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PubMed2002

Supercritical fluid extraction and high-performance liquid chromatography-diode array-electrochemical detection of signature redox compounds from sand and soil samples.

A supercritical fluid extraction procedure and a chromatographic separation/detection method were developed for the detection of Earth-based microorganisms. After microbes in a sand or a soil sample were hydrolyzed in a diluted NH(4)OH/acetone solution, several redox compounds from bacteria could be effectively extracted with trimethylamine-modified supercritical CO(2) at 35 degrees C and 300 atm. These signature redox-active compounds were separated by a reversed-phase HPLC column in an ion-pair mode and then monitored with a diode array detector and an electrochemical detector. The analytical results demonstrated the feasibility of using the reported techniques to detect the chemical signature of life in barren desert sand samples.

Bacteria↗

PubMed1993

The ligand binding signatures of the rat AT1A, AT1B and the human AT1 receptors are essentially identical.

The objective of this study was to determine whether the three isoforms of recombinant Ang II receptors (rAT1A, rAT1B and hAT1), stably and individually expressed in CHO cells, could be pharmacologically distinguished by their ligand binding signatures. Competition studies were performed to characterize the inhibition of [125I]Ang II binding to each of the cell membrane preparations by an extensive series of peptide and nonpeptide Ang II analogs. Scatchard plot analyses revealed the following binding characteristics:rAT1A-Kd = 1.27 +/- 0.14 nM; rAT1B- Site 1:Kd = 0.56 +/- 0.11 nM, Site 2: Kd = 126 +/- 23 nM; and hAT1-Site 1:Kd = 1.06 +/- 0.16 nM, Site 2: Kd = 257 +/- 55 nM. The binding of [125I]Ang II in the three preparations was similarly sensitive to inhibition by GTP gamma S. The ligand binding signatures of the three receptor isoforms are essentially the same and are illustrated by the affinity and order of potency of the following ligands: L-158,809 > or = Sar1, Ile8Ang II > saralasin Ang II > or = Ang III > EXP581 > EXP3174 > losartan > or = EXP811 > GR117,289c > EXP6803 > DuP 532 > Ang I >> PD123177. In conclusion, the two rat AT1 receptor isoforms are pharmacologically indistinguishable from each other and from that of the human.

Angiotensin II↗

PubMed1998

Histone H2A.F/Z subfamily: the smallest member and the signature sequence.

The nucleotide sequence of a 700 basepair cDNA obtained from rabbit bladder was determined. It encodes a 123 amino acid protein, which is the smallest member of histone H2A.F/Z subfamily. The known H2A.F/Z variants are highly conserved in their central core regions of about 100 amino acids but more divergent in their N- and C-terminal ends. In addition to the seven amino acid signature sequence previously known for the H2A proteins, all the cloned H2A.F/Z variants contain an identical peptide sequence, L-E-Y-L-T-A-E-V-L-E-L-A-G-N-A. This 15 amino acid motif is proposed here as the signature sequence to identify new members of the H2A.F/Z subfamily.

Amino Acid Sequence↗

PubMed2000

Disruption of galactokinase signature sequence in gal3p of Saccharomyces cerevisiae does not lead to loss of signal transduction function.

Gal3p of Saccharomyces cerevisiae is a 520-amino-acid residue protein, which activates the GAL genes in the presence of galactose by relieving the repression of Gal80p. It shows significant amino acid sequence homology to galactokinases but does not possess galactokinase activity. Deletion mutants of Gal3p were generated to identify the role of N-terminal amino acid residues required for function. The mutant versions of Gal3p could be detected on a Western blot. The Gal3p mutant lacking N-terminal 50-amino-acid residues which is disrupted for galactokinase signature sequence was found to be functional. These results suggest that the evolutionarily conserved galactokinase signature sequence present in known galactokinases may not have a role in Gal3p function.

Amino Acid Sequence↗

PubMed2002

Bacillus subtilis inorganic pyrophosphatase: the C-terminal signature sequence is essential for enzyme activity and conformational integrity.

Bacillus subtilis inorganic pyrophosphatase is the first member of a newly identified Family II of PPases. To examine the role of a signature sequence found near the C-terminus, two truncated variants and a series of site-specific mutants were produced. A truncation of 17 residues (17AATR) but also single alanine substitutions, R295A and K296A, produced inactive enzyme. Removal of 5 nonconserved terminal residues (5AATR) markedly affected enzyme stability. Replacing S294 with A, T, C, or V decreased activity, the latter two mutations showing the greatest effect. Substitutions V299I and V300I had no or minor effects, whereas V300W and V299G/V300W significantly reduced activity. The sizes of truncated proteins and the full-length PPase were indistinguishable by gel-filtration. We conclude that the C-terminus has no role in multimerization, while both its conserved and nonconserved regions are essential for full enzyme activity. The signature sequence is required for both the conformation and composition of the active site.

