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At least 919 records · Page 51Linked to original sources
PubMed2003

Quasispecies variation of porcine reproductive and respiratory syndrome virus during natural infection.

Porcine reproductive and respiratory syndrome virus (PRRSV) displays notorious genetic, antigenic, and clinical variability. Little is known, however, about the nature and extent of viral variation present within naturally infected animals. By amplifying and cloning the open reading frame 5 gene from tonsils of naturally infected swine, and by sequencing individual clones, we characterized viral diversity in nine animals from two farms. All animals harbored multiple PRRSV variants at both the nucleic and the amino acid levels. Structural variation and rates of synonymous and nonsynonymous nucleotide substitution were no different within known epitopes than elsewhere. Analysis of molecular variance indicated that differences between farms, among animals within farms, and within individual animals accounted for 92.94, 3.84, and 3.22% of the total viral genetic variability observed, respectively. PRRSV exists during natural infection as a quasispecies distribution of related genotypes. Positive natural selection for immune evasiveness does not appear to maintain this diversity.

Animals↗
PubMed2004

Atomic force microscopy studies on DNA structural changes induced by vincristine sulfate and aspirin.

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

Aspirin↗
PubMed1985

Myocardial uptake of radioactively labelled free fatty acids.

Structural variations in the carbon chain of free fatty acids influence the uptake of free fatty acids in the myocardium. To enable the use of free fatty acids in nuclear cardiology, various methods of introducing gamma-emitting isotopes have been evaluated. The uptake of various free fatty acids is described and structure-activity relationships deduced.

Animals↗
PubMed1989

Generational differences in the structure of the CES-D scale in Mexican Americans.

This study examines differences in the structure of the Center for Epidemiologic Studies Depression (CES-D) scale across three generations of Mexican Americans. The covariance structure of the items was viewed as a function of several parameter matrices. Factorial invariance was evaluated by testing a series of hypotheses involving equivalence constraints on one or more parameter matrices. The findings revealed that the proposed 12-item model fits the data within each of the three generations adequately. Although no generational differences in factor loadings were revealed, structural variations of the CES-D in measurement error variances were found. Measurement error variances associated with certain items in the older generation are significantly greater than those in the middle-aged and young generations. In addition, socioeconomic characteristics, acculturation, and health status fail to explain the observed differences in the structure of the CES-D among the three generations.

Adult↗
PubMed2005

Analysis of nucleic acid constituents by on-line capillary electrophoresis-mass spectrometry.

This review is focused on the capillary electrophoresis-mass spectrometric (CE-MS) analysis of nucleic acid constituents in the broadest sense, going from nucleotides and adducted nucleotides over nucleoside analogues to oligonucleotides. These nucleic acid constituents play an important role in a variety of biochemical processes. Hence, their isolation, identification, and quantification will undoubtedly help reveal the process of life and disease mechanisms, such as carcinogenesis, and can also be useful for antitumor and antiviral drug research to provide valuable information about mechanism of action, pharmacokinetics, pharmacodynamics, toxicity, therapeutic drug level monitoring, and quality control related to this substance class. Fundamental investigations into their structure, the search for modifications, the occurrence and biochemical impact of structural variation amongst others, are therefore of great value. In view of the related bioanalytical procedures, the coupling of CE to MS has emerged as a powerful tool for the analysis of the complex mixtures of nucleic acid constituents: CE confers rapid analysis and efficient resolution, while MS provides high selectivity and sensitivity with structural characterization of minute amounts of compound. After an introduction about the biochemical and analytical perspectives on the nucleic acid constituents, the different modes of CE used in this field of research as well as the relevant CE-MS interfaces and the difficulties associated with quantitative CE-MS are briefly discussed. A large section is finally devoted to field-oriented applications.

Electrophoresis, Capillary↗
PubMed1994

Fourier transform infrared spectroscopy and differential scanning calorimetry of transferrins: human serum transferrin, rabbit serum transferrin and human lactoferrin.

Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC) have been used to investigate the solution structure and thermal stability of human serum transferrin (HST), human lactoferrin (HLF) and rabbit serum transferrin (RST) in their diferric and apo forms. Our study shows that: (A) The secondary structure of all the proteins studied (estimated in H2O) was in the range 43-53% alpha-helix and 23-28% beta-sheet. These values differ markedly from previously reported circular dichroism (CD) data. This is attributed to the fact that FTIR and CD measure different aspects of secondary structure (hydrogen bonding and dihedral angles, respectively). (B) The secondary structural content of the proteins is not altered by iron binding or release. However, the iron-free proteins undergo a greater extent of 1H-2H exchange than the diferric proteins indicating that significant structural changes do occur upon iron binding/release. (C) The removal of iron leads to thermal destabilization of HST, HLF and RST. Structural variation in the apo transferrins is indicated by the observation of a single irreversible DSC transition for apo human lactoferrin, a double DSC transition for apo human serum transferrin (one reversible) and a broad irreversible asymmetric DSC transition for apo rabbit serum transferrin. FTIR spectroscopy shows that a distinct loss of protein secondary structure occurs at the transition temperatures shown by DSC.

Animals↗
PubMed2001

The human vomeronasal organ. III. Postnatal development from infancy to the ninth decade.

The large literature on the human vomeronasal organ (VNO) offers little consensus as to its persistence in the adult. We have already documented the existence of the VNO from embryonic day 33 through the neonatal stages. This has now been extended to human adults: 27 cadaver nasal septa, aged 2-86 y, were either dissected or decalcified, serially sectioned, stained and examined. The consistent presence of the VNO is reported as a homologue, in the form of a duct-like structure on the nasal septum at all ages. Also reported are size variability, pronounced bilateral asymmetry, a nonchemosensory pseudostratified ciliated epithelium with considerable structural variation and generally without medial-lateral differentiation, nasal septal glands opening into the VNO lumen, a lack of correlation between postnatal age and VNO size, visualisation of the human VNO with certainty by histological means alone, and a minute opening as its only visible surface feature. The human VNO is a discrete structure that should not be confused with the nasopalatine fossa, the septal mucosal pits or VNO openings.

Adult↗
PubMed2025

Extensive longevity and DNA virus-driven adaptation in nearctic Myotis bats.

The genus Myotis is one of the largest clades of bats, and exhibits some of the most extreme variation in lifespans among mammals alongside unique adaptations to viral tolerance and immune defense. To study the evolution of longevity-associated traits and infectious disease, we generated cell lines and near-complete genome assemblies for 8 closely related species of Myotis. Using genome-wide screens of positive selection, analyses of structural variation, and functional experiments in primary cells, we identify new patterns of adaptation contributing to longevity, cancer resistance, and viral interactions in bats. We show that the recurrent evolution of longevity seen in Myotis leads to some of the highest predicted increases in cancer risk across mammals and demonstrate a unique DNA damage response in primary cells of the long-lived M. lucifugus. We also find evidence of abundant adaptation in response to DNA viruses - but not RNA viruses - in Myotis and other bats in sharp contrast with other mammals, potentially contributing to the role of bats as reservoirs of zoonoses. Together, our results demonstrate how genomics and primary cells derived from diverse taxa uncover the molecular bases of extreme adaptations in non-model organisms.

Aging↗
PubMed2004

Low-velocity zone atop the 410-km seismic discontinuity in the northwestern United States.

