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PubMed2006

Serum proteomic signature for cystic fibrosis using an antibody microarray platform.

Antibody microarrays are a new proteomic technology, which we have developed as a platform for identifying a cystic fibrosis (CF)-specific serum proteomic signature. Serum samples from CF patients have been pooled and compared with equivalent pools of control sera in order to identify patterns of protein expression unique to CF. We find that the set of significantly differentially expressed proteins is enriched in protein mediators of inflammation from the NFkappaB signaling pathway, and in proteins that may be selectively expressed in CF-affected tissues such as lung and intestine. In several instances, we validate the data from the antibody microarrays by quantitative analysis with Reverse Capture Protein Microarrays. We conclude that antibody microarray technology is sensitive, quantitative, and robust, and can be useful as a proteomic platform to discriminate between sera from CF and control patients.

Adolescent↗

PubMed2006

Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa.

Interindividual variation of human mitochondrial DNA has been extensively studied over the last two decades, and its usefulness for reconstructing evolutionary relationships of extant populations has been proved. However, some mitochondrial lineages still need to be studied using a combination of larger and tailored datasets and increased level of resolution in order to shed light on their origin and on the processes underlying their present distribution. In this study, we analyze the phylogeny of the L1c haplogroup of human mitochondrial DNA using sequence data from hypervariable regions 1 and 2 obtained from 455 individuals (extracted from a total sampling of 2542 individuals) belonging to sub-Saharan African and African-American populations. We propose a substantial revision of L1c phylogeny, by introducing one new sub-haplogroup (L1c4), two new L1c1 clades (L1c1b and L1c1c), and by reassigning the previous L1c1a1 sequences to a clade which we termed L1c5. The new phylogeny encompasses distinct lineages with different evolutionary histories. In fact, based on population frequency, internal variation and mismatch distribution, we propose that L1c1b, L1c1c and L1c2 originated in Bantu ancestors, whereas L1c1a, L1c4 and L1c5 evolved among Western Pygmies. The population structure of L1c is not comparable to any known mitochondrial or, even, Y-chromosomal haplogroup, and challenges the current view that most of mtDNA variation in Pygmies might reflect admixture with Bantu or a persistence of plesiomorphic characters. In fact, the unique feature of the L1c is that it retains a signature of a phase common to the ancestors of the Bantu and Western Pygmies, while encompassing some specific sub-clades which can indicate their divergence. This allowed us to attempt a phylogenetically based assessment of the evolutionary relationships between the two groups. Taking into consideration estimates of the time to the most recent common ancestor of L1c and its clades together with archaeological and paleoclimatological evidence, we propose that the ancestors of Bantu and Western Pygmies separated between 60 and 30 kya.

Africa, Central↗

PubMed2004

Modulation of notch signaling elicits signature tumors and inhibits hras1-induced oncogenesis in the mouse mammary epithelium.

Deregulation of Notch signaling, which normally affects a broad spectrum of cell fates, has been implicated in various neoplastic conditions. Here we describe a transgenic mouse model, which demonstrates that expression of a constitutively active form of the Notch1 receptor in the mammary epithelium induces the rapid development of pregnancy/lactation-dependent neoplasms that consistently exhibit a characteristic histopathological pattern. These signature tumors retain the ability to respond to apoptotic stimuli and regress on initiation of mammary gland involution, but eventually appear to progress in subsequent pregnancies to nonregressing malignant adenocarcinomas. Additionally, we present evidence indicating that cyclin D1 is an in vivo target of Notch signals in the mammary glands and demonstrate that we can effectively inhibit Hras1-driven, cyclin D1-dependent mammary oncogenesis by transgenic expression of the Notch antagonist Deltex.

Adenocarcinoma↗

PubMed2001

Automated signature peptide approach for proteomics.

