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At least 613 records · Page 34Linked to original sources
PubMed1982

Structure and variation of human ribosomal DNA: the external transcribed spacer and adjacent regions.

A group of human ribosomal DNA (rDNA) recombinants that include the probable site for initiation of transcription have been examined for sequence polymorphism. A detailed restriction map of one rDNA insert was constructed using plasmid subclones and end-labeled segments. Comparison of 16 similar rDNA inserts by restriction and heteroduplex analysis demonstrated striking conservation of the external transcribed spacer and 18S gene regions, but defined a region where restriction sites for the enzymes Sma I, Hpa II, and Hha I become frequent or variable. This region extends for about 400--800 base pairs (bp) at the left end of the rDNA insert and is postulated to contain nontranscribed spacer sequences. The use of cloned rDNA segments as probes for the restriction analysis of genomic rDNA has demonstrated certain fixed sites in the nontranscribed spacer that do not vary significantly among different individuals or tumor cell lines. In contrast, restriction with the enzyme Sal I reveals several variable fragments, one of which has been found only in a retinoblastoma cell line.

Base Composition↗
PubMed2006

Gaussian mixture modeling of alpha-helix subclasses: structure and sequence variations.

Classification of helical structures and identification of class specific sequence features is of interest for protein structure modeling. We use geometric invariant based method to first select helix-like local conformations. These conformations are mapped in a principal component space and subjected to Gaussian mixture modeling. The largest Gaussian corresponds to the regular alpha-helix. Kinked helix and curved helix appear as a separate gaussians. Class conditional, position specific amino acid propensity analysis reveals striking difference among the three classes. In regular helix, proline propensity is significant only in the beginning and low in the rest of the region regardless of length of the helix. In kinked helix, the proline propensity has a sharp peak at the helix center, while in the curved helix, the proline propensity has a broad peak in the middle region.

Amino Acids↗
PubMed2001

Homonuclear (1)H-NMR assignment and structural characterization of human immunodeficiency virus type 1 Tat Mal protein.

The transacting transcriptional activator (Tat) is a viral protein essential for activation of the human immunodeficiency virus (HIV) genes, and it plays an important role in HIV induced immunodeficiency. We report the NMR structural characterization of the active Tat Mal variant that belongs to a highly virulent D-subtype HIV type-1 (HIV-1) strain (Mal) found mainly in Africa. A full Tat Mal protein (87 residues) is synthesized. This synthetic protein is active in a transactivation assay with HeLa cells infected with the HIV long terminal repeated noncoding sequences of the HIV-1 provirus (LTR) lac Z gene. Homonuclear (1)H-NMR spectra allows the sequential assignment of the Tat Mal spin systems. Simulating annealing generates 20 conformers with similar folding. The geometry of the mean structure is optimized with energy minimization to obtain a final structure. As the European variant (Tat Bru) the N-terminal region of Tat Mal constitutes the core, and there is a hydrophobic pocket composed of the conserved Trp 11 interacting with several aromatic residues. The two functional regions of Tat (basic and the cysteine-rich regions) are well exposed to the solvent. A short alpha-helix is observed in region V adjacent to the basic region. This alpha helix induces local structural variations compared to the NMR structure of Tat Bru, and it brings the cysteine-rich and basic regions closer. This study suggests that similar folding exists among Tat variants.

Africa↗
PubMed1980

Circadian variation in the structure of mast cells.

Circadian variation in the structure of mast cells has been demonstrated histologically. At 11.00 h the number of mast cells was increased and at 03.00 h it was significantly decreased (p less than 0.01). Morphological analysis has also supported this phenomenon.

Animals↗
PubMed2004

Differential activation and inhibition of human platelet thrombin receptors by structurally distinct alpha-, beta- and gamma-thrombin.

