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PubMed2006

Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis.

BACKGROUND: Recent, rapid growth in the quantity of available genomic data has generated many protein sequences that are not yet biochemically classified. Thus, the prediction of biochemical function based on structural motifs is an important task in post-genomic analysis. The InterPro databases are a major resource for protein function information. For optimal results, these databases should be searched at regular intervals, since they are frequently updated. RESULTS: We describe here a new program JIPS (Java GUI for InterProScan), a tool for tracking and viewing results obtained from repeated InterProScan searches. JIPS stores matches (in a local database) obtained from InterProScan searches performed with multiple versions of the InterPro database and highlights hits that have been added since the last search of the InterPro database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures. CONCLUSION: JIPS is an efficient tool for performing repeated InterProScans on large batches of protein sequences, tracking and viewing search results, and mining the collected data.

Algorithms↗
PubMed2006

Toxicity evaluation for the broad area of the asbestos mine of northern Greece.

The existing data regarding the quality of the environment in the asbestos mine of northern Greece (MABE) region related to the presence of asbestos are insufficient to determine the current pollution problem. In the present work, a first approach to this problem has been taken through a toxicity risk assessment. The environmental quality of an open air asbestos mine was evaluated over a long period of time by measuring and monitoring the concentration of asbestos fibres in air, soil and water. Air measurements were made to determine the concentration of asbestos fibres in the atmospheric air of the mine, the depositions and the nearby villages. The asbestos fibre concentration was also specified inside the building facilities of MABE. Analyses of soil, dust and water samples were carried out showing the presence of enormous quantities of chrysotile asbestos. The concentration of asbestos fibres in the atmospheric air was compared to older measurements that were taken at the same sampling points during the operation of the mine. The results of this work, in conjunction with individual researches that have been carried out in the past and with the evaluation of international standards of scientific and experience-based findings, provide a reliable framework with which to estimate the threat of MABE to its surrounding environment, and help to determine a basic criterion for the remediation and rehabilitation of the region. In addition, mathematical models based on human and animal studies were used to estimate the probability of a person developing cancer from breathing air containing asbestos fibres in the wider vicinity of the mine in order to define appropriate procedures for evaluating asbestos-related risk.

Air↗
PubMed1994

Probability of causation for lung cancer after exposure to radon progeny: a comparison of models and data.

The estimates of lung cancer risk due to the exposure to radon decay products are based on different data sets from underground mining and on different mathematical models that are used to fit the data. Diagrams of the excess relative rate per 100 working level months in its dependence on age at exposure and age attained are shown to be a useful tool to elucidate the influence that is due to the choice of the model, and to assess the differences between the data from the major western cohorts and those from the Czech uranium miners. It is seen that the influence of the choice of the model is minor compared to the difference between the data sets. The results are used to derive attributable lifetime risks and probabilities of causation for lung cancer following radon progeny exposures.

Adult↗
PubMed1998

Mining the human proteome: experience with the human lymphoid protein database.

We have undertaken an effort in the past five years aimed at developing a database of lymphoid proteins detectable by two-dimensional (2-D) polyacrylamide gel electrophoresis. The database contains 2-D patterns and derived information pertaining to: (i) polypeptide constituents of unstimulated and stimulated mature T cells and immature thymocytes; (ii) cultured T cells and cell lines that have been manipulated by transfection with a variety of constructs or by treatment with specific agents; (iii) single cell-derived T and B cell clones; (iv) cells obtained from patients with lymphoproliferative disorders and leukemia; and (v) a variety of other relevant cell populations. The database has experienced a substantial expansion in 2-D patterns it contains, numbering currently 9167 individual 2-D patterns. This number represents a fraction of the 30,682 2-D patterns maintained in our databases. The capacity to design and undertake experiments, produce high-quality 2-D patterns, and to undertake simple or rudimentary analyses of 2-D patterns to meet the basic needs of the experiments for which the 2-D gels were produced has exceeded the capacity to fully and uniformly integrate information generated from any gel image or experiment, across all images and experiments. While only a fraction of the information in the 2-D patterns contained in the lymphoid database has been mined, novel findings derived from querying the database point to the merits of this protein based approach. Additional resources have recently been put into place to mine more effectively data pertaining to protein expression in lymphoid cells.

Cell Cycle↗
PubMed2003

High-content proteomics: fluorescence multiplexing using an integrated, high-sensitivity, multiwavelength charge-coupled device imaging system.