This paper addresses the issue of automating the multidimensional chromatographic, signature peptide approach to proteomics. Peptides were automatically reduced and alkylated in the autosampler of the instrument. Trypsin digestion of all proteins in the sample was then executed on an immobilized enzyme column and the digest directly transferred to an affinity chromatography column. Although a wide variety of affinity columns may be used, the specific column used in this case was a Ga(III) loaded immobilized metal affinity chromatography (IMAC) column. Ga(III)-IMAC is known to select phosphorylated peptides. Phosphorylated peptides selected by the affinity column from tryptic digests of milk were automatically transferred to a reversed-phase liquid chromatography (RPLC) column. Further fractionation of tryptic peptides on the RPLC column was achieved with linear solvent gradient elution. Effluent from the RPLC column was electrosprayed into a time-of-flight mass spectrometer. The entire process was controlled by software in the liquid chromatograph. With slight modification, it is possible to add multiple columns in parallel at any of the single column positions to further increase throughput. Total analysis time in the tandem column mode of operation was under 2 h.

Automation↗

PubMed2002

An alternative mechanism for amidase signature enzymes.

The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain. The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.

Amidohydrolases↗

PubMed2006

Classification of renal neoplasms based on molecular signatures.

PURPOSE: Gene expression microarray studies have demonstrated distinct molecular signatures for different types of renal neoplasms based on overall gene expression patterns. However, in most of these studies the investigators used renal tumors with defined histology. We analyzed a test set of renal tumors in double-blind fashion using recently established molecular profiles of renal tumors as benchmarks. MATERIALS AND METHODS: A total of 16 consecutive nephrectomies performed for neoplasms at a single urological service were subjected to gene expression profiling using cDNA chips containing 21,632 genes. Analysis was clustered with our previously established molecular profiles of 91 histologically defined kidney neoplasms and comparative genomic microarray analysis while blinded to tumor histology and clinical information. RESULTS: With molecular analysis 9, 4, 2 and 1 tumors were classified as clear cell, papillary RCC, chromophobe RCC, and renal oncocytoma, respectively. Histopathological evaluation was concordant in 14 tumors. One of the 2 tumors with a discrepancy between molecular and pathological diagnoses was composed of oncocytoma and high grade clear cell RCC, and the other was chromophobe RCC that histologically mimicked papillary RCC. CONCLUSIONS: We report the feasibility of the molecular diagnosis and classification of unknown renal neoplasms. Molecular diagnosis appears to be reliable and comparable to the standard of urological pathology. This molecular method may be a potentially useful test for establishing an accurate diagnosis that can impact clinical management.

Carcinoma, Renal Cell↗

PubMed2002

Comparative genomic hybridization analysis of PhIP-induced mammary carcinomas in rats reveals a cytogenetic signature.

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a mutagen/carcinogen belonging to the class of heterocyclic amines (HCAs) found in cooked meats, is a known rat mammary gland carcinogen. To gain insight into the genomic alterations associated with PhIP-induced carcinogenesis, we used comparative genomic hybridization (CGH) to examine chromosomal abnormalities in rat mammary gland carcinomas induced by PhIP. The alterations were compared to those induced by 7,12-dimethylbenz[a]anthracene (DMBA), a potent and well-studied mammary carcinogen. All six PhIP-induced carcinomas examined by CGH showed losses in the same specific regions of chromosomes 2, 3, 11, 18, and X, whereas three carcinomas induced by DMBA showed no consistent patterns of chromosomal gain or loss. This indicates that PhIP has a recognizable cytogenetic signature in rat mammary gland carcinomas.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed1996

Homochirality as the signature of life: the SETH Cigar.

A characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. It is therefore suggested that a search for extra-terrestrial life can be approached as a Search for Extra-Terrestrial Homochirality (SETH). A novel miniaturized space polarimeter, called the SETH Cigar, is described which could he used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. It is believed that homochirality will be found in the subsurface layers on Mars as a relic of extinct life.

Astronomy↗

PubMed2003

Principal surface wave velocities in the point focus acoustic materials signature V(z) of an anisotropic solid.