Bacillus subtilis↗

PubMed1995

The mutagenic processing of psoralen photolesions leaves a highly specific signature at an endogenous human locus.

To assess the role of a given genotoxic agent in the etiology of human cancers, it is useful to establish the mutational specificity of this agent. The aim of this study was to investigate whether the processing of psoralen photolesions, interstrand cross-links (CL) and monoadducts (MA), leaves a specific molecular signature in the mutational events produced at an endogenous locus, HPRT. Human lymphoblasts were treated by 4,5',8-trimethylpsoralen (Me3Pso) in association with a double irradiation protocol (365 plus 365 nm) which allows us to increase the proportion of CL for a given constant number of total photoadducts. The molecular spectrum of mutations at the HPRT locus induced in these conditions was compared to the previously reported spectra of mutations induced by the same psoralen in combination with a single irradiation of either 365 nm (induction of MA and a low proportion of CL) or 405 nm (producing almost exclusively MA). In all treatment conditions, base substitutions constitute the major type of Me3Pso photoinduced mutations. The majority of base substitutions involve a T residue preferably within a 5'-TpA sequence which corresponds to the favoured sites of psoralen photoadducts. In other words, the Me3Pso photolesions induce at the endogenous HPRT locus a high specific signature. Moreover, base substitutions have been essentially found in the non-transcribed strand of the HPRT gene suggesting that the psoralen photolesions are preferentially removed from the transcribed strand. In spite of the considerable difference between the proportion of lesions of both types (CL or MA) induced in different treatment conditions, the kind of mutations and their sequence distribution are similar suggesting that the mutagenic processing of psoralen CL and MA is similar at least for the steps resulting in base substitutions.

Base Sequence↗

PubMed1999

Signature amino acid changes in latent membrane protein 1 distinguish Epstein-Barr virus strains.

Sequence variations in the Epstein-Barr virus (EBV) latent membrane protein 1 gene have been described in numerous EBV-associated tumors with some of these variations, most notably a 30-base pair deletion in the cytoplasmic carboxyl-terminal domain, suggested as associated with an increase in tumorigenicity. In this study, EBV DNA sequence was determined from 92 tissue specimens or cell lines, including nasopharyngeal carcinoma, oral hairy leukoplakia, post-transplant lymphoma, post-transplant without pathology, mononucleosis, Burkitt's lymphoma, parotid tumor, and normal from distinct geographical regions. The amino- and carboxyl-terminal sequences and, in some cases, the full-length sequences of latent membrane protein 1 were determined. Characteristic sequence patterns distinguished strains, with the carboxyl-terminal sequence being the most informative in distinguishing among the strains. Phylogenetic relationships between strains were determined, as were signature amino acid changes that discriminate between them. A correlation between strain and disease or strain and geographic location was not detected. The sequence variation and signature sequences identified at least seven distinct strains, as well as hybrid strains that apparently result from recombination.

Amino Acid Sequence↗

PubMed1996

Low-angle X-ray scattering signatures of urinary calculi.

This is the first reported use of low-angle X-ray scattering for the investigation of urinary calculi. Low-angle X-ray scattering (LAXS) measures the diffraction of a broad spectrum of X-rays at a single angle and uses a conventional diagnostic X-ray beam, and could thus be developed for use in vivo. A total of 45 calculi were investigated using this technique. Calcium oxalate stones showed a bimodal signature with peaks of almost even photon energies. Signatures for the other stone types were less well-defined. The results are discussed in more detail below. Our preliminary results show that the technique is capable of distinguishing between calcium oxalate stones and other stone types in vitro. Further work is in progress to correlate the results of this technique with objective parameters of stone hardness.

Humans↗

PubMed1998

Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria.

