Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Signature”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,063 records · Page 59Linked to original sources
PubMed2005

Spectral signatures of hydrated proton vibrations in water clusters.

The ease with which the pH of water is measured obscures the fact that there is presently no clear molecular description for the hydrated proton. The mid-infrared spectrum of bulk aqueous acid, for example, is too diffuse to establish the roles of the putative Eigen (H3O+) and Zundel (H5O2+) ion cores. To expose the local environment of the excess charge, we report how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules. Signature bands indicating embedded Eigen or Zundel limiting forms are observed in all of the spectra with the exception of the three- and five-membered clusters. These unique species display bands appearing at intermediate energies, reflecting asymmetric solvation of the core ion. Taken together, the data reveal the pronounced spectral impact of subtle changes in the hydration environment.

Journal Article↗
PubMed2005

The radiative signature of upper tropospheric moistening.

Climate models predict that the concentration of water vapor in the upper troposphere could double by the end of the century as a result of increases in greenhouse gases. Such moistening plays a key role in amplifying the rate at which the climate warms in response to anthropogenic activities, but has been difficult to detect because of deficiencies in conventional observing systems. We use satellite measurements to highlight a distinct radiative signature of upper tropospheric moistening over the period 1982 to 2004. The observed moistening is accurately captured by climate model simulations and lends further credence to model projections of future global warming.

Journal Article↗
PubMed2005

Animal evolution and the molecular signature of radiations compressed in time.

The phylogenetic relationships among most metazoan phyla remain uncertain. We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved. In contrast, the same genes robustly resolved phylogenetic relationships within a major clade of Fungi of approximately the same age as the Metazoa. The differences in resolution within the two kingdoms suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences. Furthermore, simulation analyses as well as studies of other radiations in deep time indicate that, given adequate sequence data, the lack of resolution in phylogenetic trees is a signature of closely spaced series of cladogenetic events.

Animals↗
PubMed1997

Europa's magnetic signature: report from Galileo's pass on 19 December 1996.

On 19 December 1996 as Galileo passed close to Jupiter's moon, Europa, the magnetometer measured substantial departures from the slowly varying background field of Jupiter's magnetosphere. Currents coupling Europa to Jupiter's magnetospheric plasma could produce perturbations of the observed size. However, the trend of the field perturbations is here modeled as the signature of a Europa-centered dipole moment whose maximum surface magnitude is approximately 240 nanotesla, giving a rough upper limit to the internal field. The dipole orientation is oblique to Europa's spin axis. This orientation may not be probable for a field generated by a core dynamo, but higher order multipoles may be important as they are at Uranus and Neptune. Although the data can be modeled as contributions of an internal field of Europa, they do not confirm its existence. The dipole orientation is also oblique to the imposed field of Jupiter and thus not directly produced as a response to that field. Close to Europa, plasma currents appear to produce perturbations with scale sizes that are small compared with a Europa radius.

Extraterrestrial Environment↗
PubMed1998

In situ discovery of graphite with interstellar isotopic signatures in a chondrule-free clast in an L3 chondrite

Optical and scanning electron microscopy of a chondrule-free clast in the unequilibrated L3 chondrite Khohar revealed a spherical object consisting of an aggregate of small ( approximately 2- micrometer diameter), Ni-poor (0.5 to 2.89 weight percent) metal particles and fine-grained graphite (<1-micrometer diameter). The graphite has large D and 15N excesses (deltaD approximately 1500 per mil and delta15N approximately 1300 per mil) with two isotopically distinct signatures: N rich with a high D/H ratio and N poor with a high 15N/14N ratio. These excesses are the largest D and 15N excesses observed in situ in a well-characterized phase in a meteorite. The isotopic characteristics are suggestive of an interstellar origin, probably by ion-molecule reactions at low temperature in the interstellar molecular cloud from which the solar system formed. The structure and nonchondritic composition of the metal particles suggest they did not form under equilibrium conditions in the solar nebula.

Journal Article↗
PubMed1999

Role of fluids in faulting inferred from stress field signatures

The stress orientation signature of weak faults containing high-pressure fluids has been observed for segments of the San Andreas fault system in southern California. The inferred lithostatic fluid pressures extend into the surrounding relatively intact rock in a zone scaling with the width of the interseismic strain accumulation. Repeated strain-related fracturing and crack sealing may have created low-permeability barriers that seal fluids into the network of currently active fractures.

Journal Article↗
PubMed2000

Animal behavior. Dolphins whistle a signature tune.