This paper deals with the point focus beam (PFB) acoustic materials signature V(z) of an anisotropic solid, and in particular how it tends to be dominated by a limited number of principal surface rays. These rays are associated with propagation directions in which the Rayleigh wave (RW), pseudo-surface acoustic wave (PSAW) or a lateral wave slowness has an extremum. The phenomenon is interpreted in terms of the complex azimuthally averaged reflectance function of the surface, and also explained on the basis of a ray model. We illustrate the phenomenon with a number of examples, pertaining to the surfaces of single crystal copper and a carbon-fibre epoxy composite. In the case of copper, which has a much larger acoustic impedance than the water couplant, the oscillations in V(z) are dominated by principal RW and PSAW, whereas for the composite there is no RW or pseudo-SAW to be discerned with acoustic microscopy (AM), and V(z) is dominated by principal lateral waves. The utility of PFB AM in the study of anisotropic solids is further elaborated with examples showing how V(z) is sensitive to surface orientation, and how V(z) is affected by the presence of a surface over layer. The phenomena examined in this paper expand the scope for determining materials characteristics, such as elastic constants, crystallographic orientation, residual stress and over layer properties, from PFB V(z) measurements.

Anisotropy↗

PubMed2001

Tracing sewage in the marine environment: altered signatures in Concepción Bay, Chile.

Lipid biomarkers are now widely used to trace organic matter in the marine environment. Selected compounds and ratios can be used to identify sources or processes. However, in a study of a particularly contaminated area, the expected signatures were not found (Mudge and Seguel, Bol. Soc. Chil. Quím. 42 (1997) 5). This site has been re-examined to determine why they were absent. The concentrations of sterols, fatty acids and alcohol biomarkers of 10 sediment cores from Concepción Bay, Chile, were quantified by capillary gas chromatography-mass spectrometry. The data obtained from 34 fatty acids, 28 fatty alcohols (C12-C30) and 32 sterols from the target study area, indicated that fatty acids from Concepción Bay sediments were the most abundant lipids (range 1.6-307 microg g(-1) dry wt) followed by sterols (range 0.02-25.3 microg g(-1) drywt). The sewage markers 5beta-coprostanol and epi-coprostanol were found in the areas close to the Penco-Lirquen disposal pipe. High bacterial activity was also present as indicated by the cholestanol, 18:1omega7, iso, anteiso and branched fatty acids and enhanced odd/even ratios of fatty alcohol biomarkers. The sediments from the centre of Concepción Bay had a greater marine/algal input characterized by brassicasterol and the marine fatty acids (20:4omega6, 20: 5omega3 22: 6omega3). The terrestrial contribution was mainly characterized by beta-sitosterol, C22-C26 fatty acids and confirmed by short/long chain ratio of the fatty alcohols. The distribution of these two markers indicates that the terrestrial matter passing through the sewage system is deficient in short chain fatty alcohols. The epi-coprostanol/coprostanol versus coprostanol/cholesterol plots also indicated selected removal of the stanols leaving apparently high cholesterol concentrations.

Biomarkers↗

PubMed1998

The Xylum Clot Signature Analyzer: a dynamic flow system that simulates vascular injury.

The Xylum Clot Signature Analyzer (CSA) is an automated, user-friendly, benchtop analyzer that assesses platelet function and coagulation in non-anticoagulated whole blood under physiological flow and temperature conditions. From blood drawn in a single venipuncture, the CSA measures: a) the time for platelets to occlude holes "punched" in a blood conduit (platelet hemostasis time or PHT); b) collagen-induced thrombus formation (CITF) as blood flows in a channel containing a collagen fiber; and c) clotting time (CT). Micrographs show platelet-rich thrombi in the punched holes and on the collagen surface after a run. PHT and CITF increased at lower shear rate, suggesting that shear activation of platelets is involved in hole closure and in collagen-induced thrombus formation. In blood mixed with anti-von Willebrand's factor (vWF) antibodies, anti-GPIb antibodies, aurin tricarboxylic acid (ATA), or anti-GPIIb-IIIa, PHT and CITF were prolonged, further supporting the reflection of platelet function by those parameters. At low shear rate (<1000 sec(-1)), native blood and blood treated with anti-vWF did not have significantly different PHTs or CITFs. At high shear rate (>6000 sec(-1)), the PHT and CITF of the anti-vWF-treated sample were significantly greater than those of the untreated sample. This supports the inhibition of shear-induced activation of platelets by anti-vWF in the CSA. Heparin-treated blood showed significantly longer CT, indicating that coagulation of blood under flow is inhibited by heparin. The CSA thus assess multiple aspects of hemostasis under near-physiological conditions.

