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PubMed2003

Geographical and organisational variation in the structure of primary care services: implications for study design.

AIMS: To evaluate the extent to which structural variation between English general practices is accounted for at higher organisational levels in the National Health Service (NHS). METHODS: We analysed data for 11 structural characteristics of all general practices in England. These included characteristics of general practitioners (GPs), the practice list and the services provided by practices. A four-level random effects model was used for analysis and components of variance were estimated at the levels of practice, primary care group (PCG), health authority and region. RESULTS: The proportion of single-handed practices ranged from 0% to 74% at PCG level and from 14% to 43% in different regions. The proportion of practices providing diabetes services ranged from 0% to 100% at PCG level and from 71% to 96% in different regions. The list size per GP ranged from 1314 to 2704 patients per GP at PCG level and from 1721 to 2225 at regional level. Across the 11 variables analysed, components of variance at general practice level accounted for between 43% and 95% of the total variance. The PCG level accounted for between 1% and 29%, the health authority level for between 2% and 15% and the regional level for between 0% and 13% of the total variance. Adjusting for an index of deprivation and the supply of GPs gave a median 8% decrease in the sum of variance components. CONCLUSION: Geographical and organisational variation in the structure of primary care services should be considered in designing studies in health systems such as the English NHS. Stratified designs may be used to increase study efficiency, but variation between areas may sometimes compromise generalisability.

Aged↗
PubMed1986

Variation in the structural subunit and basal protein antigens of Bacteroides nodosus fimbriae.

The fimbriae of Bacteroides nodosus play a major role in protective immunity against ovine footrot and are an important determinant in the serological classification system that divides field isolates into at least eight serogroups and 16 serotypes. Purified fimbriae contain two polypeptide antigens, the structural subunit of the fimbrial strand (molecular weight about 17,000) and a basal protein (molecular weight about 80,000), both of which exhibit structural variation. Fimbriae were prepared from all prototype strains, as well as from a number of other isolates representative of each of the B. nodosus serotypes, and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Substantial variation was observed in the electrophoretic mobility of the fimbrial subunits from the prototypes of each of the eight serogroups. With the exception of serogroup H, which is an unusual case, the apparent molecular weights of the fimbrial subunits ranged from about 16,500 in serogroup D to 19,000 in serogroup F (serotype 1); in serogroup A, B, C and E, the apparent molecular weights were clustered in the range of 17,000 to 17,500, whereas serogroup G was about 18,500. Serogroup H fimbriae appeared to consist of two smaller polypeptides, which in the prototype (H1) had apparent molecular weights of about 6,000 and 10,000 and which seem to have arisen as a consequence of an internal proteolytic nick in the original subunit. Electrophoretic variation in the fimbrial subunit was also observed between different serotypes, although with the exceptions of serogroups F and H, this was not as pronounced as between the serogroups. Examination of a number of isolates classified within the same serotypes showed that some variation, although minor, also occurred at this level. The basal antigen exhibited significant variation at all levels of the serotypic hierarchy in a manner apparently unrelated to the classification system. Among the range of isolates examined, the apparent molecular weight of this antigen varied from about 77,000 to 88,000.

Antigens, Bacterial↗
PubMed2004

Bone tissue stiffness in the mandibular condyle is dependent on the direction and density of the cancellous structure.