The development of drugs to neutralize the action of thrombin has to date focused on the alpha form of the protease. It is generally agreed that inactive prothrombin is proteolytically converted to active alpha-thrombin which may be further hydrolyzed to beta- and gamma-thrombin. While all three forms of the enzyme retain catalytic activities, only alpha-thrombin is presumed to be physiologically important. The beta- and gamma-thrombin are presumed to be degradation products of no physiological significance. Our demonstration that beta- and gamma-thrombin selectively activate PAR-4 in this and a previous report (J. Biol. Chem. 276, 21173-21183, 2001) necessitates a reevaluation of how we view their physiological roles and how we approach the pharmacological regulation of their actions. Beta-thrombin, like gamma-thrombin, at nM levels selectively activates PAR-4. This was demonstrated by full retention of aggregatory activity with platelets whose PAR-1 and GP Ib receptors were inactivated. Furthermore, the beta-thrombin response was abrogated by desensitizing platelets with suboptimal levels of the thrombin receptor activating peptide for PAR-4 (TRAP-4). For beta-thrombin and gamma-thrombin to have a physiological role, it is necessary to show they can be generated under physiological conditions. We demonstrate, for the first time, that alpha-thrombin is hydrolyzed in less than 1 min by activated factor X at physiological pH, in vitro. This implies that alpha-thrombin may be rapidly converted to beta-thrombin and/or gamma-thrombin in vivo in the proper microenvironment. The differential activation of the three platelet thrombin receptors by alpha-, beta- and gamma-thrombin implies selective structural variations between these thrombin species. Structural differences are likely to account for the marked differential responses observed with the antithrombotic, hirudin, which inhibits alpha-thrombin , is a slightly weaker inhibitor of beta-thrombin and a very weak inhibitor of gamma-thrombin -induced platelet aggregations. The converse order of inhibition is observed with the physiological protease inhibitor, alpha(1)-antitrypsin. Finally, a non-traditional inhibitor, histone-1, selectively inhibits only beta- and gamma-thrombin , primarily at the receptor level of PAR-4 rather than on the thrombin molecule. Trypsin, like beta- and gamma-thrombin , activates PAR-4 and is also inactive with TRAP-4 desensitized platelets. Therefore, it was reasoned that trypsin would be more structurally similar to gamma-thrombin than to alpha-thrombin. The analysis of the crystalline structures of alpha-, gamma-thrombin and trypsin from the databases confirm that this is the case. These findings should help to elucidate structure-function relationships of the different thrombins and may aid in the development of new anti-thrombotic drugs.

Factor Xa↗
PubMed2006

Structures of DNA-linked nanoparticle aggregates.

The room-temperature structure of DNA-linked gold nanoparticle aggregates is investigated using a combination of experiment and theory. The experiments involve extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30 base-pair DNA. The theoretical studies use calculated spectra for models of the aggregate structures to determine which structure matches the observations. These models include diffusion-limited cluster-cluster aggregation (DLCA), reaction-limited cluster-cluster aggregation (RLCA), and compact (nonfractal) cluster aggregation. The diameter of the nanoparticles used in the experiments is larger than has been considered previously, and this provides greater sensitivity of spectra to aggregate structure. We show that the best match between experiment and theory occurs for the RLCA fractal structures. This indicates that DNA hybridization takes place under irreversible conditions in the room-temperature aggregation. Some possible structural variations which might influence the result are considered, including the edge-to-edge distance between nanoparticles, variation in the diameter of the nanoparticles, underlying lattice structures of on-lattice compact clusters, and positional disorders in the lattice structures. We find that these variations do not change the conclusion that the room-temperature structure of the aggregates is fractal. We also examine the variation in extinction at 260 nm as temperature is increased, showing that the decrease in extinction at temperatures below the melting temperature is related to a morphological change from fractal toward compact structures.

DNA↗
PubMedDate not supplied

Multiplanar variations in the structural characteristics of cancellous bone.

A quantitative serial sectioning technique and a video-imaging procedure were used to obtain precise (20-microns voxels, in a 5 mm x 6 mm x 7 mm test volume) digital images of lumbar vertebral cancellous bone specimens. Conventional stereological image analyses were performed on this data to determine multiplanar (bulk) and surface planar variations in cancellous structural properties. Based upon an error analysis of subgroups of the complete serial planar images, our findings suggest that, for a plane resolution of 20 microns, sectioning at an increment < or = 100 microns along an axis is necessary to obtain accurate data of bulk structural properties of cancellous bone. Planar structural variations obtained from the serial sections of cancellous bone revealed a high degree of complexity and heterogeneity of the bone architecture. Bone area centers deviated from the section centroid and showed a helical variation along the primary or superior--inferior loading axis of samples. In comparison with the base planes (perpendicular to the superior-inferior axis), the lateral planes (parallel to the superior-inferior axis) of spine samples showed smaller mean values of structural indices and a more oriented structure. This structural anisotropy may be related to the functional mechanical anisotropy of the samples.

Adult↗
PubMed1988

Assignments of 31P NMR resonances in oligodeoxyribonucleotides: origin of sequence-specific variations in the deoxyribose phosphate backbone conformation and the 31P chemical shifts of double-helical nucleic acids.