Biological Assay↗

PubMed2001

Generating protein three-dimensional fold signatures using inductive logic programming.

Inductive logic programming (ILP) has been applied to automatically discover protein fold signatures. This paper investigates the use of topological information to circumvent problems encountered during previous experiments, namely (1) matching of non-structurally related secondary structures and (2) scaling problems. Cross-validation tests were carried out for 20 folds. The overall estimated accuracy is 73.37+/-0.35%. The new representation allows us to process the complete set of examples, while previously it was necessary to sample the negative examples. Topological information is used in approximately 90% of the rules presented here. Information about the topology of a sheet is present in 63% of the rules. This set of rules presents characteristics of the overall architecture of the fold. In contrast, 26% of the rules contain topological information which is limited to the packing of a restricted number of secondary structures, as such, the later set resembles those found in our previous studies.

Algorithms↗

PubMedDate not supplied

Protein expression signatures and lysosomal stability in Mytilus edulis exposed to graded copper concentrations.

Protein expression and lysosomal stability were observed in Mytilus edulis exposed to 0, 20, 40, 60, and 80 ppb copper sulfate for 24 h in a static exposure system. Haemolymph was removed from each mussel and analyzed for lysosomal damage using the Neutral Red retention assay expressed as the ratio of lysosomal size to cell area, the lysosomal destabilization ratio. Gill tissue from the same individuals was dissected, homogenized and the proteins extracted and then separated using two-dimensional gel electrophoresis. Two-dimensional protein maps from each concentration were analyzed using MELANIE II 2D gel analysis software (Biorad). Lysosomal damage increased with each dosage, with LDRs ranging from 0.18 +/- 0.01 at 0 ppb copper sulfate to 0.32 +/- 0.11 at 80 ppb copper sulfate. Orthogonal comparisons showed that the control, 20 and 40 ppb classes together differed significantly (P < 0.05) from the 60 and 80 ppb classes together. Specific protein expression signatures were identified at each dosage.

Animals↗

PubMedDate not supplied

Protein expression signatures: an application of proteomics.

The methods of proteomics, the study of the protein complement of the genome, are applicable to environmental testing. Sets of proteins specific to different stressors can be isolated using computer imaging software. Individual proteins can be identified by mass spectrometry. The Protein Expression Signatures (PES) obtained have potential in diagnosing adverse factors in the environment. The challenge is to demonstrate their feasibility in complex environments. We have shown that PES for three endocrine disrupting compounds in trout (Onchorhynchus mykiss), can be detected in mixed sewage effluent. Other studies support these results. As protein databases expand, identification becomes routine, and capture molecules specific to each protein are developed, the possibility of simple field tests for multiple stressors becomes real.

Animals↗

PubMed2004

Lead contamination and isotope signatures in the urban environment of Hong Kong.

