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PubMedDate not supplied

ADME transcriptome in Hispanic versus White donor livers: evidence of a globally enhanced NR1I3 (CAR, constitutive androstane receptor) gene signature in Hispanics.

Previous studies have found that, compared with Whites, Hispanic donor livers had elevated expression of CYP2 enzymes, gene products regulated by the constitutive androstane receptor (CAR). The objectives of the current study were to determine (1) the CAR activation signature in human liver (2) whether other drug detoxification (absorption, distribution, metabolism and excretion (ADME)) genes were differentially expressed in Hispanic versus White livers, and (3) the extent of overlap in the CAR and Hispanic liver transcriptomes. The CAR transcriptome (ADME genes differentially expressed following phenobarbital versus vehicle treatment of human hepatocytes) and the Hispanic liver transcriptome (ADME genes differentially expressed in Hispanic versus White livers) were identified using Affymetrix oligonucleotide arrays. Quantitative real-time polymerase chain reaction (PCR) was used to verify candidate genes in a larger sample size. Comparison of the CAR and Hispanic liver ADME transcriptomes revealed a significant association between the gene changes. Sixty-four per cent of the ADME genes induced more than twofold by phenobarbital were also induced in Hispanics, and 14% of the ADME genes repressed more than twofold by phenobarbital were repressed in Hispanics. In conclusion, compared with Whites, Hispanic donor livers have increased expression of many genes that are transcriptionally regulated by CAR. This result has practical implications to the drug treatment of Hispanic patients.

Adolescent↗

PubMed2026

Occupationally relevant vibrations and the brain: frequency-dependent proteomics signatures in a rat model.

INTRODUCTION: Occupational exposure to whole-body vibration (WBV), particularly in agricultural environments, has been associated with adverse cognitive and physiological effects. This study examined the neurophysiological impact of WBV in a rat model at 4 Hz and 30 Hz, frequencies representative of off-road and on-road vehicle operation. METHODOLOGY: Forty-four Sprague-Dawley rats were assigned to control (0 Hz), low-frequency (4 Hz), or high-frequency (30 Hz) vibration conditions. After three days of exposure, brain tissues were collected and analyzed using mass spectrometry-based proteomics to identify differentially expressed proteins. RESULTS: Proteomic profiling revealed distinct, frequency-dependent alterations in brain protein expression. Compared with controls, 32 cognition-related proteins were differentially regulated at 4 Hz and 29 at 30 Hz, with 13 differing between the two vibration conditions. Principal component analysis showed clear separation among groups, indicating unique proteomic signatures for each exposure frequency. Functional enrichment and protein-protein interaction analyses demonstrated involvement of synaptic plasticity, cytoskeletal organization, calcium regulation, and neurotransmitter release. Exposure to 4 Hz was associated with the upregulation of proteins involved in calcium homeostasis and synaptic integrity, suggesting potential disruption of cognitive processes. In contrast, 30 Hz increased the expression of proteins related to axonal guidance and neuroprotection, indicating a less clearly adverse response that may reflect adaptive or potentially beneficial effects. DISCUSSION: These findings provide new insight into biological mechanisms underlying WBV-induced cognitive changes and underscore the importance of vibration frequency in shaping neurophysiological outcomes. They also establish a foundation for future studies integrating proteomics with behavioural assessments in animals and humans.

Animals↗

PubMed1999

S values are not a signature for a significant contribution of neutrons to the radiation dose received by atomic-bomb survivors.

PURPOSE: It has been proposed previously that the ratio of complete to incomplete translocations as seen by fluorescence in situ hybridization (FISH), the S value, can be a cytogenetic fingerprint of exposure to radiation of different qualities. Results from a previous study suggested that the S value is approximately 10 for sparsely ionizing radiations such as X- and gamma-rays, and 2 for densely ionizing radiations. Based on FISH data of atomic-bomb (A-bomb) survivors, which showed an S value of 3.25, a significant neutron component to A-bomb radiation was suggested. To examine the possibility, the present in vitro study was conducted using X-rays. MATERIALS AND METHODS: Human blood lymphocytes were exposed to X-rays and first metaphases were examined with FISH using DNA probes for chromosomes 1, 2 and 4. RESULTS: The S value was 3.16 for X-rays, which differs from approximately 10 as reported previously, and not larger than the 3.25 obtained from the blood lymphocytes of A-bomb survivors. CONCLUSIONS: S values seem to vary among laboratories even after exposure of cells to sparsely ionizing radiations. Data from this study show that S values are not a signature for a significant contribution of neutrons to the radiation dose received by A-bomb survivors in Hiroshima.

