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PubMed2004

Trefoil factor 3 overexpression in prostatic carcinoma: prognostic importance using tissue microarrays.

BACKGROUND: Human intestinal trefoil factor 3 (TFF3) is a member of a family of polypeptides encoded by a cluster of genes on chromosome 21. Through gene expression profiling studies TFF3 mRNA has been found to be overexpressed in prostate cancer. METHODS: We used immunochemistry on tissue microarrays and software tools, collectively referred to as TMAJ, for online assessment of staining to analyze samples from 294 primary tumors and 61 metastatic lesions. RESULTS: Applying a cutoff of 20% of cells staining as positive, the frequency of staining was 18.8% in normal (51 of 272) and 47.0% in primary tumors (126 of 268), P < 0.0001, Wilcoxon rank sum). Expression of TFF3 in metastatic prostate cancer was similar to that in primary tumors. TFF3 expression was not associated with time to biochemical recurrence, development of distant metastasis, or death due to prostate cancer. Scoring data derived from visual estimation of expression correlated highly with semi-automated image analysis using the Automated Cellular Imaging System (ACIS) from Chromavision, Inc. CONCLUSIONS: These studies validate that TFF3 is overexpressed at the protein level in a subset of primary and metastatic prostate cancers, show the first use of the TMAJ database, and demonstrate the ability to semi-automatically scan and score immunohistochemically stained tissue microarray slides.

Biomarkers, Tumor↗
PubMed2002

Pressure ulcers in intensive care patients: a review of risks and prevention.

OBJECTIVE: Review of the literature concerning pressure ulcers in the intensive care setting. DATA SOURCE AND STUDY SELECTIONS: Computerized databases (Medline from 1980 until 1999 and CINAHL from 1982 until 1999). The indexing terms for article retrieval were: "pressure ulcers", "pressure sores", "decubitus", and "intensive care". Nineteen articles met the selection criteria, and seven more were found from the references of these articles. One thesis was also analyzed. RESULTS: Data on prevention, incidence, and costs of pressure ulcers in ICU patients are scarce. Overall there are no conclusive studies on the identification of pressure ulcer risk factors. None of the existing risk-assessment scales was developed especially for use in ICU patients. It is highly questionable to what extent these scales can be used in this setting as they are not even reliable in "standard care". The following risk factors might play a role in pressure ulcer development: duration of surgery and number of operations, fecal incontinence and/or diarrhea, low preoperative protein and albumin concentrations, disturbed sensory perception, moisture of the skin, impaired circulation, use of inotropic drugs, diabetes mellitus, too unstable to turn, decreased mobility, and high APACHE II score. The number of patients per study ranged from 5 from 638. The definition of "pressure ulcer" varied widely between authors or was not mentioned. CONCLUSIONS: Meaningful comparison cannot be made between the various studies because of the use of different grading systems for pressure ulcers, different methods of data collection, different (or lack of) population characteristics, unreported preventive measures, and the use of different inclusion and exclusion criteria. There is a need for well-conducted studies covering all these aspects.

APACHE↗
PubMed1999

Probing for drug-induced multiplex signal transduction pathways using high resolution two-dimensional gel electrophoresis: application to beta-adrenoceptor stimulation in the rat C6 glioma cell.

Whole-cell [(32)P]-protein phosphorylation assays and two-dimensional gel electrophoresis (2-DGE) were applied to the analysis of the beta-adrenoceptor (betaAR)-linked signal transduction pathway. Rat C6 glioma cells were stimulated with isoproterenol and the protein lysates were resolved by 2-DGE. Two dimensional [(32)P]-phosphoprotein 'maps' were generated depicting the modulation of intracellular proteins after isoproterenol stimulation versus unstimulated cells. A total of 274 distinct phosphoprotein spots were detected, of which 200 were up-regulated, 69 were down-regulated, and 5 remained unchanged. An evaluation of isoproterenol's activity across several kinase pathways was performed using a computer-generated 2-DGE template incorporating the location and identification of individual signaling phosphoprotein intermediaries. The template served as a 'reference map' for drug treatment comparisons. We observed a significant increase in the phosphorylation states of several nuclear transcription factors, notably CREB-1, ATF-1, NFkappaB/IkappaBalpha and ELK-1, but not c-Jun. A parallel series of radioimmunoprecipitation studies confirmed our 2-DGE findings. Moreover, isoproterenol increased the phosphorylation state of PKC and of several MAPK-dependent pathway kinases which correlated with a significant increase in their endogenous kinase activity. Isoproterenol's effects on PKA, PKC and ERK-dependent activities were blocked by propranolol, a betaAR antagonist. In conclusion, an acute isoproterenol stimulus induced multiplex pathway modulation via the betaAR in the C6 glioma cell indicating that signaling pathway cross-talk is an essential feature for the regulation of cellular function. Moreover, the immediate advantages of the 2-DGE analytical approach were apparent, and further development of the protein database will provide a valuable tool to screen for broad-based drug-mediated signaling activities.