Dolphins are remarkably intelligent creatures renowned for their ability to imitate manmade sounds and for producing individual signature whistles that enable them to recognize each other. Now, in his Perspective, Tyack discusses new findings showing that vocal imitation is important for communication among bottlenose dolphins in the wild (Janik). Apparently, bottlenose dolphins, when they are separated in the wild, address each other by matching each other's whistles.

Animals↗
PubMed1995

Auroral signature of comet Shoemaker-Levy 9 in the jovian magnetosphere.

The electrodynamic interaction of the dust and gas comae of comet Shoemaker-Levy 9 with the jovian magnetosphere was unique and different from the atmospheric effects. Early theoretical predictions of auroral-type processes on the comet magnetic field line and advanced modeling of the time-varying morphology of these lines allowed dedicated observations with the Hubble Space Telescope Wide Field Planetary Camera 2 and resulted in the detection of a bright auroral spot. In that respect, this observation of the surface signature of an externally triggered auroral process can be considered as a "magnetospheric active experiment" on Jupiter.

Extraterrestrial Environment↗
PubMed2025

Proteomic analysis reveals distinct cerebrospinal fluid signatures across genetic frontotemporal dementia subtypes.

We used an untargeted mass spectrometric approach, tandem mass tag proteomics, for the identification of proteomic signatures in genetic frontotemporal dementia (FTD). A total of 238 cerebrospinal fluid (CSF) samples from the Genetic FTD Initiative were analyzed, including samples from 107 presymptomatic (44 C9orf72, 38 GRN, and 25 MAPT) and 55 symptomatic (27 C9orf72, 17 GRN, and 11 MAPT) mutation carriers as well as 76 mutation-negative controls ("noncarriers"). We found shared and distinct proteomic alterations in each genetic form of FTD. Among the proteins significantly altered in symptomatic mutation carriers compared with noncarriers, we found that a set of proteins including neuronal pentraxin 2 and fatty acid binding protein 3 changed across all three genetic forms of FTD and patients with Alzheimer's disease from previously published datasets. We observed differential changes in lysosomal proteins among symptomatic mutation carriers with marked abundance decreases in MAPT carriers but not other carriers. Further, we identified mutation-associated proteomic changes already evident in presymptomatic mutation carriers. Weighted gene coexpression network analysis combined with gene ontology annotation revealed clusters of proteins enriched in neurodegeneration and glial responses as well as synapse- or lysosome-related proteins indicating that these are the central biological processes affected in genetic FTD. These clusters correlated with measures of disease severity and were associated with cognitive decline. This study revealed distinct proteomic changes in the CSF of patients with genetic FTD, providing insights into the pathological processes involved in the disease. In addition, we identified proteins that warrant further exploration as diagnostic and prognostic biomarker candidates.

Humans↗
PubMed2005

Atazanavir signature I50L resistance substitution accounts for unique phenotype of increased susceptibility to other protease inhibitors in a variety of human immunodeficiency virus type 1 genetic backbones.

Substitution of leucine for isoleucine at residue 50 (I50L) of human immunodeficiency virus (HIV) protease is the signature substitution for atazanavir (ATV) resistance. A unique phenotypic profile has been associated with viruses containing the I50L substitution, which produces ATV-specific resistance and increased susceptibility to most other approved HIV protease inhibitors (PIs). The basis for this unique phenotype has not been clearly elucidated. In this report, a direct effect of I50L on the susceptibility to the PI class is described. Cell-based protease assays using wild-type and PI-resistant proteases from laboratory and clinical isolates and in vitro antiviral assays were used to demonstrate a strong concordance between changes in PI susceptibility at the level of protease inhibition and changes in susceptibility observed at the level of virus infection. The results show that the induction of ATV resistance and increased susceptibility to other PIs by the I50L substitution is likely determined at the level of protease inhibition. Moreover, the I50L substitution functions to increase PI susceptibility even in the presence of other primary and secondary PI resistance substitutions. These findings may have implications regarding the optimal sequencing of PI therapies necessary to preserve PI treatment options of patients with ATV-resistant HIV infections.

Amino Acid Substitution↗
PubMed1991

Carbohydrate signatures of aquatic macrophytes and their dissolved degradation products as determined by a sensitive high-performance ion chromatography method.