Variation in the apparent stiffness of cancellous bone is generally ascribed to variation in cancellous structure and density, while the bone tissue stiffness is assumed to be constant. The purpose of the present study was to examine whether the bone tissue stiffness is dependent on the direction and density of the cancellous structure. Bone tissue stiffness was estimated by combining mechanical testing and micro-finite element (micro-FE) modeling on cylindrical bone specimens obtained from the human mandibular condyle. One set of specimens was tested in the vertical direction of the condyle (n = 39) and another set in the transverse direction (n = 30). The cancellous structure of the specimens was characterized by micro-CT. The apparent bone stiffnesses predicted by the FE model correlated strongly (r2 = 0.91) with the measured apparent bone stiffnesses. Apparent bone stiffness in the transverse direction was considerably smaller than that in the vertical direction. In contrast, the predicted bone tissue stiffness was significantly larger in the transverse direction (E = 13.70 GPa) than in the vertical direction (E = 11.87 GPa). In addition, bone tissue stiffness correlated negatively with the bone volume fraction and directional sensitivity of the bone tissue stiffness increased with a decrease of bone volume fraction. The results suggest that the transversely oriented trabeculae in the mandibular condyle are stiffer and more mineralized than the vertically oriented trabeculae and that bone loss is compensated by an increase in the degree of mineralization.

Aged↗
PubMed2026

Genome-wide variation analysis of two Salvia hispanica L. genotypes and implication for associations with metabolic and adaptive traits.

BACKGROUND: Advances in next-generation sequencing have accelerated genome-wide exploration of genetic diversity in underutilized oilseed crops. Salvia hispanica L. (chia), a high-nutrient pseudocereal rich in omega-3 fatty acids, is increasingly valued for its health benefits and commercial potential, yet it remains poorly characterized at the genomic level. Understanding the scale and nature of genomic variation is essential for improving complex traits such as oil yield, stress tolerance, and seed quality. METHODS: Two contrasting chia genotypes, Black-chia (CACH-B) and White- chia (CACH-W), were resequenced using the Bio-Resequencing Toolkit (BRT) pipeline. High-coverage sequencing, with a mapping rate exceeding 99% and an average depth of approximately 28×, facilitated the detection and annotation of single-nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy-number variations (CNVs), and structural variants (SVs). The functional classification of variant impacts enabled the identification of genes potentially linked to metabolic and adaptive traits. RESULTS: A total of 1.97 million SNPs, 401,493 InDels, 836 CNVs, and 15,288 SVs were identified across the chia genome. Notably, approximately 53% of exonic SNPs were non-synonymous (dN/dS ≈ 1.28), predominantly affecting lipid metabolism, transcriptional regulation, and stress response pathways, potentially altering key agronomic traits. In addition, CNV hotspots were concentrated in chromosomes 3 and 6, overlapping MYB, WRKY, and bZIP transcription factor loci, may potentially be involved in stress tolerance and yield. Furthermore, structural rearrangements, including inversions and duplications within the FAD2, FAD3, and CYP450 gene clusters, were potentially associated with seed pigmentation and omega-3 biosynthesis, pointing to their potential breeding relevance. Observed heterozygosity (Hₒ ≈ 0.71) and nucleotide diversity (π ≈ 7 × 10-3) indicated moderate to high allelic richness. In addition, the low FST value (0.038) indicates substantial genomic similarity between the two genotypes. CONCLUSION: This study presents the first comprehensive map integrating SNPs, CNVs, and SVs in S. hispanica L. The results reveal a structurally dynamic genome characterized by substantial sequence and structural variation, providing valuable insights into genomic diversity and potential adaptive mechanisms in chia. The coexistence of high SNP diversity and abundant structural variation underpins chia's nutritional specialization and environmental resilience. These results deliver a foundational genomic resource for marker-assisted breeding, genome-wide association studies, and the development of climate-resilient chia cultivars.

Copy-number variation, structural variation↗
PubMed1988

Structural and antigenic variation of the structural protein VP3 in serotype 1 poliovirus isolated from vaccinees.

High resolution two-dimensional PAGE was used to analyse protein variation among serotype 1 poliovirus isolates. Viruses isolated from patients with recent histories of vaccination with live attenuated poliovirus were compared with prototype serotype 1 poliovaccine. The nonvaccine Mahoney and Brunenders strains of serotype 1 poliovirus were also analysed. The overall protein profile was conserved but the structural protein VP3 varied in its net charge among the viruses. Eight out of 14 clinical virus isolates had VP3 with a net basic charge identical to serotype 1 polio vaccine, whereas the remaining clinical isolates had an acidic VP3 similar to the nonvaccine type 1 strains. The altered VP3 mobility correlated with a change in antigenicity as determined by monoclonal antibodies directed to the neutralization site located on VP3. The data clearly illustrated the suitability of two-dimensional PAGE in analysing protein mutations in attenuated vaccine virus excreted by vaccinees.