Animals↗
PubMed2005

The rat blood-brain barrier transcriptome.

The blood-brain barrier (BBB) is the cellular interface between the circulating blood and neural environment, and is created by apposed endothelial cells and their intercellular tight junctions. Many aspects of how the BBB functions at the molecular level remain unresolved; therefore, we report for the first time a comprehensive gene expression profile of rat brain microvessels using serial analysis of gene expression (SAGE). We assembled a full and quantitative SAGE catalog containing 101,364 tags, of which 33% of the tags matched known genes, 51% matched expressed sequence tags (ESTs) in the Unigene database, and 16% of the tags were unassigned. The transcriptome catalog contains many new and novel transcripts among known BBB genes. A large compliment of junctional proteins and an extensive assortment of facilitated carrier and ATP-dependent transporters are included. To identify microvessel-enriched transcripts, we compared the microvessel SAGE catalog to cortex and hippocampus SAGE catalogs. This resulted in identification of 864 genes, including several known for their abundant expression at the BBB, such as the transferrin receptor (TrnR). Sorting enriched genes based on function revealed groups that encode transporters (11%), receptors (5%), proteins involved in vesicle trafficking (4%), structural proteins (10%), and components of signal transduction pathways (17%). This genomic repertoire emphasizes the unique cellular phenotype existing within the brain and further implicates the BBB as a mediator between the brain and periphery. These results may provide a useful resource and reference point from which to determine the effects of different physiological, developmental, and disease processes on BBB gene expression.

Animals↗
PubMed2001

Safety aspects of pharmacological GH therapy in adults.

The consequences of "pharmacological" growth hormone administration have been studied in a number of conditions, including those characterized by high rates of catabolism. The majority of studies have reported favourable effects on metabolism but recent reports indicate that GH treatment results in increased mortality in critically ill humans. The objective of the study was to assess the safety of large doses of rhGH therapy in human adults. Original trials were identified by searching MEDLINE (1966-March 2000) and the Cochrane database (2000). References of all identified trials were also inspected for more studies. All relevant trials in which GH had been administered to non-GH-deficient (GHD) adult humans were selected from. Outcomes such as death, clinically significant change in function, change in length of hospital stay or need for treatment, and adverse effects were sought. Studies were selected, quality-assessed and passed suitable for inclusion by two independent reviewers. Those studies that were placebo-controlled with satisfactory randomization were considered for inclusion. Twenty-one reports were included in the review. A wide range of patient groups were studied by a variety of investigators, employing a range of doses and duration of GH treatment. The study protocols differed markedly. The majority of studies were small and were designed and/or powered to enable identification of specific effects on nutritional status, protein metabolism, level of function or quality of life. Only two studies were designed to assess safety issues and mortality. In these, GH treatment was associated with a marked increase in mortality in critically ill ICU patients, with a range of diagnoses. Multi-organ failure and the effects of sepsis/infection accounted for most of the excess mortality. In addition morbidity, in terms of length of ICU stay, was increased by GH administration. Other less marked effects were increased fluid retention and hyperglycaemia as a consequence of GH administration. Functional improvement following GH therapy was documented in some studies. There have been few studies assessing the safety aspects of "pharmacological" GH treatment in adult humans. Two well-designed reports indicate that GH administration results in increased morbidity and mortality in a wide variety of critically ill subjects across a spectrum of age ranges. The mechanism(s) of the GH-associated mortality remain poorly understood. Based on current trial evidence, pharmacological GH treatment cannot be recommended for widespread use in critically ill subjects. Well-conducted and reported randomized trials are still needed to inform practice as to whether GH administration will be safe in specific illness categories.