The sugar contents of emergent macrophytes from a freshwater lake, a freshwater swamp, and a salt marsh in the southeastern United States were examined together with the dissolved free sugars produced during macrophyte degradation and in natural water samples collected adjacent to macrophyte stands. Simultaneous separation of up to 13 neutral and 2 amino sugars together with 3 uronic acids and muramic acid was achieved by anion-exchange high-performance ion chromatography. As little as 10 pmol or a concentration of 20 nM sugar can be detected by pulsed amperometry, a greater sensitivity for sugar quantification than that of previously reported detection techniques used in conjunction with either gas or liquid chromatographic systems. Optimum conditions for hydrolysis of plant material by using trifluoroacetic acid were determined, and internal standards were used to quantify losses due to matrix effects and solid-phase extraction of samples. Our data demonstrate that ratios of certain indicator sugars in undegraded macrophytes differ significantly from ratios of dissolved free sugars formed during macrophyte degradation, reflecting the complex processes (biological and physical) involved in vascular plant degradation in aquatic ecosystems. Natural water samples collected adjacent to macrophyte beds contained dissolved free sugars at concentrations of 620 nM (lake), 890 nM (freshwater swamp), and 2,300 nM (salt marsh). Sugar signatures of these natural water samples were similar to those of macrophyte degradation products.

Journal Article↗
PubMed1997

Phosphorus effects on the mycelium and storage structures of an arbuscular mycorrhizal fungus as studied in the soil and roots by analysis of Fatty Acid signatures.

The distribution of an arbuscular mycorrhizal (AM) fungus between soil and roots, and between mycelial and storage structures, was studied by use of the fatty acid signature 16:1(omega)5. Increasing the soil phosphorus level resulted in a decrease in the level of the fatty acid 16:1(omega)5 in the soil and roots. A similar decrease was detected by microscopic measurements of root colonization and of the length of AM fungal hyphae in the soil. The fatty acid 16:1(omega)5 was estimated from two types of lipids, phospholipids and neutral lipids, which mainly represent membrane lipids and storage lipids, respectively. The numbers of spores of the AM fungus formed in the soil correlated most closely with neutral lipid fatty acid 16:1(omega)5, whereas the hyphal length in the soil correlated most closely with phospholipid fatty acid 16:1(omega)5. The fungal neutral lipid/phospholipid ratio in the extraradical mycelium was positively correlated with the level of root infection and thus decreased with increasing applications of P. The neutral lipid/phospholipid ratio indicated that at high P levels, less carbon was allocated to storage structures. At all levels of P applied, the major part of the AM fungus was found to be present outside the roots, as estimated from phospholipid fatty acid 16:1(omega)5. The ratio of extraradical biomass/intraradical biomass was not affected by the application of P, except for a decrease at the highest level of P applied.

Journal Article↗
PubMed2001

Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment.

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802-805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.

Anaerobiosis↗
PubMed2005

A method adapting microarray technology for signature-tagged mutagenesis of Desulfovibrio desulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments.

Signature-tagged mutagenesis (STM) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. To date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. We used a mini-Tn10 transposon-bearing plasmid, pBSL180, that efficiently and randomly mutagenized Desulfovibrio desulfuricans G20 in addition to Shewanella oneidensis MR-1. Using these organisms as model sediment-dwelling anaerobic bacteria, we developed a new screening system, modified from former STM procedures, to identify genes that are critical for sediment survival. The screening system uses microarray technology to visualize tags from input and output pools, allowing us to identify those lost during sediment incubations. While the majority of data on survival genes identified will be presented in future papers, we report here on chemotaxis-related genes identified by our STM method in both bacteria in order to validate our method. This system may be applicable to the study of numerous environmental bacteria, allowing us to identify functions and roles of survival genes in various habitats.

Anaerobiosis↗
PubMed2005

Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk.

We have compared the proteomic profiles of L. lactis subsp. cremoris NCDO763 growing in the synthetic medium M17Lac, skim milk microfiltrate (SMM), and skim milk. SMM was used as a simple model medium to reproduce the initial phase of growth of L. lactis in milk. To widen the analysis of the cytoplasmic proteome, we used two different gel systems (pH ranges of 4 to 7 and 4.5 to 5.5), and the proteins associated with the cell envelopes were also studied by two-dimensional electrophoresis. In the course of the study, we analyzed about 800 spots and identified 330 proteins by mass spectrometry. We observed that the levels of more than 50 and 30 proteins were significantly increased upon growth in SMM and milk, respectively. The large redeployment of protein synthesis was essentially associated with an activation of pathways involved in the metabolism of nitrogenous compounds: peptidolytic and peptide transport systems, amino acid biosynthesis and interconversion, and de novo biosynthesis of purines. We also showed that enzymes involved in reactions feeding the purine biosynthetic pathway in one-carbon units and amino acids have an increased level in SMM and milk. The analysis of the proteomic data suggested that the glutamine synthetase (GS) would play a pivotal role in the adaptation to SMM and milk. The analysis of glnA expression during growth in milk and the construction of a glnA-defective mutant confirmed that GS is an essential enzyme for the development of L. lactis in dairy media. This analysis thus provides a proteomic signature of L. lactis, a model lactic acid bacterium, growing in its technological environment.