A number of proteins have been identified that contain prominent sequence signatures that are uniquely shared by the members of the Deinococcus-Thermus genera and the cyanobacterial species but which are not found in any of the other eubacterial or archaebacterial homologs. The proteins containing such sequence signatures include (1) the DnaJ/Hsp40 family of proteins, (2) DNA polymerase I, (3) the protein synthesis elongation factor EF-Tu, and (4) the elongation factor EF-Ts. A strong affinity of the Deinococcus-Thermus species to cyanobacteria is also seen in the phylogenetic trees based on Hsp70 and DnaJ sequences. These results provide strong evidence of a close and specific evolutionary relationship between species belonging to these two eubacterial divisions.

Amino Acid Sequence↗

PubMed2006

Parent-offspring communication in the Nile crocodile Crocodylus niloticus: do newborns' calls show an individual signature?

Young Nile crocodiles Crocodylus niloticus start to produce calls inside the egg and carry on emitting sounds after hatching. These vocalizations elicit maternal care and influence the behaviour of other juveniles. In order to investigate the acoustic structure of these calls, focusing on a possible individual signature, we have performed acoustic analyses on 400 calls from ten young crocodiles during the first 4 days after hatching. Calls have a complex acoustic structure and are strongly frequency modulated. We assessed the differences between the calls of the individuals. We found a weak individual signature. An individual call-based recognition of young by the mother is thus unlikely. In other respects, the call acoustic structure changes from the first to the fourth day after hatching: fundamental frequency progressively decreases. These modifications might provide important information to the mother about her offspring--age and size--allowing her to customize her protective care to best suit the needs of each individual.

Acoustics↗

PubMed2000

Sonoclot signature during normal pregnancy.

OBJECTIVE: The Sonoclot analyser provides global measurement of haemostasis, including plasma coagulation, platelet function and fibrinolysis. Benefits of its use in cardiovascular and hepatic surgery are well-documented and it may be useful in managing obstetric complications. The aim of this study was to determine ranges of the Sonoclot variables for normal pregnancy. DESIGN: Prospective and longitudinal study. SETTING: Antenatal outpatient clinic, university hospital. PATIENTS: Forty-seven healthy women were studied; forty-two completed normal pregnancies and gave birth to healthy infants. INTERVENTIONS: None. MEASUREMENTS AND RESULTS: Sonoclot signatures were performed at 10-15, 32-34 and 38-40 weeks of gestation and at 8 weeks postpartum. Haemoglobin concentration, haematocrit, platelet count, fibrinogen and activated partial thromboplastin time (APTT) were analysed with normal results. Sonact time and peak time were significantly decreased and clot rate and secondary rate were significantly increased during pregnancy compared with 8 weeks postpartum, indicating hypercoagulability. There were no significant changes in these variables during pregnancy. There were no changes in peak amplitude and downward rate. A significant correlation was found between sonact time and APTT, and between clot rate and APTT. CONCLUSIONS: We found the Sonoclot analyser simple to handle and the signatures easy to interpret. The ranges for the Sonoclot variables apply throughout pregnancy. The ranges for sonact time, clot rate, secondary rate and peak time during pregnancy differed from the ranges at 8 weeks postpartum.

Adult↗

PubMed2006

The glycine residues G551 and G1349 within the ATP-binding cassette signature motifs play critical roles in the activation and inhibition of cystic fibrosis transmembrane conductance regulator channels by phloxine B.

The cystic fibrosis transmembrane conductance regulator (CFTR) protein contains a canonical ATP-binding cassette (ABC) signature motif, LSGGQ, in nucleotide binding domain 1 (NBD1) and a degenerate LSHGH in NBD2. Here, we studied the contribution of the conserved residues G551 and G1349 to the pharmacological modulation of CFTR chloride channels by phloxine B using iodide efflux and whole-cell patch clamp experiments performed on the following green fluorescent protein (GFP)-tagged CFTR: wild-type, delF508, G551D, G1349D, and G551D/G1349D double mutant. We found that phloxine B stimulates and inhibits channel activity of wild-type CFTR (Ks = 3.2 +/- 1.6 microM: , Ki = 38 +/- 1.4 microM: ) and delF508 CFTR (Ks = 3 +/- 1.8 microM: , Ki = 33 +/- 1 microM: ). However, CFTR channels with the LSGDQ mutated motif (mutation G551D) are activated (Ks = 2 +/- 1.13 microM: ) but not inhibited by phloxine B. Conversely, CFTR channels with the LSHDH mutated motif (mutation G1349D) are inhibited (Ki = 40 +/- 1.01 microM: ) but not activated by phloxine B. Finally, the double mutant G551D/G1349D CFTR failed to respond not only to phloxine B stimulation but also to phloxine B inhibition, confirming the importance of both amino acid locations. Similar results were obtained with genistein, and kinetic parameters were determined to compare the pharmacological effects of both agents. These data show that G551 and G1349 control the inhibition and activation of CFTR by these agents, suggesting functional nonequivalence of the signature motifs of NBD in the ABC transporter CFTR.