Chromosome Breakage↗

PubMed2000

Factors influencing stable isotope ratios in CH4 and CO2 within subenvironments of freshwater wetlands: implications for delta-signatures of emissions.

Much uncertainty still exists regarding spatial and temporal variability of stable isotope ratios (13C/12C and D/H) in different CH4-emission sources. Such variability is especially prevalent in freshwater wetlands where a range of processes can influence stable isotope compositions, resulting in variations of up to approximately 50% for delta13C-CH4 and approximately 50% for deltaD-CH4 values. Within a temperate-zone bog and marsh situated in southwestern Ontario, Canada, gas bubbles in pond sediments exhibit only minor seasonal and spatial variation in delta13C-CH4, deltaD-CH4 and delta13C-CO2 values. In pond sediments, CO2 appears to be the main source of carbon during methanogenesis either directly via CO2 reduction or indirectly through dissimilation of autotrophic acetate. In contrast, CH4 production occurs primarily via acetate fermentation at shallow depths in peat soils adjacent to ponds at each wetland. At greater depths within soils, sigmaCO2 and H2O increasingly exert an influence on delta13C- and deltaD-CH4 values. Secondary alteration processes (e.g., methanotrophy or diffusive transport) are unlikely to be responsible for depth-related changes in stable isotope values of CH4. Recent models that attempt to predict deltaD-CH4 values in freshwater environments from D/H ratios in local precipitation do not adequately account for such changes with depth. Subenvironments (i.e., soil-forming and open water areas) in wetlands should be considered separately with respect to stable isotope signatures in CH4 emission models.

Atmosphere↗

PubMed2005

Geochemical signatures (C, N, delta13C, delta15N, metals) of suspended matter in the river Weisse Elster (central Germany): their seasonal and flow-related distribution 1997-2001.

Geochemical studies of carbon, nitrogen, delta13C, delta15N as well as Fe, Mn, Cd, Zn, Cr and Hg in suspended matter taken from the river Weisse Elster (central Germany) between 1997 and 2001 reveal significant changes to the composition of the organic sediment load, which correlate with the hydrological period and flow rate. Using C/N ratios and the isotope values of carbon and nitrogen as source indicators, it was found that the organic suspended matter fractions in hydrological winter periods comprise both resuspended mortal plankton material from the riverbed and terrigenous C3 plant material from the clastic input. During the 6 month summer periods, increased bioproductivity results in more dissolved carbon and mineral nitrogen compounds being taken up by the freshly formed aquatic organic substance (freshwater plankton). These compounds stem from bacterial breakdown processes affecting organic components of the river sediment and/or the peripheral soil zone. Increasing fractions of freshwater plankton during the summer period are accompanied by an increase in the nitrogen content and by isotope signatures shifting (delta13C to lower but delta15N to higher values) in the suspended matter. Seasonally opposite correlations between metal contents (e.g. Cd, Zn, Cr, Hg and Fe) and the carbon and nitrogen levels of suspended matter (significantly positive in winter and significantly negative in summer) show that in suspended matter these elements mostly bind to resuspended mortal (rather than the freshly formed living aquatic) organic substance. According to long-term measuring series, between 1993 and 2002 the levels of heavy metals (especially cadmium) in the suspended matter of the river Weisse Elster decreased. Similarly, between 1997 and 2001 the oxygen level in the river Weisse Elster improved. This caused the faster breakdown of organic substance on the riverbed, resulting in the increased uptake of 15N-rich nitrogen compounds into the fresh aquatic organic substance formed every year, and an increase in the conversion of dissolved manganese in the water into insoluble manganese compounds in the river sediment.

Carbon↗

PubMedDate not supplied

A novel method for GPCR recognition and family classification from sequence alone using signatures derived from profile hidden Markov models.