The seismic discontinuity at 410 km depth in the Earth's mantle is generally attributed to the phase transition of (Mg,Fe)2SiO4 (refs 1, 2) from the olivine to wadsleyite structure. Variation in the depth of this discontinuity is often taken as a proxy for mantle temperature owing to its response to thermal perturbations. For example, a cold anomaly would elevate the 410-km discontinuity, because of its positive Clapeyron slope, whereas a warm anomaly would depress the discontinuity. But trade-offs between seismic wave-speed heterogeneity and discontinuity topography often inhibit detailed analysis of these discontinuities, and structure often appears very complicated. Here we simultaneously model seismic refracted waves and scattered waves from the 410-km discontinuity in the western United States to constrain structure in the region. We find a low-velocity zone, with a shear-wave velocity drop of 5%, on top of the 410-km discontinuity beneath the northwestern United States, extending from southwestern Oregon to the northern Basin and Range province. This low-velocity zone has a thickness that varies from 20 to 90 km with rapid lateral variations. Its spatial extent coincides with both an anomalous composition of overlying volcanism and seismic 'receiver-function' observations observed above the region. We interpret the low-velocity zone as a compositional anomaly, possibly due to a dense partial-melt layer, which may be linked to prior subduction of the Farallon plate and back-arc extension. The existence of such a layer could be indicative of high water content in the Earth's transition zone.

Journal Article↗
PubMed2002

NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding protein.

We have solved the solution structure of the peptidyl-prolyl cis-trans isomerase (PPIase) domain of the trigger factor from Mycoplasma genitalium by homo- and heteronuclear NMR spectroscopy. Our results lead to a well-defined structure with a backbone rmsd of 0.23 A. As predicted, the PPIase domain of the trigger factor adopts the FK506 binding protein (FKBP) fold. Furthermore, our NMR relaxation data indicate that the dynamic behavior of the trigger factor PPIase domain and of FKBP are similar. Structural variations when compared to FKBP exist in the flap region and within the bulges of strand 5 of the beta sheet. Although the active-site crevice is similar to that of FKBP, subtle steric variations in this region can explain why FK506 does not bind to the trigger factor. Sequence variability (27% identity) between trigger factor and FKBP results in significant differences in surface charge distribution and the absence of the first strand of the central beta sheet. Our data indicate, however, that this strand may be partially structured as "nascent" beta strand. This makes the trigger factor PPIase domain the most minimal representative of the FKBP like protein family of PPIases.

Amino Acid Sequence↗
PubMed2003

Enzymatic synthesis of hydrophilic undecylenic acid sugar esters and their biodegradability.

To enhance water solubility of 10-undecylenic acid, which has anti-fungus, anti-bacterial and anti-virus activity, D-glucose, trehalose and sucrose were regioselectively esterified with vinyl 10-undecylenic acid ester in dimethyl formamide by a commercial protease, Bioprase conc., from Bacillus subtilis. 6-O-(10-Undecylenoyl) D-glucose, 6-O-(10-undecylenoyl) trehalose and 1'-O-(10-undecylenoyl) sucrose were obtained. The influence of structural variation by changing the sugar moiety was analyzed the surface tension and biodegradability.

Bacillus subtilis↗
PubMed2003

Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signal.

Secondary structures of the most conserved part of the mt 16S rRNA gene, domains IV and V, have been recently analysed in a comparative study. However, full secondary structures of the mt LSU rRNA molecule are published for only a few insect species. The present study presents full secondary structures of domains I, II, IV and V of Odonates and one representative of mayflies, Ephemera sp. The reconstructions are based on a comparative approach and minimal consensus structures derived from sequence alignments. The inferred structures exhibit remarkable similarities to the published Drosophila melanogaster model, which increases confidence in these structures. Structural variance within Odonates is homoplastic, and neighbour-joining trees based on tree edit distances do not correspond to any of the phylogenetically expected patterns. However, despite homoplastic quantitative structural variation, many similarities between Odonates and Ephemera sp. suggest promising character sets for higher order insect systematics that merit further investigations.

Animals↗
PubMed1990

Iron environment in ferritin with large amounts of phosphate, from Azotobacter vinelandii and horse spleen, analyzed using extended X-ray absorption fine structure (EXAFS).