ATP-Binding Cassette Transporters↗

PubMed2000

Conserved structural features in class I major fimbrial subunits (Pilin) in gram-negative bacteria. Molecular basis of classification in seven subfamilies and identification of intrasubfamily sequence signature motifs which might Be implicated in quaternary structure.

Type 1 and P-pili are prototype members of Class I fimbriae produced by Gram-negative bacteria. Despite common structural characteristics, the low level of amino acid sequence conservation among the Class I major fimbrial subunits (pilins) indicates considerable evolutionary distance between members of this superfamily. We highlight here structural relatedness between Class I pilins from their two-dimensional sequence analysis using hydrophobic cluster analysis (HCA) and secondary structure predictions (PHD program). We present evidence that all members of the Class I pilin family have clear structural relatedness and suggest that classification based on phylogenetic analysis of Class I pilins into seven subfamilies correlates with differences in structural properties of the amino acid sequences. Using a sensitive alignment process (HCA), we identified 29 residues in topohydrophobic positions which probably play a prominent role in folding. The most striking aspects that distinguish the different pilin subfamilies are (i) large variation in the length of the loops connecting the structurally conserved regions and (ii) intrasubfamily sequence signature motifs located on regions predicted to be in the beta-conformation. We suggest that these "intrasubfamily sequence signature motifs" are part of interactive surfaces which participate in subunit-subunit interactions. These motifs prove highly useful in characterizing and classifying new Class I fimbriae that have not yet been described and whose sequence diverges appreciably from those of characterized groups. (After the submission of our manuscript, the experimental structure of Class I pilus subunits was published. In light of these actual pilin structures, a comparison has been made between the predicted results and the crystal structure in the Note Added in Proof.)

Amino Acid Motifs↗

PubMed1998

Identification of a hotspot for transformation of Neisseria meningitidis by shuttle mutagenesis using signature-tagged transposons.

Shuttle mutagenesis using signature-tagged transposons was employed to generate a library of individually tagged mutants of the Neisseria meningitidis strain B1940, which belongs to serogroup B. The use of tagged transposons allowed us to monitor for enrichment for single mutants during the process of shuttle mutagenesis, by amplification of the tags and subsequent sequence determination. Enrichment of a single clone occurred during the transformation of the meningococci with transposon-containing plasmid DNA. Sequence determination around the site of transposon insertion revealed that the transposon had mutagenized a previously unknown locus, which was designated hrtA (high rate of transformation). hrtA-mediated transformation was independent of TnMax5 and tag sequences, and it most probably involved recombination events. The hrtA locus is restricted to meningococci and gonococci and is present in few apathogenic neisserial species. Chromosomal mapping of hrtA and six further hrt sites revealed a random distribution of highly transforming DNA fragments on the meningococcal chromosome. In conclusion, our data demonstrate that shuttle mutagenesis of naturally competent bacteria using signature-tagged transposons allows the isolation of chromosomal DNA fragments, which exhibit a high transformation efficiency, and which, therefore, are likely to be involved in horizontal gene transfer.

Base Sequence↗

PubMed2005

Prediction of beta-strand packing interactions using the signature product.

The prediction of beta-sheet topology requires the consideration of long-range interactions between beta-strands that are not necessarily consecutive in sequence. Since these interactions are difficult to simulate using ab initio methods, we propose a supplementary method able to assign beta-sheet topology using only sequence information. We envision using the results of our method to reduce the three-dimensional search space of ab initio methods. Our method is based on the signature molecular descriptor, which has been used previously to predict protein-protein interactions successfully, and to develop quantitative structure-activity relationships for small organic drugs and peptide inhibitors. Here, we show how the signature descriptor can be used in a Support Vector Machine to predict whether or not two beta-strands will pack adjacently within a protein. We then show how these predictions can be used to order beta-strands within beta-sheets. Using the entire PDB database with ten-fold cross-validation, we have achieved 74.0% accuracy in packing prediction and 75.6% accuracy in the prediction of edge strands. For the case of beta-strand ordering, we are able to predict the correct ordering accurately for 51.3% of the beta-sheets. Furthermore, using a simple confidence metric, we can determine those sheets for which accurate predictions can be obtained. For the top 25% highest confidence predictions, we are able to achieve 95.7% accuracy in beta-strand ordering. [Figure: see text].

