not detectable in the pooled control sample (cohort 1 CFS-related proteome). Multilogistic regression analysis (GLM) of cohort 2 detected 10 proteins that were shared by CFS individuals and the cohort 1 CFS-related proteome, but were not detected in control samples. Detection of >or=1 of a select set of 5 CFS-related proteins predicted CFS status with 80% concordance (logistic model). The proteins were alpha-1-macroglobulin, amyloid precursor-like protein 1, keratin 16, orosomucoid 2 and pigment epithelium-derived factor. Overall, 62 of 115 proteins were newly described. CONCLUSION: This pilot study detected an identical set of central nervous system, innate immune and amyloidogenic proteins in cerebrospinal fluids from two independent cohorts of subjects with overlapping CFS, PGI and fibromyalgia. Although syndrome names and definitions were different, the proteome and presumed pathological mechanism(s) may be shared.

Adolescent↗

PubMed2003

Open architecture expression profiling of plant transcriptomes and gene discovery using GeneCalling technology.

The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling technology is an open architecture system capable of assaying more than 95% of genes expressed in a tissue. Unlike the closed systems, GeneCalling is not dependent upon an existing sequence or clone database. GeneCalling uses as low as 50 pg of the cDNA from samples and identifies cDNA fragments that are differentially modulated within a set of samples. With the use of 96 pairs of restriction enzymes, more than 30,000 cDNA fragments are routinely assayed to identify those that are differentially modulated. Specific processes, such as SeqCalling, Trace Poisoning, and GeneCall Poisoning, are set up to not only confirm the known genes, but also to clone and analyze unknown and novel genes that have an interesting expression profile. GeneCalling has been successfully applied to expression profiling of several plant and fungal species, and resulted in identification and characterization of genes that are useful in commercial applications towards improving agriculturally important traits in plants.

DNA, Complementary↗

PubMed1998

A integrative molecular information system.

Methods of biotechnology allow the isolation, sequencing, and synthesis of molecular structures. Molecular database systems are available, which allow the worldwide data access. Methods and concepts of bioinformatics are important for the analysis of these molecular data, which represent complex regulatory networks. In this paper we present the architecture of our molecular information system.

Biotechnology↗

PubMed2003

[MGAP-A microbe genome annotation platform].

A Microbe Genome Annotation Platform (MGAP) was developed and applied to the cynobacterium PCC7002 genome annotation. Various bioinformatics software tools from sequence analysis to gene identification and function prediction were implemented in MGAP. Protein sequence databases SWISSPROT and PDBseq, protein information resource InterPro and COG were also integrated in the platform. The web interface of MGAP has the functionality to display a circular map of gene distribution and GC contents throughout the genome. Detailed information such as the DNA and protein sequence, the location of genes on chromosomes can be viewed by clicking the corresponding object within the map. MGAP is based on a PC/Linux system affordable for small biological laboratories and has the advantage of using free software tools including MySQL, Apache and Perl.

Cyanobacteria↗

PubMed2006

Augmented assessment as a means to augmented reality.

Rigorous scientific assessment of educational technologies typically lags behind the availability of the technologies by years because of the lack of validated instruments and benchmarks. Even when the appropriate assessment instruments are available, they may not be applied because of time and monetary constraints. Work in augmented reality, instrumented mannequins, serious gaming, and similar promising educational technologies that haven't undergone timely, rigorous evaluation, highlights the need for assessment methodologies that address the limitations of traditional approaches. The most promising augmented assessment solutions incorporate elements of rapid prototyping used in the software industry, simulation-based assessment techniques modeled after methods used in bioinformatics, and object-oriented analysis methods borrowed from object oriented programming.

Computer Simulation↗

PubMed2006

Protein expression in a transformed trabecular meshwork cell line: proteome analysis.

PURPOSE: Characterization of the human trabecular meshwork (TM) proteome is hindered by the small mass of intact tissue and the slow growth of cultured cell strains. We have previously characterized a transformed TM cell strain (GTM3) that demonstrates many of the same protein expression and cell signaling systems of nontransformed cell strains. The aim of this study was to initiate a proteomic survey of GTM3 cells as the initial step toward characterization of the complete human TM proteome. METHODS: GTM3 cells were cultured to confluence, harvested and solubilized in urea/Nonidet. The protein extract (600 mug) was focused in immobilized isoelectric focusing (IEF) strips, separated by 10% SDS PAGE, and visualized with colloidal Coomassie Blue. Spots of interest were excised, destained, and the contained proteins subjected to in-gel reduction, derivatization, and tryptic digestion. Tryptic peptides were extracted and analyzed by electrospray LC/MS/MS. Protein identification was made using the TurboSequest search algorithm and a recent version of the nonredundant human protein database downloaded from the National Center for Biotechnology Information (NCBI). RESULTS: Eighty-seven (87) primary proteins and 93 variants of these proteins were identified. A website was created (TM proteome) that combines data such as graphic spot location within the gel, peptide sequence, apparent and calculated pI, apparent and calculated mass, percentage of coverage, and protein informatic website links. CONCLUSIONS: Proteomic analysis of a transformed human TM cell line has been initiated combining preparative two-dimensional PAGE separation, LC/MS/MS analysis of major proteins, and bioinformatic cataloging of the data. Further investigation of data from the transformed cell strain will be used in a comparative fashion for spot identification of analytical proteomic gels of human TM tissue and cultured normal cells. These initial data will form the base from which the characterization of protein expression in the normal and glaucomatous TM can be accomplished.

Cell Line, Transformed↗

PubMed2005

Proteome analysis of maternal serum samples for trisomy 21 pregnancies using ProteinChip arrays and bioinformatics.

A surface-enhanced laser desorption/ionization time of flight (SELDI-TOF)-based ProteinChip System was used as a tool for rapid discovery and identification of protein patterns in serum that discriminate between trisomy 21 and unaffected pregnancies. We analyzed 24 serum samples from women carrying a trisomy 21 pregnancy and 32 with an unaffected pregnancy, ranging from 10.0 to 14.0 weeks of gestation. The resulting protein profiles were submitted to a clustering algorithm, a rule extraction, a rating, and a rule base construction step. For the generated combined rule base, the specificity and sensitivity for the prediction of a trisomy 21 pregnancy reach 97% and 91%, respectively.

Computational Biology↗

PubMed2006

VANTED: a system for advanced data analysis and visualization in the context of biological networks.

BACKGROUND: Recent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes. RESULTS: We present VANTED, a tool for the visualization and analysis of networks with related experimental data. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks, e. g. metabolic pathways or classification hierarchies. Visualization and navigation methods support the visual exploration of the data-enriched networks. Statistical methods allow analysis and comparison of multiple data sets such as different developmental stages or genetically different lines. Correlation networks can be automatically generated from the data and substances can be clustered according to similar behavior over time. As examples, metabolite profiling and enzyme activity data sets have been visualized in different metabolic maps, correlation networks have been generated and similar time patterns detected. Some relationships between different metabolites were discovered which are in close accordance with the literature. CONCLUSION: VANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at http://vanted.ipk-gatersleben.de.

Algorithms↗

PubMed2005

A streamlined approach to high-throughput proteomics.

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis.

Automation↗

PubMed2004

BIAS: Bioinformatics Integrated Application Software.

MOTIVATION: We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. AVAILABILITY: BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. CONTACT: hallett@mcb.mcgill.ca.

Computational Biology↗

PubMed2003

Combining medical informatics and bioinformatics toward tools for personalized medicine.

OBJECTIVES: Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. METHODS: Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). RESULTS: Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. CONCLUSIONS: A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

Biomedical Research↗