G-protein coupled receptors (GPCRs) constitute a broad class of cell-surface receptors, including several functionally distinct families, that play a key role in cellular signalling and regulation of basic physiological processes. GPCRs are the focus of a significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs, whereas they still comprise the best potential targets for drug design. Taking into account the excess of data derived by genome sequencing projects, the use of computational tools for automated characterization of novel GPCRs is imperative. Typical computational strategies for identifying and classifying GPCRs involve sequence similarity searches (e.g. BLAST) coupled with pattern database analysis (e.g. PROSITE, BLOCKS). The diagnostic method presented here is based on a probabilistic approach that exploits highly discriminative profile Hidden Markov Models, excised from low entropy regions of multiple sequence alignments, to derive potent family signatures. For a given query, a P-value is obtained, combining individual hits derived from the same family. Hence a best-guess family membership is depicted, allowing GPCRs' classification at a family level, solely using primary structure information. A web-based version of the application is freely available at URL: http:/bioinformatics.biol.uoa.gr/PRED-GPCR.

Databases, Factual↗

PubMed1998

Group specific antibodies against the putative AMP-binding domain signature SGTTGXPKG in peptide synthetases and related enzymes.

The superfamily of adenylate forming enzymes including peptide synthetases, acyl-CoA synthetases and insect luciferases is readily identified by the signature sequence SGTTGXPKG. This sequence including an invariant lysyl residue is located in a disordered loop region and was predicted to be of significant antigenicity. Antibodies were generated employing YTSGTTGRPKGC attached to bovine serum albumin and have been successfully used to identify respective enzymes and adenylate forming domains in multienzyme systems. These include the delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetases of Aspergillus nidulans and Acremonium chrysogenum, gramicidin S synthetase 1 and tyrocidine synthetase 1 from Bacillus brevis, acetyl-CoA synthetase from Alcaligenes eutrophus and a putative peptide synthetase from Metarhizium anisopliae. Weaker or no reactions are observed when the amino acid in position X in the protein is non-basic or hydrophobic, which is respectively the case for gramicidin S synthetase 1 and luciferase.

Adenosine Monophosphate↗

PubMed2025

MicroRNAs signatures in small extracellular vesicles for psychological resilience in young adults using machine learning.

AIMS: Psychological resilience refers to an individual's capacity to adapt to adverse events. MicroRNAs (miRNAs) play a crucial role in regulating post-transcriptional processes, while small extracellular vesicles (sEVs) act as transport vehicles. This study aimed to employ genome-wide profiling to identify and validate differences in the expression of resilience-associated sEV-miRNAs between low resilience (LR) and high resilience (HR) in young adults. METHODS: Eighty participants were divided into LR or HR based on the Connor - Davidson Resilience Scale (CD-RISC). The expression levels of the target sEV-miRNAs in LR and HR were compared and analyzed. RESULTS: Expression analyses demonstrated significant differences in let-7b, miR-151b, miR-335, and miR-193a between LR and HR (p < 0.01), with let-7b showing the highest discriminative ability. The AUC values for each sEV-miRNA ranged from 0.74 to 0.94, based on logistic regression and three machine learning models: random forest, support vector machine, and eXtreme gradient boosting. Based on leave-one-out cross-validation in different models, the combined four sEV-miRNAs demonstrated strong performance for detecting LR (AUC = 0.87-0.90). Sex-specific differences were also observed, with female participants showing more pronounced resilience signatures in targeted sEV-miRNAs. CONCLUSIONS: These findings suggest that sEV-miRNAs hold potential as biomarkers for psychological resilience in young adults.

Humans↗

PubMed2026

Lesion-specific oral microbiome signatures and predicted carcinogenic pathways in oral squamous cell carcinoma: a paired-site study in Pakistan.