Adolescent↗
PubMedDate not supplied

Use of lysozyme as a standard for evaluating the effectiveness of a proteomics process.

Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including sample preparation, enzymatic digestion, HPLC, mass spectrometry, and database searching. By using this internal standard, digestion issues including rearrangements, semi-tryptic fragments, and modifications were monitored. In addition, control of the HPLC process including column performance was achieved. The use of the lysozyme standard allowed easy optimization of mass spectral conditions including data dependent and collision induced dissociation settings. The use of this internal standard in a study of differential protein expression in rat serum samples is presented.

Animals↗
PubMed2004

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.

UNLABELLED: Despite increasing numbers of computational tools developed to predict cis-regulatory sequences, the availability of high-quality datasets of transcription factor binding sites limits advances in the bioinformatics of gene regulation. Here we present such a dataset based on a systematic literature curation and genome annotation of DNase I footprints for the fruitfly, Drosophila melanogaster. Using the experimental results of 201 primary references, we annotated 1367 binding sites from 87 transcription factors and 101 target genes in the D.melanogaster genome sequence. These data will provide a rich resource for future bioinformatics analyses of transcriptional regulation in Drosophila such as constructing motif models, training cis-regulatory module detectors, benchmarking alignment tools and continued text mining of the extensive literature on transcriptional regulation in this important model organism. AVAILABILITY: http://www.flyreg.org/ CONTACT: cbergman@gen.cam.ac.uk.

Binding Sites↗
PubMed2006

EMAGE: a spatial database of gene expression patterns during mouse embryo development.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods.

Animals↗
PubMed2003

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins.

A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.

Animals↗
PubMed2001

Sequence complexity of disordered protein.

Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins.

Artificial Intelligence↗
PubMed1994

Guidelines for the interpretation of laboratory findings in birds and mammals with unknown reference ranges: plasma biochemistry.

The results of analyses of plasma samples from healthy and sick adult birds and mammals of a wide range of species were used to calculate reference ranges and clinical ranges for 11 biochemical variables (calcium, sodium, chloride, total protein, albumin, globulin, inorganic phosphate, potassium, bicarbonate, urea and creatinine concentrations) in six mammalian Orders (Primata, Carnivora, Pinnipedia, Proboscidea, Perissodactyla and Artiodactyla) and six avian Orders (Ciconiiformes, Gruiformes, Pelecaniformes, Psittaciformes, Falconiformes and Strigiformes). The patterns of variation between Orders for the different biochemical variables were then used to provide guidelines for the interpretation of plasma biochemistry results in the species in these Orders for which there are no reference data. The observed clinical ranges provide an indication of the potential diagnostic value of each variable.

Animal Diseases↗
PubMedDate not supplied

A hierarchical clustering approach for large compound libraries.

A modified version of the k-means clustering algorithm was developed that is able to analyze large compound libraries. A distance threshold determined by plotting the sum of radii of leaf clusters was used as a termination criterion for the clustering process. Hierarchical trees were constructed that can be used to obtain an overview of the data distribution and inherent cluster structure. The approach is also applicable to ligand-based virtual screening with the aim to generate preferred screening collections or focused compound libraries. Retrospective analysis of two activity classes was performed: inhibitors of caspase 1 [interleukin 1 (IL1) cleaving enzyme, ICE] and glucocorticoid receptor ligands. The MDL Drug Data Report (MDDR) and Collection of Bioactive Reference Analogues (COBRA) databases served as the compound pool, for which binary trees were produced. Molecules were encoded by all Molecular Operating Environment 2D descriptors and topological pharmacophore atom types. Individual clusters were assessed for their purity and enrichment of actives belonging to the two ligand classes. Significant enrichment was observed in individual branches of the cluster tree. After clustering a combined database of MDDR, COBRA, and the SPECS catalog, it was possible to retrieve MDDR ICE inhibitors with new scaffolds using COBRA ICE inhibitors as seeds. A Java implementation of the clustering method is available via the Internet (http://www.modlab.de).

Algorithms↗
PubMed2005

MSAID: multiple sequence alignment based on a measure of information discrepancy.