Antigenic Variation↗
PubMed1995

Variation in the primary structure of waxy proteins (granule-bound starch synthase) in diploid cereals.

The molecular weights of waxy proteins, by SDS-PAGE, and the N-terminal amino acid sequences of mature protein and of V8 protease-induced fragments were determined in diploid cereals. The homology of the primary structure was relatively high among cereals examined here, and there appeared to be a common sequence, V-F-V-G-A-E-M-A, in the vicinity of the N terminus. Based on the amino acid sequences, these cereals could be divided into two groups, including corn and rice in one and diploid wheat, four Aegilops species, rye, and barley in the other. In diploid wheat and Aegilops species there were substitutions of amino acids in the primary structure. Variations of this sort suggest that the primary structure of waxy proteins would provide clues to the phylogenetic relations in the wheat group.

Amino Acid Sequence↗
PubMed1999

Variations in cell and structure populations along the length of murine small intestine.

Previous workers have reported a range of structural variations occurring along the length of small intestine. These studies have concentrated on the major intestinal components with little information available on the intersite variation of other members of a highly heterogeneous population. Using resin histology, the current study has collected data per circumference for all definable structural features within the murine intestinal wall, along with measurements for epithelial, muscle, nerve and connective tissue areas, and villous height and cryptal depth. Seven different sites along the length of the small intestine were examined. Following statistical comparisons a number of features exhibited no intersite variation; these were numbers of villi, submucosal vessels, myenteric nerve plexus profiles, inner muscle nuclei and apoptotic bodies as well as measurements for tissue areas and cryptal depth. Variations were seen between sites for crypts, enterocytes, villous and cryptal stromal cells, cryptal goblet cells, cryptal non-secretory epithelial cells, Paneth cells, endocrine cells, intra-epithelial lymphocytes, submucosal nerve plexus profiles, outer muscle nuclei and mitotic figures. A reduced villous height was observed caudally. Certain correlations between villous height/crypt number and constituent parameters have been noted. The results provide a complete description of how each definable structural feature within the gut wall varies at regular intervals along the length of the small intestine in C57 BL mice. A number of previously unreported variations have been described. The work provides a comprehensive data bank for future intestinal investigations.

Analysis of Variance↗
PubMed2004

Variations in content and structure of glycosaminoglycans of the vitreous gel from different mammalian species.

The vitreous of all species is composed of essentially the same type of extracellular matrix macromolecules organized to a transparent gel. In this study, the composition and fi ne chemical structure of the glycosaminoglycans (GAGs) in the vitreous gel from sheep and goat were determined and compared with those of human and pig vitreous gels. The results showed that, in all examined species; hyaluronan (HA) was the predominant GAG, whereas chondroitin sulphate (CS) was the minor one. In the vitreous gel of the most relative species, i.e. sheep and goat, higher amounts of both of HA and CS were estimated as compared with pig and human tissues. The distribution of hydrodynamic sizes of HA and CS was significantly differed among different species. All HA preparations consisted of molecules with great variability in hydrodynamic sizes. The relative proportions of the large HA molecules (size >1.8 x 10(6) kDa) were significantly higher in sheep and goat as compared with human and pig vitreous gel. The length of CS chains was also of larger size in sheep and goat (50 and 58 kDa, respectively) than the respective chains in human and pig vitreous gel (38 and 28 kDa, respectively). The sulphation patterns of CS preparations were determined following enzymic treatments, HPLC and capillary electrophoretic analyses. The human vitreous-derived CS chains showed quite different sulphation profile than that of CS isolated from other species, since 4-sulphated disaccharides were identified as the dominant moiety. In conclusion, significant compositional and structural variations between the vitreous matrixes of different species at the GAG level were identified. The functional significance of these species-dependent variations is discussed.