BACKGROUND: Oral squamous cell carcinoma accounts for over 90% of oral neoplasms. Despite therapeutic advances, the lack of reliable, non-invasive biomarkers and delayed diagnosis continues to impede effective clinical management. By combining paired lesion and non-lesion sampling with predictive metagenomics analysis, our study addresses this gap and advances the current understanding of microbiome‒tumor interactions. METHODS: We analyzed 92 buccal swab samples from 39 OSCC patients and 14 healthy controls using 16S rRNA gene (V3-V4) sequencing. Taxonomic profiling was conducted using QIIME2 and SILVA/eHOMD databases, functional pathways were predicted using PICRUSt2, and hub taxa were identified through co-abundance network analysis. RESULTS: Microbial community structure differed significantly across lesion, non-lesion, and healthy sites (PERMANOVA, p = 0.001). Lesions were enriched with Selenomonas infelix and Treponema vincentii, while healthy controls harbored Streptococcus oralis and Gemella haemolysans. Co-abundance network analysis revealed lesion-specific hub species, notably T. vincentii, strongly correlated with predicted activation of pyrimidine biosynthesis pathways (r = 0.69, q < 1E-6), suggesting predicted metabolic alterations in the tumor microenvironment. Non-lesion sites were also characterized by two hub species, Prevotella melaninogenica and Segatella oulorum. CONCLUSION: Our findings define a lesion-specific microbial signature of OSCC characterized by the depletion of health-associated taxa, enrichment of pro-inflammatory pathobionts, and predicted associations with metabolic pathways implicated in carcinogenesis. These alterations reflect a predicted functionally altered tumor microenvironment.

16S rRNA gene↗

PubMed1999

Signature sequences for the galectin-4 subfamily.

Galectins are a distinct family of animal lectins that have a cation-independent affinity for beta-galactoside sugars and share characteristic amino acid sequences. The cDNA encoding rabbit bladder galectin-4 has been cloned and sequenced (GenBank accession no. AF091738). The deduced 328 amino acid sequence predicts a multidomain structure consisting of an N-terminal peptide (19 residues) and two carbohydrate recognition domains (130 residues each) connected by a linker region (49 residues). Comparison of rabbit galectin-4 with related proteins reveals that two peptide motifs, M-A-F/Y-V-P-A-P-G-Y-Q-P-T-Y-N-P-T-L-P-Y in the N terminus and A-F-H-F-N-P-R-F-D-G-W-D-K-V-V-F in the first carbohydrate recognition domain are highly conserved in human, pig, rat, and mouse galectin-4 as well as in mouse galectin-6. The two peptide motifs are proposed here as the signature sequences to identify new members of the galectin-4 subfamily.

Amino Acid Sequence↗

PubMed2004

Pathogenic profiles and molecular signatures of antinuclear autoantibodies rescued from NZM2410 lupus mice.

Two outstanding questions concerning antinuclear antibodies (ANAs) in lupus involve their pathogenic potential and their molecular signatures. To address these questions, a panel of 56 antinuclear and 47 nonnuclear binding monoclonal antibodies was rescued from four seropositive NZM2410 lupus mice. The monoclonals varied in their reactivity to nucleosomes, ssDNA, dsDNA, and glomerular substrate. A large fraction of the antibodies demonstrated apparent polyreactivity (to DNA, histones, and glomerular antigens) due to bound, DNase-1 sensitive nuclear antigenic bridges. Although nephrophilic immunoglobulin (Ig) M and IgG antibodies were the most pathogenic, the dsDNA-binding antibodies were modestly so; in contrast, antinucleosome antibodies were clearly not pathogenic. Compared with the nonnuclear antigen-binding monoclonal antibodies rescued from the same mice, ANAs exhibited increased utilization of VH5/7183 genes and highly cationic heavy chain (HC) CDR3 regions. Most intriguingly, the CDR3 regions of the ANAs exhibited alternating arginine/lysine peaks at H96, H98, and H100, with neutral troughs at H95, H97, and H99. To summarize, glomerular-binding anti-dsDNA antibodies appear to be the most pathogenic variety of lupus autoantibodies. The presence of an alternating charge pattern in their HC CDR3 regions appears to be a prominent hallmark of ANAs.

Amino Acid Sequence↗

PubMed2000

Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.