It is now possible to unambiguously assign all 31P resonances in the 31P NMR spectra of oligonucleotides by either two-dimensional NMR techniques or site-specific 17O labeling of the phosphoryl groups. Assignment of 31P signals in tetradecamer duplexes, (dTGTGAGCGCTCACA)2, (dTAT-GAGCGCTCATA)2, (dTCTGAGCGCTCAGA)2, and (dTGTGTGCGCACACA)2, and the dodecamer duplex d(CGTGAATTCGCG)2 containing one base-pair mismatch, combined with additional assignments in the literature, has allowed an analysis of the origin of the sequence-specific variation in 31P chemical shifts of DNA. The 31P chemical shifts of duplex B-DNA phosphates correlate reasonably well with some aspects of the Dickerson/Calladine sum function for variation in the helical twist of the oligonucleotides. Correlations between experimentally measured P-O and C-O torsional angles and results from molecular mechanics energy minimization calculations show that these results are consistent with the hypothesis that sequence-specific variations in 31P chemical shifts are attributable to sequence-specific changes in the deoxyribose phosphate backbone. The major structural variation responsible for these 31P shift perturbations appears to be P-O and C-O backbone torsional angles which respond to changes in the local helical structure. Furthermore, 31P chemical shifts and JH3'-P coupling constants both indicate that these backbone torsional angle variations are more permissive at the ends of the double helix than in the middle. Thus 31P NMR spectroscopy and molecular mechanics energy minimization calculations appear to be able to support sequence-specific structural variations along the backbone of the DNA in solution.

Base Sequence↗
PubMed1996

Population genetic comparisons among eight populations using allele frequency and sequence data from three microsatellite loci.

Eight different population samples (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese) were studied using the tetranucleotide short tandem repeat systems HumTHO1 (THO1), Hum VWFA31 (VWA) and HumACTBP2 (ACTBP2). Ten alleles were differentiated in THO1, 11 alleles in VWA and 28 alleles in ACTBP2. THO1 showed 1 bp deletions in the repeat region, VWA sequence and structure variations of the 4-bp repeat motif and ACTBP2 sequence, structure and length variations in the repeat array and deletions/insertions (1-6 bp) in the flanking regions. A phylogenetic tree was constructed (UPGMA method) leading to branches which grouped Germans and Turks, Japanese and Chinese, and Papuans and Australian aborigines.

Asian People↗
PubMed2001

Genetic variation in 16S-23S rDNA internal transcribed spacer regions and the possible use of this genetic variation for molecular diagnosis of Bacteroides species.

The structural variation in 16S-23S rDNA internal transcribed spacer regions (ITS) among Bacteroides species was assessed by PCR amplification and sequencing analysis, and its possible use for molecular diagnosis of these species was evaluated. Ninety strains of the genus Bacteroides, including the species B. distasonis, B. eggerthii, B. fragilis, B. ovatus, B. thetaiotaomicron, B. uniformis and B. vulgatus, produced one to three ITS amplification products with sizes ranging from 615 to 810 bp. Some Bacteroides strains could be differentiated at species level on the basis of ITS amplification patterns and restriction fragment length polymorphism (RFLP) analysis using a four-nucleotide-recognizing enzyme, Msp I. The results of sequence analysis of ITS amplification products revealed genes for Ile-tRNA and Ala-tRNA in all strains tested. The nucleotide sequence, except for that in tRNA-coding regions, was highly variable and characteristic for each species, but a common sequence among B. fragilis, B. thetaiotaomicron and B. ovatus was observed. A digoxigenin-labeled oligonucleotide probe (named FOT1), which was designed from this conserved sequence, specifically hybridized to the ITS amplification products from B. fragilis, B. thetaiotaomicron and B. ovatus. These results suggest that the ITS region is a useful target for the development of rapid and accurate techniques for identification of Bacteroides species.

Bacteroides↗
PubMed2005

Ectomycorrhizas associated with a relict population of Dryas octopetala in the Burren, western Ireland II. Composition, structure and temporal variation in the ectomycorrhizal community.

The composition, structure and temporal variation of ectomycorrhizal (EM) communities associated with mountain avens (Dryas octopetala) in grass heaths of the Burren, western Ireland were assessed by using soil core sampling in two permanent plots and 30 other sites (196 cores in total). Of the 34 different EM types observed, 11 were common and constituted over 80% of the EM biomass. Four EM types, Craterellus lutescens, Tomentella sp., Dryadirhiza fulgens and Cenococcum geophilum were the most abundant as measured by EM length and frequency of occurrence in cores. The species profile and relative abundances were very similar in cores from the permanent plots and different sites in the Burren, indicating that they were all representative of the same EM community. The below-ground EM community in both plots was compared with production of basidiomes, and the latter was found to be an unreliable indicator of EM community structure. Temporal variation in the EM community was assessed by repeated core sampling of the two permanent plots over a 14-month period (between March 1998 and May 1999). No statistically significant shifts in EM abundance were found between sampling dates, probably as a consequence of the large variation in EM abundance between core samples over the sampling period. No significant relationship was found between rainfall, soil moisture or soil temperature and fluctuations in EM abundance. Patterns of total EM abundance and fluctuations in EM diversity were strongly correlated between the two permanent plots over the sampling period. Temporal fluctuations in the dominant EM type, Craterellus lutescens, were similar in both plots with respect to mycorrhizal length, biomass and relative abundance, and the patterns between both plots were positively correlated. EM diversity was negatively correlated with biomass of ectomycorrhizas of Craterellus lutescens in both plots, but it was significant only in plot 1.