The iron core of proteins in the ferritin family displays structural variations that include phosphate content as well as the number and the degree of ordering of the iron atoms. Earlier studies had shown that ferritin iron cores naturally high in phosphate, e.g., Azotobacter vinelandii (AV) ferritin (Fe:P ratio = 1:1.7), had decreased long-range order. Here, the influence of phosphate on the local structure around iron in ferritin cores is reported, comparing the EXAFS of AV ferritin, reconstituted ferritin [the protein coats of horse spleen ferritin mixed with Fe(II) with and without phosphate at pH 7] (Fe:P ratio = 1:0.25), and native horse spleen ferritin (Fe:P ratio = 1:0.125); reconstituted horse spleen ferritin without phosphate was indistinguishable from native horse spleen ferritin (HSF) in the analysis. In contrast, when the phosphate content was high in AV ferritin and horse spleen ferritin reconstituted with phosphate, the average iron atom had five to six phosphorus neighbors at 3.17 A. Moreover, the number of detectable iron neighbors was lower when phosphate was high or present during reconstitution (2-3 vs 5-6), and the interatomic distance was longer (3.50 vs 3.03 A), indicating that some phosphate bridges neighboring iron atoms. However, the decrease in the number of detectable iron-iron neighbors compared to HSF and the higher number of Fe-P interactions relative to Fe-Fe interactions suggest that some phosphate ligands were chain termini, or blocked crystal growth, and/or introduced defects which contributed both to the long-range disorder and to altered redox properties previously observed in AV ferritin.

Animals↗
PubMed2005

Variations in Helicobacter pylori lipopolysaccharide to evade the innate immune component surfactant protein D.

Helicobacter pylori is a common and persistent human pathogen of the gastric mucosa. Surfactant protein D (SP-D), a component of innate immunity, is expressed in the human gastric mucosa and is capable of aggregating H. pylori. Wide variation in the SP-D binding affinity to H. pylori has been observed in clinical isolates and laboratory-adapted strains. The aim of this study was to reveal potential mechanisms responsible for evading SP-D binding and establishing persistent infection. An escape variant, J178V, was generated in vitro, and the lipopolysaccharide (LPS) structure of the variant was compared to that of the parental strain, J178. The genetic basis for structural variation was explored by sequencing LPS biosynthesis genes. SP-D binding to clinical isolates was demonstrated by fluorescence-activated cell sorter analyses. Here, we show that H. pylori evades SP-D binding through phase variation in lipopolysaccharide. This phenomenon is linked to changes in the fucosylation of the O chain, which was concomitant with slipped-strand mispairing in a poly(C) tract of the fucosyltransferase A (fucT1) gene. SP-D binding organisms are predominant in mucus in vivo (P = 0.02), suggesting that SP-D facilitates physical elimination. Phase variation to evade SP-D contributes to the persistence of this common gastric pathogen.

Carbohydrate Sequence↗
PubMed2003

Modulation of sodium channels by the oxadiazine insecticide indoxacarb and its N-decarbomethoxylated metabolite in rat dorsal root ganglion neurons.

The effects of the oxadiazine insecticide indoxacarb and its N-decarbomethoxylated metabolite (DCJW) on tetrodotoxin-resistant (TTX-R) voltage-gated sodium channels in rat dorsal ganglion neurons were studied using the whole-cell patch clamp technique. Indoxacarb and DCJW suppressed the peak amplitude of action potentials, and DCJW exhibited a faster time course and higher potency than indoxacarb in the blocking effects. In voltage-clamp experiments, indoxacarb and DCJW suppressed TTX-R sodium currents in a time-dependent manner without a steady-state level of suppression. IC50 values for indoxacarb and DCJW on TTX-R sodium currents were estimated to be 10.7 and 0.8 microM after 25 min of bath application, respectively. DCJW was about 10 times more potent than indoxacarb in blocking TTX-R sodium currents. Although the suppressive effects of indoxacarb were partially reversible after washout with drug-free external solution, no recovery of sodium current was observed in DCJW treated neurons after prolonged washout. In current-voltage relationships, both indoxacarb and DCJW blocked the sodium currents to the same degree in the entire range of membrane potentials. The sodium conductance-voltage curve was not shifted along the voltage axis by indoxacarb and DCJW at 10 microM. In contrast, the steady-state inactivation curves were shifted in the hyperpolarizing direction by indoxacarb as well as by DCJW. Based on these results, it was concluded that indoxacarb and DCJW potently blocked the TTX-R sodium channel in rat DRG neurons with hyperpolarizing shifts of the steady-state inactivation curves, suggesting preferential association of the insecticides to the inactivated state of sodium channels. The small structural variation between indoxacarb and DCJW resulted in clear differences in potency for blocking sodium channels and reversibility after washout.