The Duffy blood group locus, which encodes a chemokine receptor, is characterized by three alleles-FY*A, FY*B, and FY*O. The frequency of the FY*O allele, which corresponds to the absence of Fy antigen on red blood cells, is at or near fixation in most sub-Saharan African populations but is very rare outside Africa. The FST value for the FY*O allele is the highest observed for any allele in humans, providing strong evidence for the action of natural selection at this locus. Homozygosity for the FY*O allele confers complete resistance to vivax malaria, suggesting that this allele has been the target of selection by Plasmodium vivax or some other infectious agent. To characterize the signature of directional selection at this locus, we surveyed DNA sequence variation, both in a 1.9-kb region centered on the FY*O mutation site and in a 1-kb region 5-6 kb away from it, in 17 Italians and in a total of 24 individuals from five sub-Saharan African populations. The level of variation across both regions is two- to threefold lower in the Africans than in the Italians. As a result, the pooled African sample shows a significant departure from the neutral expectation for the number of segregating sites, whereas the Italian sample does not. The FY*O allele occurs on two major haplotypes in three of the five African populations. This finding could be due to recombination, recurrent mutation, population structure, and/or mutation accumulation and drift. Although we are unable to distinguish among these alternative hypotheses, it is likely that the two major haplotypes originated prior to selection on the FY*O mutation.

Africa South of the Sahara↗

PubMed2000

Evidence for Stellar Streaming in the Cores of Elliptical Galaxies: A Kinematic Signature of Mergers?

We present evidence for non-Gaussian velocity fields within the cores of luminous elliptical galaxies. This evidence is based on high signal-to-noise ratio, medium-resolution spectroscopy of the cores of early-type members of the Virgo and Coma Clusters obtained with the Wisconsin-Indiana-Yale-NOAO 3.5 m telescope. The Virgo data were acquired using an integral-field unit (DensePak), which allows the velocity field to be sampled over a variety of spatial scales. The Coma data were obtained through single 2&arcsec; diameter fibers. The cross-correlation profiles of luminous elliptical galaxies show considerable structure, often having several features with amplitudes as high as 10% that of the cross-correlation peak itself. This structure is most obvious within a radius of 1&farcs;5 (at Virgo), or </=100 pc, and is nearly undetectable when the data are binned over R<15", or </=1 kpc. Similar features are found in the single-fiber spectra of the luminous elliptical galaxies in the Coma Cluster, suggesting that they are ubiquitous in giant elliptical galaxies. Interestingly, only the most luminous elliptical galaxies show these phenomena; the central regions of lower luminosity elliptical galaxies have regular Gaussian-like profiles. We interpret this kinematic structure as "stellar streaming" and suggest that these phenomena could be a relic signature of the merger history of luminous elliptical galaxies.

Journal Article↗

PubMed2003

Past exposure to densely ionizing radiation leaves a unique permanent signature in the genome.

Speculation has long surrounded the question of whether past exposure to ionizing radiation leaves a unique permanent signature in the genome. Intrachromosomal rearrangements or deletions are produced much more efficiently by densely ionizing radiation than by chemical mutagens, x-rays, or endogenous aging processes. Until recently, such stable intrachromosomal aberrations have been very hard to detect, but a new chromosome band painting technique has made their detection practical. We report the detection and quantification of stable intrachromosomal aberrations in lymphocytes of healthy former nuclear-weapons workers who were exposed to plutonium many years ago. Even many years after occupational exposure, more than half the blood cells of the healthy plutonium workers contain large (>6 Mb) intrachromosomal rearrangements. The yield of these aberrations was highly correlated with plutonium dose to the bone marrow. The control groups contained very few such intrachromosomal aberrations. Quantification of this large-scale chromosomal damage in human populations exposed many years earlier will lead to new insights into the mechanisms and risks of cytogenetic damage.

Alpha Particles↗

PubMed2003

Mussel disturbance dynamics: signatures of oceanographic forcing from local interactions.