Animals↗
PubMed2003

Quantifying phylogenetically structured environmental variation.

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.

Analysis of Variance↗
PubMed2004

Allozyme variation and structure of the Canarian endemic palm tree Phoenix canariensis (Arecaceae): implications for conservation.

Electrophoretic analysis of 18 allozyme loci was used to estimate the levels and structuring of genetic variation within and among natural populations of the protected endemic palm species from the Canary Islands (Phoenix canariensis) to evaluate its genetic relationship with the widespread congener P. dactylifera, and to assess comparatively the genetic variation in the populations where the two species coexist with morphologically intermediate plants (mixed populations). Our survey revealed that the within-population component explains roughly 75% of the genetic variation levels detected in P. canariensis (A=1.59; P=41.8; He=0.158), which rank higher than those reported for other species of the Arecaceae. A Principal Component analysis (PCA) based on allele frequencies consistently separates populations of P. canariensis and P. dactylifera, and reveals a close genetic relationship between P. canariensis and the mixed populations. Reduced levels of genetic variation in P. canariensis with respect to P. dactylifera, the fact that the genetic makeup of the Canarian endemic (with no unique alleles) is a subset of that found in P. dactylifera, and the high genetic identity between both species strongly suggest that P. canariensis is recently derived from a common ancestor closely related to P. dactylifera.

Arecaceae↗
PubMed1998

Alterations in chromosome structure and variations in the inherent radiation sensitivity of human cells.

Variations in the inherent radiosensitivity of both tumor cells and the normal tissues that surround them play an important role in tumor response to radiation therapy. In vitro studies suggest that variations in radiation sensitivity both between different tissues and within a specific histology are a reflection of differences in the rate and fidelity of rejoining of chromosome breaks. Cells of radiosensitive cell lines rejoin breaks more slowly and with less fidelity than those of more resistant cell lines. Differences in radiation sensitivity are also associated with variations in chromosome structure as detected by nucleoid-based assays. A model is presented to suggest that the radiation sensitivity of a cell line is a reflection of its transcriptional architecture, the number and genomic location of its actively transcribing regions. Also, it is proposed that chromosome breaks induced at or near transcriptionally active regions of the genome are rejoined preferentially and with greater fidelity than breaks induced at other regions of the genome.

Chromosome Aberrations↗
PubMed1983

Bovine tracheal cartilage proteoglycans. Variations in structure and composition with age.

The variation with age in structure and composition of proteoglycans from bovine tracheal cartilage was studied from fetal life to 12 years of age. Cartilage content of proteoglycans as related to collagen was found to increase with age. The extractability of the proteoglycans decreases markedly with age. Extracted proteoglycans were characterized and change during growth and maturation as follows: 1. They contain fewer chondroitin sulfate chains. The chains are of constant size; but at higher ages they are more highly sulfated, primarily with 6-sulfate groups. 2. They contain an increasing number of constant size keratan sulfate chains, while the number of O-linked oligosaccharides (structurally related to the keratan sulfate linkage region to protein) decreases. 3. They become smaller, at least partially, as a result of an increasing proportion of a smaller size proteoglycan. 4. They have a higher protein content. The changes can largely be attributed to an early shift (up to 22 months of age) from a predominating large chondroitin sulfate rich proteoglycan in the youngest cartilage to increasing proportions of a distinct, smaller keratan sulfate rich proteoglycan. During subsequent aging all molecular parameters as well as proportions of subpopulations of proteoglycans remain rather constant.

Aging↗
PubMed2006

Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals.