The detection of proteins in 2-D gels and their subsequent identification by MS is still the "gold standard" in proteomics. Fluorescent detection has increasingly replaced colorimetric and radiometric detection on gels and blots. The reasons for this are multiple and varied and include higher sensitivity, better quantitation, increased dynamic range, speed, safety and ease of use. Unlike other methods, fluorescent protein detection is also typically very consistent in response from protein to protein and in many cases is compatible with MS methods for protein identification. The superior sensitivity and benefits achieved by fluorescent techniques have spurred the development of instrumentation capable of delivering precise, sensitive, high-resolution image acquisition over a wide variety of excitation and emission wavelengths. This report focuses on applications using the highly sensitive, charge-coupled device based ProXPRESS multilabel imager, readily configurable for image acquisition over a wide variety of wavelengths (380-700 nm and ultraviolet (UV)) using xenon lamp or UV excitation. The ability to simultaneously detect enzyme activities or protein modifications with different color fluorescent probes in addition to total protein amounts (multiplexing) allows the further mining of proteomic data content from a single set of protein samples. To this end, the development of instrumentation that enables a multiplexing strategy will become central to in-depth proteomic studies. The ProXPRESS maximizes the efficiency of experimental strategies that require flexibility and multicolor fluorescence detection.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2006

Combined use of photosynthetic enzyme complexes and microalgal photosynthetic systems for rapid screening of wastewater toxicity.

Because of the often episodic nature of wastewater toxicity, routine monitoring using expensive and time consuming tests can constitute an inefficient means of toxicity evaluation, particularly when negative results are generated. Cost-effective screening tests enabling the rapid detection of effluent toxicity are clearly needed, and they should be used to rapidly determine where in-depth investigations should be focused. The LuminoTox is a recently-developed screening test enabling the rapid determination of wastewater toxicity. This test is based on the inhibition of chlorophyll fluorescence emitted by photosynthetic systems. The combined use of photosynthetic enzyme complexes (PECs), isolated from higher plants, and whole photosynthetic organisms (algae) allows a wide range of toxic inhibitors to be detected within 10-15 min. The detection thresholds obtained for individual toxic chemicals indicate that algae are less sensitive to metal cations than PECs, because of the algal cell wall being ion selective. However, other toxic chemicals, such as phenolic compounds and nitrogen ammonia, acting on the last constituents of the photosynthetic enzyme complex that are degraded during the PEC extraction process, are more easily detected with algae after just 10 min of exposure. The combination of PECs and algae is not only useful for rapid toxicity screening, but yields results that are as sensitive as those of standard bioassays. Toxicity data generated with mining industry effluents demonstrate that PECs routinely prove to be as sensitive as daphnia, while algal sensitivity is comparable to that of the standard trout bioassay. An important feature of LuminoTox and algal photosynthetic system testing, however, resides in the production of their rapid and sensitive responses (10-15 min) in comparison with those of the more traditional tests (48-96 h for daphnia and trout, respectively).

Eukaryota↗
PubMed2006

Synergy between Competitive Intelligence (CI), Knowledge Management (KM) and Technological Foresight (TF) as a strategic model of prospecting--the use of biotechnology in the development of drugs against breast cancer.

The aim of this paper is to demonstrate the synergy between Competitive Intelligence, Knowledge Management and Technological Foresight, and to emphasize the proposal of a strategic model of data prospecting as a mechanism to support decision-making in regard to three approaches for sustainable development and innovation: technological, social and economic. The use of biotechnology in the development of drugs against breast cancer is the case study. The article shows the results of data and text mining in specialized medical and patent databases, identifying the most frequently cited drugs, as well as the authors of research, and the inventors of new technology at the beginning of the 21st century. In addition, the study includes reference to Brazilian competence in breast cancer area, the international trends in drugs for treatment of this cancer, leading international institutions and Brazilian competencies. A framework is presented, which could serve as a guide and support for the decision-making process.

Biotechnology↗
PubMed2006

The application of systems biology to drug discovery.

Recent advances in the 'omics' technologies, scientific computing and mathematical modeling of biological processes have started to fundamentally impact the way we approach drug discovery. Recent years have witnessed the development of genome-scale functional screens, large collections of reagents, protein microarrays, databases and algorithms for data and text mining. Taken together, they enable the unprecedented descriptions of complex biological systems, which are testable by mathematical modeling and simulation. While the methods and tools are advancing, it is their iterative and combinatorial application that defines the systems biology approach.

Animals↗
PubMed2005

Toxicity of uranium and copper individually, and in combination, to a tropical freshwater macrophyte (Lemna aequinoctialis).