Action Potentials↗
PubMed1992

Membrane cofactor protein.

MCP serves to down-regulate the activation of complement on host tissue. It performs this function by serving as a cofactor for the factor I-mediated cleavage of C3b and C4b. MCP is most likely an intrinsic regulator, i.e., it primarily protects its home cell. The wide tissue distribution of MCP mirrors this critical function of host cell protection. With the exception of erythrocytes, every cell and tissue examined expresses this protein. MCP is represented as two broad heterogeneous bands on SDS-PAGE with M(r)s of 51,000-58,000 and 59,000-68,000. The quantity of each form expressed is inherited in an autosomal codominant fashion. In most cells and cell lines, four isoforms of MCP predominate and arise by alternative splicing of a single MCP gene. All forms possess four repeating modules of--60 aminoacids, an area enriched in serines, threonines, and prolines [(STP), probable site of O-linked glycosylation], a short area of unknown function, a transmembrane domain, and a cytoplasmic tail. The isoforms differ, however, in the length and composition of the STP region and in the cytoplasmic tail. Alternative splicing of a single exon within the STP region determines the protein phenotype. Alternative splicing at the COOH_terminus gives rise to two distinct cytoplasmic tails. The biological significance of these structural variations in the STP and cytoplasmic tail regions is being investigated.

Animals↗
PubMed2003

Enzymatic synthesis of trehalose esters having lipophilicity.

To improve trehalose lipophilicity, trehalose was regioselectively esterified with vinyl fatty acid esters in dimethyl formamide by protease from Bacillus subtilis to give 6-O-lauroyltrehalose, 6-O-myristoyltrehalose, 6-O-palmitoyltrehalose, 6-O-stearoyltrehalose, 6-O-oleoyltrehalose and 6-O-linoleoyltrehalose. The influence of structural variation by changing fatty acid substitute was examined by measurement of the surface tension and biodegradability.

Bacillus subtilis↗
PubMed2001

Structural adaptation of enzymes to low temperatures.

A systematic comparative analysis of 21 psychrophilic enzymes belonging to different structural families from prokaryotic and eukaryotic organisms is reported. The sequences of these enzymes were multiply aligned to 427 homologous proteins from mesophiles and thermophiles. The net flux of amino acid exchanges from meso/thermophilic to psychrophilic enzymes was measured. To assign the observed preferred exchanges to different structural environments, such as secondary structure, solvent accessibility and subunit interfaces, homology modeling was utilized to predict the secondary structure and accessibility of amino acid residues for the psychrophilic enzymes for which no experimental three-dimensional structure is available. Our results show a clear tendency for the charged residues Arg and Glu to be replaced at exposed sites on alpha-helices by Lys and Ala, respectively, in the direction from 'hot' to 'cold' enzymes. Val is replaced by Ala at buried regions in alpha-helices. Compositional analysis of psychrophilic enzymes shows a significant increase in Ala and Asn and a decrease in Arg at exposed sites. Buried sites in beta-strands tend to be depleted of VAL: Possible implications of the observed structural variations for protein stability and engineering are discussed.

Alanine↗