The source and the extent of Pb pollution in the urban environment of Hong Kong were investigated at five different urban settings selected on the basis of their annual average daily traffic (AADT) varying from less than 100 to 61,700. In addition, a small distant island without any traffic was selected to establish the possible baseline values. The surface environmental samples studied consisted of street and tunnel dusts, gully sediments, and a limited number of roadside topsoils. The analytical results clearly indicated variable degrees of Pb contamination in these urban settings. However, the level of contamination varied significantly among different types of samples collected at the same location. Pb concentrations of roadside topsoils (79+/-22 micrograms/g) and gully sediments (278+/-88 micrograms/g) were lower than those of the corresponding road dusts (327+/-54 micrograms/g). The Pb isotope compositions in different urban settings varied considerably. The bedrock in the small island had the lowest Pb concentration (12 micrograms/g) but with the highest 206Pb/207Pb ratio (1.2206), whereas the tunnel ceiling dusts with the highest level of Pb (1410 micrograms/g) had the lowest 206Pb/207Pb ratio (1.1062). Despite the significant differences in vehicle types and traffic volumes, and the presence of several different petroleum retailers in Hong Kong, the Pb isotope ratios of road dusts (206Pb/207Pb: 1.1553+/-0.0043, 208Pb/207Pb: 2.4408+/-0.0084) varied within a relatively narrow range among all the five urban sampling sites. On the other hand, the Pb isotopic compositions of gully sediments (206Pb/207Pb: 1.1515+/-0.0145, 208Pb/207Pb: 2.4322+/-0.0198) varied noticeably within the same setting, but were reasonably comparable across the different study sites. In general, the 206Pb/207Pb ratios of road dusts can be used to estimate the direct contribution from automobile emissions, whereas those of gully sediments might reflect the effects of the mixing of different anthropogenic sources. The Pb isotope signatures in the urban environment of Hong Kong clearly suggested that anthropogenic Pb in the environment originated from Pb ore with a low 206Pb/207Pb ratio (such as the Australian Pb ore and similar sources in Southeast Asia) were significantly different from those of the anthropogenic Pb present in the neighboring Pearl River Delta (PRD) region.

Air Pollutants↗

PubMed2001

Glutamate receptor channel signatures.

Genes encoding glutamate receptor channel subunits were identified in genomes from Drosophila melanogaster and Caenorhabditis elegans by homology search with amino acid sequences that participate in the conserved channel pore. The predicted sequences of the putative glutamate receptor subunits revealed a distinct channel pore signature for each receptor subtype and for most of them, related members were found in C. elegans and Drosophila.

Amino Acid Sequence↗

PubMed1995

Dinucleotide relative abundance extremes: a genomic signature.

Early biochemical experiments established that the set of dinucleotide odds ratios or 'general design' is a remarkably stable property of the DNA of an organism, which is essentially the same in protein-coding DNA, bulk genomic DNA, and in different renaturation rate and density gradient fractions of genomic DNA in many organisms. Analysis of currently available genomic sequence data has extended these earlier results, showing that the general designs of disjoint samples of a genome are substantially more similar to each other than to those of sequences from other organisms and that closely related organisms have similar general designs. From this perspective, the set of dinucleotide odds ratio (relative abundance) values constitute a signature of each DNA genome, which can discriminate between sequences from different organisms. Dinucleotide-odds ratio values appear to reflect not only the chemistry of dinucleotide stacking energies and base-step conformational preferences, but also the species-specific properties of DNA modification, replication and repair mechanisms.

Animals↗

PubMed2003

Trimethylbenzoic acids as metabolite signatures in the biogeochemical evolution of an aquifer contaminated with jet fuel hydrocarbons.

Evolution of trimethylbenzoic acids in the KC-135 aquifer at the former Wurtsmith Air Force Base (WAFB), Oscoda, MI was examined to determine the functionality of trimethylbenzoic acids as key metabolite signatures in the biogeochemical evolution of an aquifer contaminated with JP-4 fuel hydrocarbons. Changes in the composition of trimethylbenzoic acids and the distribution and concentration profiles exhibited by 2,4,6- and 2,3,5-trimethylbenzoic acids temporally and between multilevel wells reflect processes indicative of an actively evolving contaminant plume. The concentration levels of trimethylbenzoic acids were 3-10 orders higher than their tetramethylbenzene precursors, a condition attributed to slow metabolite turnover under sulfidogenic conditions. The observed degradation of tetramethylbenzenes into trimethylbenzoic acids obviates the use of these alkylbenzenes as non-labile tracers for other degradable aromatic hydrocarbons, but provides rare field evidence on the range of high molecular weight alkylbenzenes and isomeric assemblages amenable to anaerobic degradation in situ. The coupling of actual tetramethylbenzene loss with trimethylbenzoic acid production and the general decline in the concentrations of these compounds demonstrate the role of microbially mediated processes in the natural attenuation of hydrocarbons and may be a key indicator in the overall rate of hydrocarbon degradation and the biogeochemical evolution of the KC-135 aquifer.

Benzoates↗