The recent hapmap effort has placed focus on the application of genome-wide SNP analysis to assess the contribution of genetic variability, particularly SNPs, to traits such as disease. Here, we describe the utility of genome-wide SNP analysis in the direct detection of extended homozygosity and structural genomic variation. We use this approach to assess the frequency of genomic alterations resulting from the lymphoblast immortalization and culture processes commonly used in cell repositories. We have assayed 408 804 SNPs in 276 DNA samples extracted from Epstein-Barr virus immortalized cell lines, which were derived from lymphocytes of elderly neurologically normal subjects. These data reveal extended homozygosity (contiguous tracts >5 Mb) in 9.5% (26/272) and 340 structural genomic alterations in 182 (66.9%) DNA samples assessed, 66% of which did not overlap with previously described structural variations. Examination of DNA extracted directly from the blood of 30 of these subjects confirmed all examined instances of extended homozygosity (6/6), 75% of structural genomic alteration <5 Mb in size (12/16) and 13% (1/8) of structural genomic alteration >5 Mb in size. These data suggest that structural genomic variation is a common phenomenon in the general population. While a proportion of this variability may be caused or its relative abundance altered by the immortalization and clonal process this will have only a minor effect on genotype and allele frequencies in a large cohort. It is likely that this powerful methodology will augment existing techniques in the identification of chromosomal abnormalities.

Aged↗
PubMed2026

Structural genome variation drives adaptation of the xylose-fermenting yeast Scheffersomyces stipitis to lignocellulosic hydrolysates.

Second-generation (2G) bioethanol from lignocellulosic feedstocks is a sustainable alternative to fossil fuels. However, its production is constrained by the poor performance of industrial microbes in hydrolysates that are generated during biomass pretreatment. Scheffersomyces stipitis is a native xylose fermenting yeast and a promising platform for 2G bioethanol production, and adaptive evolution under hydrolysate stress has yielded strains with enhanced performance. However, the chromosomal basis of this adaptation is unknown. Here, we demonstrate that chromosome scale structural variation, rather than point mutations, underlies the improved phenotype of the evolved strains. By integrating long- and short-read genome sequencing, we identify two major chromosomal rearrangements in the top performing isolate: a reciprocal translocation between chromosomes 1 and 2 that disrupts the NUDIX hydrolase gene YSA1, and the formation of a mitotically stable 175&#xa0;kb minichromosome derived from chromosome 5. Functional analyses show that disruption of YSA1 enhances xylose utilisation and ethanol yield, while the minichromosome contributes to improved performance in hydrolysate conditions. These findings provide direct evidence that balanced rearrangements and minichromosome formation can be selected during prolonged stress and can generate adaptive phenotypes. Taken together, our study establishes genome reorganisation as a key driver of adaptation in S. stipitis.

Xylose↗
PubMed1983

Variant class II molecules from H-2 haplotypes in wild mouse populations: functional characteristics of closely related class II gene products.

Independently derived haplotypes found in wild populations of mice often express class II molecules antigenically related to specific alleles of the A molecules defined in laboratory mice. Tryptic peptide fingerprint comparisons of these antigenically related molecules indicate that they have similar, or possibly identical, primary structures in the A alpha, A beta, or both subunits. By using the Ak and Ap families of independently derived, antigenically related A molecules, we examined the effect that minor structural variations in the A molecule have on allorecognition by T lymphocytes. Data obtained indicate that a) minor structural variations in the A molecule can effect, although not always, major functional changes in allorecognition, b) changes in allorecognition are always detected when the A beta subunit contains structural variations, but not necessarily when the A alpha subunit contains structural variations, and c) more than one site in the A molecule can be recognized by alloreactive T lymphocytes. These results can be interpreted as indicating that specific sites within the A molecule are critically involved in allorecognition and that structural variations must affect these sites to elicit major changes in allorecognition.

Alleles↗
PubMed2006

Photoelectron spectroscopy of the bis(dithiolene) anions [M(mnt)2]n- (M = Fe - Zn; n = 1, 2): changes in electronic structure with variation of metal center and with oxidation.