Copper (Cu) and uranium (U) are of potential ecotoxicological concern to tropical freshwater biota in northern Australia, as a result of mining activities. Few data are available on the toxicity of U, and no data are available on the toxic interaction of Cu and U, to freshwater biota. This study determined the toxicity of Cu and U individually, and in combination, to a tropical freshwater macrophyte, Lemna aequinoctialis (duckweed), in a synthetic soft water (27 degrees C; pH, 6.5; hardness, 40 mg CaCO3 l-1, alkalinity, 16 mg CaCO3 l-1), typical of many fresh surface waters in coastal northern Australia. The growth rate of L. aequinoctialis decreased with increasing Cu or U concentrations, with the concentration of Cu inhibiting growth by 50% (EC50) being 16+/-1.0 microg l-1, with a minimum detectable effect concentration (MDEC) of 3.2 microg l-1. The concentration of U inhibiting growth by 50% (EC50) was 758+/-35 microg l-1 with a MDEC of 112 microg l-1. The EC50 value for the exposure of L. aequinoctialis to equitoxic mixtures of Cu and U was significantly (P0.05) higher than one toxic unit (1.35; 95% confidence interval, 1.18-1.52), indicating that the combined effects of Cu and U are less than additive (antagonistic). Therefore, inhibition of the growth rate of L. aequinoctialis was reduced when Cu and U were present in equitoxic mixtures, relative to individual metal exposures. Since non-additive (e.g. antagonistic) interactions of metal mixtures cannot be predicted using current mixture models, these results have important potential implications for the protection of freshwater ecosystems through the derivation of national water quality guidelines.

Animals↗
PubMed2006

Beta-sheet folding mechanisms from perturbation energetics.

Amide backbone and sidechain mutagenesis data can be used in combination with kinetic and thermodynamic measurements to understand the energetic contributions of backbone hydrogen bonding and the hydrophobic effect to the acquisition of beta-sheet structure. For example, it has been revealed that loop 1 of the WW domain forms in the transition state, consistent with the emerging theme that reverse turn formation is rate limiting in beta-sheet folding. A distinct subset of WW domain residues principally influences thermodynamic stability by forming hydrogen bonds and hydrophobic interactions that stabilize the native state. Energetic data and sequence mining reveal that only a small subset of the molecular information contained in sequences or observed in high-resolution structures is required to generate folded functional beta-sheets, consistent with evolutionary robustness.

Animals↗
PubMed2005

Genic microsatellite markers in plants: features and applications.

Expressed sequence tag (EST) projects have generated a vast amount of publicly available sequence data from plant species; these data can be mined for simple sequence repeats (SSRs). These SSRs are useful as molecular markers because their development is inexpensive, they represent transcribed genes and a putative function can often be deduced by a homology search. Because they are derived from transcripts, they are useful for assaying the functional diversity in natural populations or germplasm collections. These markers are valuable because of their higher level of transferability to related species, and they can often be used as anchor markers for comparative mapping and evolutionary studies. They have been developed and mapped in several crop species and could prove useful for marker-assisted selection, especially when the markers reside in the genes responsible for a phenotypic trait. Applications and potential uses of EST-SSRs in plant genetics and breeding are discussed.

Chromosome Mapping↗
PubMedDate not supplied

Models-of-data and models-of-processes in the post-genomic era.

As we are entering the post-genomic era, models-of-data, such as mining and filtering methods for gene sequences and microarrays and the clustering of co-expressed genes, must be complemented with models-of-processes that explain relationships between genomic information and phenomena at biochemical and physiological levels. Many of these models will have the structure of compartment models, whose conceptualization, identification and analysis will fundamentally benefit from the seminal work of John Jacquez. The article indicates with three vignettes that non-linear compartment models in the formulation of biochemical systems theory are viable candidates for post-genomic models-of-processes.

Animals↗
PubMed1998

Microarrays: biotechnology's discovery platform for functional genomics.

Advances in microarray technology enable massive parallel mining of biological data, with biological chips providing hybridization-based expression monitoring, polymorphism detection and genotyping on a genomic scale. Microarrays containing sequences representative of all human genes may soon permit the expression analysis of the entire human genome in a single reaction. These 'genome chips' will provide unprecedented access to key areas of human health, including disease prognosis and diagnosis, drug discovery, toxicology, aging, and mental illness. Microarray technology is rapidly becoming a central platform for functional genomics.

Biotechnology↗
PubMedDate not supplied

Large-scale quantitative proteomic study of PUMA-induced apoptosis using two-dimensional liquid chromatography-mass spectrometry coupled with amino acid-coded mass tagging.

By coupling two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) with amino acid-coded mass tagging (AACT), we have greatly increased the analytical throughput and sequence coverage of MS-based methods for proteome-wide quantitation. The dynamic range and reproducibility of this 2D-LC-AACT quantitative approach were evaluated by profiling the mixtures with different ratios of E. coli cells grown in either regular or AACT medium. A SQL-based high thoughput MASCOT data analysis tool was developed for proteomic data sorting and mining. We investigated the early stage of apoptosis by inducing the p53 upregulated modulator of apoptosis (PUMA) through the analyses of the relative ratios of the pairwise isotope signals that were originated from the control and labeled PUMA-induced cells. In 20-hour 2D-LC-MS/MS run, 480 proteins were conclusively identified, and more than half of them were quantified. A noteworthy change in the quantitative profile was that histones and a ubiquitin conjugate protein UBC9, which are involved in DNA double-strand break (DSB) repair were significantly down-regulated in the PUMA-overexpressing apoptotic cells, suggesting the detection of DSB in the apoptotic process. The quantitative profiling efficiency of this approach was compared with the gel-based quantitative analysis scheme.