We propose an algorithm of global multiple sequence alignment that is based on a measure of what we call information discrepancy. The algorithm follows a progressive alignment iteration strategy that makes use of what we call a function of degree of disagreement (FDOD). MSAID begins with distance calculation of pairwise sequences, based on FDOD as a numerical scoring measure. In the next step, the resulting distance matrix is used to construct a guide tree via the neighbor-joining method. The tree is then used to produce a multiple alignment. Current alignment is next used to produce a new matrix and a new tree (with FDOD scoring measure again). This iterative process continues until convergence criteria (or a stopping rule) are satisfied. MSAID was tested and compared with other prior methods by using reference alignments from BAliBASE 2.01. For the alignments with no large N/C-terminal extensions or internal insertions MSAID received the top overall average in the tests. Moreover, the results of testing indicate that MSAID performs as well as other alignment methods with an occasional tendency to perform better than these prior techniques. We, therefore, believe that MSAID is a solid and reliable method of choice, which is often (if not always) superior to other global alignment techniques.

Algorithms↗
PubMed1997

Assessment of pseudo-energy potentials by the best-five test: a new use of the three-dimensional profiles of proteins.

We propose a new assessment, called the best-five test, for the pseudo-energy potential empirically derived from the protein structural database. The object of the test is the three-dimensional (3D) profiles of proteins, which are directly connected to the pseudo-energy potentials. In the 3D profile, the fitness of each amino acid type is ranked at each residue site of a protein. A site whose native residue type is ranked within the best-five out of 20 amino acids is regarded as satisfactory and the ratio of the satisfactory sites over all the sites of all the proteins examined is indicative of the efficiency of the pseudo-energy potential employed. We applied the test to our potential function consisting of four terms; side-chain packing, hydration, backbone hydrogen-bonding and local conformation, by setting various kinds of definitions for each term. Through this test, the validity of the minus average operation is confirmed, where the energy level of potential functions is adjusted by referring to the random-environmental state of the proteins. Especially in the side-chain packing function, the success ratio increases from about 30 to 50% with this operation. Failure without the operation is ascribed to bulky hydrophobic residues, which almost always occupy higher ranking positions in the 3D profile table. A maximum success ratio of 55.6% was attained with the final potential set consisting of the above four terms. The efficiency of the final set was further checked in the fold-recognition test for distantly related proteins. The best-five test is a new use of the 3D profile table for assessing the ability of the pseudo-energy potentials.

Amino Acid Sequence↗
PubMed2005

["Iodine allergy": point of view].

OBJECTIVE: The aim of this literature review is to suggest a diagnostic and a preventive attitude in patients having presented an immediate hypersensitivity reaction due to an iodinated drug. DATA SOURCES: Literature review. Data were searched in the Medline database from 1967 to 2004 in English and French language. Complementary references were selected from the bibliography of selected references or from authors' personal databases. The following key-words were used separately or combined: Hypersensitivity, Immediate; Allergy; Contrast Media; Povidone-Iodine; Iodine; Iodine Compounds; Iodides; Amiodarone; Seafood, Parvalbumins; Tropomyosin. STUDY SELECTION: Randomized studies, epidemiological studies, original articles, clinical cases, and letters to the editor were selected. DATA SYNTHESIS: The implication of iodine has never been demonstrated during allergic hypersensitivity reactions due to iodinated drugs. However, IgE-mediated allergic hypersensitivity reactions have been published with contrast media or iodinated antiseptics and will be described in this development. In a wider sense, allergic hypersensitivity reactions due to seafood are evoked because often improperly considered as a risk factor of allergic reaction to iodinated drugs. The allergenic determinant responsible of patient sensitization is not known for iodinated contrast media, but is probably due to povidone in case of iodine povidone. In fish, the allergen is described as the protein M. There has also been strong immunological evidence that tropomyosin is a cross-reactive allergen among crustaceans and molluscs (shellfishs). In case of hypersensitivity reaction occurring with iodinated drug, an allergological assessment is required to confirm the immune mechanism, to identify the culprit drug or substance and to identify cross-reactivity especially with iodinated contrast media. CONCLUSION: Asking a patient if he/she is "allergic to iodine" is a question that should be avoided because its significance is null. A diagnosis of drug allergy, essentially relying on clinical symptoms, biological tests and cutaneous tests, is required to take adequate preventive measures.