Ascomycota↗
PubMed2006

Silica pattern formation in diatoms: species-specific polyamine biosynthesis.

Diatoms are eukaryotic, unicellular algae that are well known for the intricate architecture of their silica-based cell walls. Species identification is mainly based on variations of their hierarchically organized silica structures. Particularly striking silica frameworks are found among diatoms that belong to the genus Coscinodiscus. Recent work indicates an important role for long-chain polyamines in guiding silica precipitation as well as in silica-pattern formation. Here we demonstrate that polyamines, even if isolated from closely related diatom species, exhibit substantial structural differences. Structural variations include the overall chain length, the degree of methylation, positions of secondary amino functionalities, and, unexpectedly, site-specific incorporation of a quaternary ammonium functionality. These findings support a specific role for polyamines in creating silica nanostructures.

Biogenic Polyamines↗
PubMed2004

Constructing diffeomorphic representations for the groupwise analysis of nonrigid registrations of medical images.

Groupwise nonrigid registrations of medical images define dense correspondences across a set of images, defined by a continuous deformation field that relates each target image in the group to some reference image. These registrations can be automatic, or based on the interpolation of a set of user-defined landmarks, but in both cases, quantifying the normal and abnormal structural variation across the group of imaged structures implies analysis of the set of deformation fields. We contend that the choice of representation of the deformation fields is an integral part of this analysis. This paper presents methods for constructing a general class of multi-dimensional diffeomorphic representations of deformations. We demonstrate, for the particular case of the polyharmonic clamped-plate splines, that these representations are suitable for the description of deformations of medical images in both two and three dimensions, using a set of two-dimensional annotated MRI brain slices and a set of three-dimensional segmented hippocampi with optimized correspondences. The class of diffeomorphic representations also defines a non-Euclidean metric on the space of patterns, and, for the case of compactly supported deformations, on the corresponding diffeomorphism group. In an experimental study, we show that this non-Euclidean metric is superior to the usual ad hoc Euclidean metrics in that it enables more accurate classification of legal and illegal variations.

Algorithms↗
PubMed1997

Sequence conservation in the attachment glycoprotein and antigenic diversity among bovine respiratory syncytial virus isolates.

Partial nucleotide sequences were determined from the coding regions of the attachment glycoprotein (G) mRNAS of eight isolates of bovine respiratory syncytial virus (BRSV). The antigenic characteristics of 18 field and reference isolates were analyzed using the reactivity patterns of monoclonal antibodies (MAbs) directed against the human respiratory syncytial virus (HRSV) and BRSV G. fusion protein (F), nucleoprotein (N), and phosphoprotein (P), by radioimmunoprecipitation and immunofluorescence assays. The MAb reaction patterns demonstrated some random antigenic differences among the isolates, but for the most part were cross-reactive to the viral protein epitopes, especially on the F protein. Structural differences in the F and P proteins were observed among BRSV isolates; the P protein migrated at three different apparent molecular weights on PAGE gels. Antigenic and structural variation occurs among isolates, however, the structural differences in the P protein did not correlate with the antigenic differences among the F, N and P proteins. The G mRNA nucleotide sequence identities were high, ranging from 94.1 to 99.9%, and the predicted amino acid sequence identities ranged from 89.9 to 99.6%. Variance was due to substitution point mutations. The G protein ectodomains contained areas of sequence divergence flanking a highly conserved region, with four cysteine residues, which is analogous to the putative HRSV receptor binding domain. The high sequence and amino acid identities and random antigenic diversity among the isolates indicates that the BRSV isolates analyzed belong in a monophyletic group.

Amino Acid Sequence↗
PubMed1985

Mammalian fertilization as seen with the scanning electron microscope.

For several years we have been looking at mammalian gametes and their interactions with the scanning electron microscope (SEM). Examining the images produced by the SEM has given us a three-dimensional view of sperm, eggs, and egg investments. We are particularly impressed with the structural variation among gametes of different mammalian species. In this short report we examine the structure of mammalian spermatozoa, eggs, zonae pellucidae, and cumuli. Our observations and those of others have led us to believe that variation in gamete structure and function may have evolved as a mechanism for reproductive isolation of mammalian species.

Animals↗