Local interactions, biotic and abiotic, can have a strong influence on the large-scale properties of ecosystems. However, ecological models often explore the influence of local biotic interactions where physical disturbance is included as a large-scale and imposed source of variability but is not allowed to interact with biotic processes at the local scale. In marine intertidal communities dominated by mussels, wave disturbances create gaps in the mussel bed that recover through a successional sequence. We present a lattice model of mussel disturbance dynamics that allows local interactions between wave disturbance and mussel recolonization, in which each cell of the lattice can be empty, occupied by a mussel bed element, or disturbed (which corresponds to a newly disturbed cell that has unstable edges). As in natural ecosystems, wave disturbance can also spread from disturbed to adjacent occupied cells, and recolonization can also spread from occupied to adjacent empty cells. We first validate the local rules from artificial gap experiments and from natural gap monitoring along the Oregon coast. We analyze the properties of the model system as a function of different oceanographic forcings of productivity and disturbance. We show that the mussel bed can go through phase transitions characterized by a large sensitivity of mussel cover and patterns to oceanographic forcings but also that criticality (scale invariance) is observed over wide ranges of parameters, which suggests self-organization. We also show that spatial patterns in the intertidal can provide a robust signature of local processes and can inform about oceanographic regimes. We do so by comparing the large-scale patterns of the simulation (scaling exponents) with field data, which suggest that some experimental sites are close to criticality. Our results suggest that regional patterns in disturbed populations can be explained by local biotic and abiotic processes submitted to oceanographic forcing.

Animals↗

PubMed2004

Identification of I50L as the signature atazanavir (ATV)-resistance mutation in treatment-naive HIV-1-infected patients receiving ATV-containing regimens.

Atazanavir (ATV) is a once-daily human immunodeficiency virus (HIV) protease inhibitor (PI) shown to be effective and well tolerated. ATV has a distinct resistance profile relative to other PIs, with susceptibility maintained against 86% of isolates resistant to 1-2 PIs. Clinical isolates obtained from PI-naive patients designated as experiencing virologic failure while receiving ATV-containing regimens contained a unique isoleucine-to-leucine substitution at amino acid residue 50 (I50L) of the HIV-1 protease. The I50L substitution, observed in all isolates exhibiting phenotypic resistance to ATV, emerged in a variety of different backgrounds and was most frequently accompanied by A71V, K45R, and/or G73S. Viruses containing an I50L substitution were growth impaired, displayed ATV-specific resistance, and had increased susceptibilities (</=0.4 of reference strain) to other PIs. Comparison of viruses bearing I50L with those bearing I50V revealed specific resistance to ATV and amprenavir, respectively, with no evidence of cross-resistance. The unique I50L substitution is the signature mutation for resistance to ATV.

Atazanavir Sulfate↗

PubMed1999

X-ray scatter signatures for normal and neoplastic breast tissues.

Measurements of breast tissue scattering properties have been made in an energy dispersive x-ray diffraction system over the momentum transfer range of 0.70 to 3.50 nm(-1). One hundred samples of excised tissue have been used. Results from the diffraction system have been compared with the histological analysis for each individual sample. It has been found that tissue types can be characterized on the basis of the shape of the scatter spectrum and on its relative intensity. The shapes are significantly different between tissue types in the range 1.0 to 1.8 nm(-1) and suggest that if particular values of momentum transfer are monitored, a discriminating signal could be obtained. Analysis of the maximum intensity in the signature also reveals a change of up to a factor of 2 between adipose and fat-free tissues.

Adolescent↗

PubMed2003

An HIV type 1 subtype B founder effect in Korea: gp160 signature patterns infer circulation of CTL-escape strains at the population level.

HIV-1 subtype B predominates in the Republic of Korea. Phylogenetic analyses of sequences for complete nef genes and env gene fragments encoding the V3 loop have identified a major monophyletic Korean subclade that is distinct from Western subtype B sequences in the Los Alamos HIV Sequence Database. This was investigated further by sequence analysis of complete env genes recovered from the DNA of peripheral blood mononuclear cells for matched groups of Koreans, four patients per group, previously assigned as being infected with either Korean or Western strains. The phylogenetic classifications were confirmed and analysis of the translation products identified 32 amino acid signature pattern differences, dispersed throughout gp160, which differentiate the two subclades. Twenty-three of these positions map to epitopes recognized by HLA-I-restricted cytotoxic T-lymphocytes (CTL) as catalogued in the Los Alamos HIV Immunology Database. The remaining nine map at or close to sites predicted to be targets for immunoproteasomes that are involved in producing peptides that bind to MHC Class I. These results suggest that a founder effect in the Korean population is based on the spread of CTL-escape/host-adapted HIV-1 strains.

Databases, Factual↗