Animals↗
PubMed2005

Signature-tagged transposon mutagenesis studies demonstrate the dynamic nature of cecal colonization of 2-week-old chickens by Campylobacter jejuni.

We have constructed plasmids to be used for in vitro signature-tagged mutagenesis (STM) of Campylobacter jejuni and used these to generate STM libraries in three different strains. Statistical analysis of the transposon insertion sites in the C. jejuni NCTC 11168 chromosome and the plasmids of strain 81-176 indicated that their distribution was not uniform. Visual inspection of the distribution suggested that deviation from uniformity was not due to preferential integration of the transposon into a limited number of hot spots but rather that there was a bias towards insertions around the origin. We screened pools of mutants from the STM libraries for their ability to colonize the ceca of 2-week-old chickens harboring a standardized gut flora. We observed high-frequency random loss of colonization proficient mutants. When cohoused birds were individually inoculated with different tagged mutants, random loss of colonization-proficient mutants was similarly observed, as was extensive bird-to-bird transmission of mutants. This indicates that the nature of campylobacter colonization in chickens is complex and dynamic, and we hypothesize that bottlenecks in the colonization process and between-bird transmission account for these observations.

Animals↗
PubMed2005

13C incorporation into signature fatty acids as an assay for carbon allocation in arbuscular mycorrhiza.

The ubiquitous arbuscular mycorrhizal fungi consume significant amounts of plant assimilated C, but this C flow has been difficult to quantify. The neutral lipid fatty acid 16:1omega5 is a quantitative signature for most arbuscular mycorrhizal fungi in roots and soil. We measured carbon transfer from four plant species to the arbuscular mycorrhizal fungus Glomus intraradices by estimating (13)C enrichment of 16:1omega5 and compared it with (13)C enrichment of total root and mycelial C. Carbon allocation to mycelia was detected within 1 day in monoxenic arbuscular mycorrhizal root cultures labeled with [(13)C]glucose. The (13)C enrichment of neutral lipid fatty acid 16:1omega5 extracted from roots increased from 0.14% 1 day after labeling to 2.2% 7 days after labeling. The colonized roots usually were more enriched for (13)C in the arbuscular mycorrhizal fungal neutral lipid fatty acid 16:1omega5 than for the root specific neutral lipid fatty acid 18:2omega6,9. We labeled plant assimilates by using (13)CO(2) in whole-plant experiments. The extraradical mycelium often was more enriched for (13)C than was the intraradical mycelium, suggesting rapid translocation of carbon to and more active growth by the extraradical mycelium. Since there was a good correlation between (13)C enrichment in neutral lipid fatty acid 16:1omega5 and total (13)C in extraradical mycelia in different systems (r(2) = 0.94), we propose that the total amount of labeled C in intraradical and extraradical mycelium can be calculated from the (13)C enrichment of 16:1omega5. The method described enables evaluation of C flow from plants to arbuscular mycorrhizal fungi to be made without extraction, purification and identification of fungal mycelia.

Carbon Isotopes↗
PubMed2006

Use of single-point genome signature tags as a universal tagging method for microbial genome surveys.

We developed single-point genome signature tags (SP-GSTs), a generally applicable, high-throughput sequencing-based method that targets specific genes to generate identifier tags from well-defined points in a genome. The technique yields identifier tags that can distinguish between closely related bacterial strains and allow for the identification of microbial community members. SP-GSTs are determined by three parameters: (i) the primer designed to recognize a conserved gene sequence, (ii) the anchoring enzyme recognition sequence, and (iii) the type IIS restriction enzyme which defines the tag length. We evaluated the SP-GST method in silico for bacterial identification using the genes rpoC, uvrB, and recA and the 16S rRNA gene. The best distinguishing tags were obtained with the restriction enzyme Csp6I upstream of the 16S rRNA gene, which discriminated all organisms in our data set to at least the genus level and most organisms to the species level. The method was successfully used to generate Csp6I-based tags upstream of the 16S rRNA gene and allowed us to discriminate between closely related strains of Bacillus cereus and Bacillus anthracis. This concept was further used successfully to identify the individual members of a defined microbial community.

Bacillus anthracis↗