Anti-Infective Agents, Local↗
PubMed1997

FDA perspective on specifications for biotechnology products--from IND to PLA.

Quality standards are obligatory throughout development, approval and post-marketing phases of biotechnology-derived products, thus assuring product identity, purity, and potency/strength. The process of developing and setting specifications should be based on sound science and should represent a logical progression of actions based on the use of experiential data spanning manufacturing process validation, consistency in production, and characterization of relevant product properties/attributes, by multiple analytical means. This interactive process occurs in phases, varying in rigour. It is best described as encompassing a framework which starts with the implementation of realistic/practical operational quality limits, progressing to the establishment/adoption of more stringent specifications. The historical database is generated from preclinical, toxicology and early clinical lots. This supports the clinical development programme which, as it progresses, allows for further assay method validation/refinement, adoption/addition due to relevant or newly recognized product attributes or rejection due to irrelevance. In the next phase, (licensing/approval) specifications are set through extended experience and validation of both the preparative and analytical processes, to include availability of suitable reference standards and extensive product characterization throughout its proposed dating period. Subsequent to product approval, the incremental database of test results serves as a natural continuum for further evolving/refining specifications. While there is considerable latitude in the kinds of testing modalities finally adopted to establish product quality on a routine basis, for both drugs and drug products, it is important that the selection takes into consideration relevant (significant) product characteristics that appropriately reflect on identity, purity and potency.

Antibodies, Monoclonal↗
PubMed2005

A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization.

We have determined the effect of mutations involving isoleucine and valine (i.e., mutations I-->V and V-->I) on the stability of Escherichia coli thioredoxin. Despite the similarity in chemical structure (V and I differ only in a methyl group), we find that many environments are optimized to a significant extent for either V or I. We find, furthermore, that a plot of effect of hydrophobic mutations on stability versus packing density shows a strikingly simple pattern that clearly reflects evolutionary structural optimization. The existence of such patterns suggests the possibility of rationalizing (and perhaps even predicting) mutation effects on protein stability on the basis of evolutionary models. By "evolutionary model" we specifically refer in this context to a model for mutation effects on stability in which certain physical features of the mutated residue environments are evaluated from an assumption regarding how such environments have been selected during protein evolution (as opposed to a purely "physical model" in which those features would be derived from some kind of energetics analysis of the protein structural characteristics). To illustrate this novel approach and provide general guidelines for its application, we develop here a simple evolutionary model that successfully explains the effect of the I<-->V mutations on thioredoxin stability.

Algorithms↗
PubMed1996

A cyanobacterial gene that interferes with the phosphotransfer signal transduction involved in the osmoregulatory expression of ompC and ompF in Escherichia coli.

Synechococcus sp. PCC7942 is a phototrophic cyanobacterium. In this study we cloned a Synechococcus gene that has a striking effect on the production of the Escherichia coli outer membrane proteins, OmpC and OmpF, provided that this gene was introduced by a multicopy plasmid into the heterologous cells. This multicopy gene in E. coli cells was able to specifically shut off the production of both OmpC and OmpF at the level of transcription. The nucleotides were sequenced for this gene, named sis, and its gene product was purified from E. coli to near homogeneity. A computer-aided search found that the deduced amino acid sequence consisting of 138 residues is novel, with no significant similarity to any other protein in the databases. Since the transcription of ompC and ompF is regulated by the regulatory factors EnvZ and OmpR, through phosphotransfer signal transduction, we explored the inhibitory effect of Sis in various genetic backgrounds as to envZ and ompR. In particular, the inhibitory effect of Sis was observed even in an DeltaenvZ background, but was not observed in a certain background in which the ompC and ompF transcription was supported by a mutant OmpR that can function in a phosphorylation-independent manner. These results suggested that the EnvZ kinase may not be the direct target of Sis, but rather that the process(es) concerning the phosphorylation and/or dephosphorylation of the OmpR protein may be affected by Sis. However, no direct effect of Sis was seen in an in vitro OmpR-phosphorylation assay with the purified OmpR and Sis proteins. Based on these results, possible functions of Sis are discussed with special reference to the phosphotransfer signal transduction in E. coli.

Amino Acid Sequence↗