A detailed understanding of the electronic structures of transition metal bis(dithiolene) centers is important in the context of their interesting redox, magnetic, and optical properties. The electronic structures of the series [M(mnt)2]n- (M = Fe - Zn; mnt = 1,2-S2C2(CN)2; n = 1, 2) were examined by a combination of photodetachment photoelectron spectroscopy and density functional theory calculations, providing insights into changes in electronic structure with variation of the metal center and with oxidation. Significant changes were observed for the dianions [M(mnt)2]2- due to stabilization of the metal 3d levels from Fe to Zn and the transition from square-planar to tetrahedral coordination about the metal center (Fe-Ni, D(2h) --> Cu D2 --> Zn, D(2d). Changes with oxidation from [M(mnt)2]2- to [M(mnt)2]1- were largely dependent on the nature of the redox-active orbital in the couple [M(mnt)2](2-/1-). In particular, the first detachment feature for [Fe(mnt)2]2- originated from a metal-based orbital (Fe(II) --> Fe(III)) while that for [Fe(mnt)2]1- originated from a ligand-based orbital, a consequence of stabilization of Fe 3d levels in the latter. In contrast, the first detachment feature for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- originated from the same ligand-based orbital in both cases, a result of occupied Ni 3d levels being stabilized relative those of Fe 3d and occurring below the highest energy occupied ligand-based orbital for both of [Ni(mnt)2]2- and [Ni(mnt)2]1- . The combined data illustrate the subtle interplay between metal- and ligand-based redox chemistry in these species and demonstrate changes in their electronic structures with variation of metal center, oxidation, and coordination geometry.

Journal Article↗
PubMed1983

Genetic control of lipid transport in mice. II. Genes controlling structure of high density lipoproteins.

Genetic factors controlling the structure of high density lipoproteins (HDL) in mice have been examined. Surveys of inbred strains of mice revealed genetic structural variations of the two major apolipoproteins of mouse HDL, apolipoproteins A-I and A-II. The structural variations alter the charge of the proteins as judged by isoelectric focusing of HDL under denaturing conditions. The structural variations are inherited as single Mendelian genes exhibiting co-dominant expression. The structural gene for mouse apolipoprotein A-II, designated Alp-2, resides on mouse chromosome 1, tightly linked to Ly-m20, a lymphocyte alloantigen locus. Previous studies, as well as our results, suggest that the structural gene for mouse apolipoprotein A-I, designated Alp-1, is on mouse chromosome 9. The genetic structural variation for apo-A-I results in a shift in the charge of the entire family of apo-A-I isoforms, indicating that they are all encoded by a common structural gene. The structure of intact HDL, examined primarily by electrophoretic techniques, exhibits numerous and complex phenotypes among different strains of mice. One variation, controlling the density and possibly the size of HDL, has been studied in two sets of recombinant inbred strains of mice. The results indicate that the variation is controlled by a single major gene that is either tightly linked to or identical with the Alp-2 gene on chromosome 1. In addition to structural variation, inbred strains of mice exhibited considerable quantitative variation of plasma HDL. Thus, the mouse provides a useful model system for examining the genetic control of mammalian HDL structure and regulation.

Animals↗
PubMed1986

The stimulants and hallucinogens under consideration: a brief overview of their chemistry and pharmacology.

The substances under review are a heterogeneous set of compounds from a pharmacological point of view, though many have a common phenylethylamine structure. Variations in structure lead to marked changes in potency and characteristic action. The introductory material presented here is meant to provide a set of chemical and pharmacological highlights of the 28 substances under consideration. The most commonly used names or INN names, Chemical Abstract (CA) names and numbers, and elemental formulae are provided in the accompanying figures. This provides both some basic information on the substances and a starting point for the more detailed information that follows in the individual papers by contributors to the symposium.

Animals↗