Amino Acids↗
PubMed2006

Delta-thalassemia in Cyprus.

To help clarify the hematological picture of patients who may be positive for beta- and delta-globin gene mutations, the following study was carried out. Our aim was to identify the delta-globin gene mutations found in the Greek Cypriot population, their frequencies and the Hb A2 values associated with them. Seventy-four samples were selected from a random sample of 5,030 individuals, and the database of the Molecular Genetics Thalassaemia Department containing diagnostic analyses data was also mined for relevant information. Four novel for Cyprus delta-globin gene mutations: -30 (T-->C), Hb A2-Wrens [delta98(FG5)Val-->Met, GTG-->ATG], IVS-I-2 (T-->C) and Hb A2-Yokoshima [delta25(B7)Gly-->Asp (GGT-->GAT)] were identified. Hb A2-Yialousa [delta27(B9)Ala-->Ser, GCC-->TCC], Hb A2-Yokoshima, Hb A2-Troodos [delta116(G18)Arg-->Cys, CGC-->TGC], Hb A2-Pelendri [delta141(H19)Leu-->Pro, CTG-->CCG], codon 4 [delta4(A1)Thr-->Ile], codon 59 (-A), Hb A2-Wrens, IVS-II-897 (A-->G), IVS-I-2, -55 (T-->C) and -30 bring the total to 11 delta-globin alleles found in the Greek Cypriot population. Hb A2-Yialousa is the most common mutation followed by codon 4, with frequencies of 60.7 and 17.8%, respectively.Hb A2 levels above 1.9% have been found to indicate a significantly reduced possibility for the presence of a delta-globin gene mutation in this population. For Hb A2 levels of 1.7 and 1.8% the possibility of a delta-globin gene mutation rises to 90.9% and reaches 100% for lower Hb A2 levels. The frequency of all the mutant delta-globin chromosomes in the sample is 0.0067 and the carrier frequency is 1.26%.

Chi-Square Distribution↗
PubMed2004

Use of a directional spray system design to control respirable dust and face gas concentrations around a continuous mining machine.

A laboratory study assessed the impacts of water spray pressure, face ventilation quantity, and line brattice setback distance on respirable dust and SF6 tracer gas concentrations around a continuous mining machine using a sprayfan or directional spray system. Dust levels were measured at locations representing the mining machine operator and the standard and off-standard shuttle car operators, and in the return airway. The results showed that changes in all three independent variables significantly affected log-transformed dust levels at the three operator sampling locations. Changes in setback distance impacted return airway dust levels. Laboratory testing also identified numerous variable interactions affecting dust levels. Tracer gas levels were measured on the left and right sides of the cutting drum and in the return. Untransformed gas levels around the cutting drum were significantly affected by changes in water pressure, face ventilation quantity, and setback distance. Only a few interactions were identified that significantly affected these concentrations. Gas levels in the return airway were grouped by face ventilation quantity. Return gas levels measured at the low curtain quantity were generally unaffected by changes in water pressure or curtain setback distance. At the high curtain quantity, return airway gas levels were affected by curtain setback distance. A field study was conducted to assess the impact of these parameters in an actual mining operation. These data showed that respirable dust levels may have been impacted by a change in water pressure and, to a lesser extent, by an increase in curtain setback distance. A series of tracer gas pulse tests were also conducted during this study. The results showed that effectiveness of the face ventilation was impacted by changes in curtain flow quantity and setback distance. Laboratory testing supported similar conclusions.

Caustics↗
PubMed2003

Coupled two-way clustering server.

UNLABELLED: The CTWC server provides access to the software, CTWC1.00, that implements Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data AVAILABILITY: Free, at http://ctwc.weizmann.ac.il. SUPPLEMENTARY INFORMATION: The site has a link to an example which provides figures and detailed explanations

Algorithms↗
PubMed2004

A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays.

MOTIVATION: The radioactivity labeled DNA array platform is a robust and accurate way for a high-throughput measurement of gene expression levels in biological samples. Despite its high degree of sensitivity and reproducibility, this platform has several sources of variation. These are related to the presence of saturation effects in the array images and impede the degree of accuracy at which gene expression levels are determined. RESULTS: Here we describe a simple, but effective, approach for combining expression data from a series of autoradiographic exposures of variable length. This technique increases the sensitivity of this array platform by detecting low-expressed genes at longer exposures. It also improves the measurement accuracy of highly abundant genes by considering only values from the linear portion of dependency between the exposure times and gene intensities. As a result, the described approach improves the outcome of the subsequent steps of array data normalization and mining.

Algorithms↗