Amino Acid Sequence↗

PubMed2024

Cross-platform proteomics signatures of extreme old age.

In previous work, we used a SomaLogic platform targeting approximately 5000 proteins to generate a serum protein signature of centenarians that we validated in independent studies that used the same technology. We set here to validate and possibly expand the results by profiling the serum proteome of a subset of individuals included in the original study using liquid chromatography tandem mass spectrometry (LC-MS/MS). Following pre-processing, the LC-MS/MS data provided quantification of 398 proteins, with only 266 proteins shared by both platforms. At 1% FDR statistical significance threshold, the analysis of LC-MS/MS data detected 44 proteins associated with extreme old age, including 23 of the original analysis. To identify proteins for which associations between expression and extreme-old age were conserved across platforms, we performed inter-study conservation testing of the 266 proteins quantified by both platforms using a method that accounts for the correlation between the results. From these tests, a total of 80 proteins reached 5% FDR statistical significance, and 26 of these proteins had concordant pattern of gene expression in whole blood generated in an independent set. This signature of 80 proteins points to blood coagulation, IGF signaling, extracellular matrix (ECM) organization, and complement cascade as important pathways whose protein level changes provide evidence for age-related adjustments that distinguish centenarians from younger individuals. The comparison with blood transcriptomics also highlights a possible role for neutrophil degranulation in aging.

Humans↗

PubMed2026

Integration of methylome and transcriptome reveals age-associated signatures of stage-specific dynamics and regulatory remodeling in dogs.

Aging in mammals is characterized by widespread yet coordinated epigenetic alterations. However, integrative analyses of DNA methylation and gene expression in dogs remain largely unexplored, particularly within genetically homogeneous single-breed populations. To elucidate the molecular signatures of canine aging, we profiled the genome-wide methylome and transcriptome of clinically healthy beagle dogs representing three distinct age groups. Global methylation levels were highly conserved across individuals, yet both methylation and gene expression variability increased progressively with aging. This epigenetic drift was not stochastic but structured by genomic context, as reduced CpG-gene associations indicated a gradual loss of epigenetic control over transcription. We further observed stage-related methylation change patterns across the three age groups, including early-shift, late-shift, and progressive patterns. These groups showed partially overlapping but distinct hallmark associations, suggesting links to different age-related biological processes. Together, these findings indicate that canine epigenetic aging involves multifaceted molecular changes across adulthood and support dogs as a useful model for investigating conserved molecular signatures of aging.

Beagle dog↗

PubMed1985

Stochastic analysis of myoelectric temporal signatures for multifunctional single-site activation of prostheses and orthoses.

This paper is concerned with a stochastic time-series analysis of the temporal signatures of myoelectric (ME) signals including the determination of model order and sampling rate. The paper considers the use of time-series parameters for the activation of artificial limbs for high-level amputees, of stimulation electrodes or of powered braces for paralysed persons, in several degrees of freedom, from a single or two surface-electrode pairs at locations where considerable ME cross-talk exists. The multifunctional capability from a single site is based on the differences between the time-series (TS) parameters for different muscle activation patterns at the same ME site, these differences being thus used for limb function discrimination via easily trainable muscle activation patterns at the vicinity of the electrode site. Specifically, the analysis is in terms of identifying the AR parameters of a time-domain autoregressive (AR) signature model both for the complete ME spectrum and for parts thereof, and in terms of the autocorrelation of the signal and of the models residual. Determination of sampling rate and of model orders is discussed in detail. It is shown that, using online real-time analysis, differences in the AR time-series parameters can be observed for different trainable patterns of muscle activation, at the same electrode location, even at the same ME power levels, as long as considerable cross-talk exists at the electrode site. These parameter differences can be accentuated if one considers the AR parameters for lower-frequency spectral windows. A case is made in this paper for employing TS analysis to squeeze out information in a distinct but low-level ripple of the low frequency spectrum of the signal. This information tends to be ignored in frequency domain, but is all that the AR parameters care for in TS analysis, since they are not concerned, with a flat-average low-frequency spectrum, i.e., its white-noise-like part, which is the residual term of the AR Model and not an AR parameter. Discrimination between different functions from a single electrode-site, at even the same power level, is thus shown to require considerable cross-talk at the given site, and to require the consideration of only the low-frequency part of the spectrum.

Artificial Limbs↗