SEARCH · Search PubMed

Results for “Structure variation”

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

SourceResearch connectionFrom yearThrough year

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

At least 649 records · Page 36Linked to original sources

PubMed2004

Recognition and separation of single particles with size variation by statistical analysis of their images.

Macromolecules may occupy conformations with structural differences that cannot be resolved biochemically. The separation of mixed molecular populations is a pressing problem in single-particle analysis. Until recently, the task of distinguishing small structural variations was intractable, but developments in cryo-electron microscopy hardware and software now make it possible to address this problem. We have developed a general strategy for recognizing and separating structures of variable size from cryo-electron micrographs of single particles. The method uses a combination of statistical analysis and projection matching to multiple models. Identification of size variations by multivariate statistical analysis was used to do an initial separation of the data and generate starting models by angular reconstitution. Refinement was performed using alternate projection matching to models and angular reconstitution of the separated subsets. The approach has been successful at intermediate resolution, taking it within range of resolving secondary structure elements of proteins. Analysis of simulated and real data sets is used to illustrate the problems encountered and possible solutions. The strategy developed was used to resolve the structures of two forms of a small heat shock protein (Hsp26) that vary slightly in diameter and subunit packing.

Computer Simulation↗

PubMed2026

SynFlow: an interactive online genome structural variant viewer.

MOTIVATION: Structural variations (SVs), including inversions, translocations (TRAs), duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chromosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern genomics. While SV detection has advanced, most visualization methods produce static plots that fall short when researchers, particularly in comparative genomics, need to interactively explore large datasets, zoom into specific genomic regions, or dynamically filter structural events in real time. RESULTS: To address this gap, we introduce SynFlow, a lightweight, web-based interactive application specifically designed for exploring and visualizing SVs identified by SyRI. We demonstrate that SynFlow can reproduce complex static synteny plots published in literature, but transforms them into dynamic, shareable visualizations that support real-time filtering, reordering, and deep exploration of specific SVs, including TRAs. SynFlow is available as a web server and offers multiple entry points: browsing precomputed datasets (e.g. banana and grapevine genomes), uploading user-provided SyRI outputs, or running an integrated workflow to produce and visualize SVs on the fly. AVAILABILITY AND IMPLEMENTATION: https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/synflow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow.

Software↗

PubMed2025

Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.

Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.

Reproductive Isolation↗

PubMed2026

Lineage-associated small inversions disrupt dosT, dnaE2, and a promoter-adjacent region in some Mycobacterium tuberculosis isolates.

UNLABELLED: Large molecular inversions in the genome of Mycobacterium tuberculosis (Mtb) due to factors like the presence of insertion sequences and transposases are widely known. However, smaller inversions within coding sequences and non-coding control elements are rarely reported. The present study aims to identify inversions and their potential impact on Mtb biology in a lineage-specific manner. Structural variants (SVs) could only be detected by long reads. For this, we simulated long reads by de novo assembling the short-read sequencing data sets and subsequently aligned representative strains from each lineage using the Progressive Mauve algorithm. Independently, long-read sequencing from the Pacific Biosciences platform was acquired and analyzed using the structural variant identification method. Variants were merged, and Fisher's exact test was carried out to identify the inversion association with lineages. To visualize deoxyribonucleic acid (DNA) features, the DNA-features-viewer tool was used. Simulated reads from short-read sequencing gave indications of lineage (L)-specific inversions. The long-read sequencing approach led to the identification of seven unique inversions: two positively associated with L1, one positively associated with L3, two negatively associated with L4, and two positively associated with L3 but negatively associated with L4 (P < 0.05). The inversions encompassed primarily non-essential genes like sdaA, dosT, Rv2026c, dnaE2, Rv1341, Rv1342, and lprD. An interesting inversion was observed in the upstream control element of purB and Rv0776c. The study sheds light on small inversions that may be causing alterations in expression, formation of fusion genes, and nonsense mutations that may have a role in lineage-specific phenotypic changes. IMPORTANCE: The role of mutations like SNPs and INDELs and their association with drug resistance is well known in Mycobacterium tuberculosis (Mtb). However, structural variations, especially inversions, are largely overlooked and unreported. In this paper, publicly available whole-genome sequencing datasets from Illumina and Pacific Biosciences-Oxford Nanopore Technologies platform have been used to detect inversions and report seven unreported Mtb lineage-specific small inversions.

Mycobacterium tuberculosis↗

PubMed2026

Pan-genome characterization of the maize 4CL gene family and its dynamic responses to abiotic stress.

1.Pan-genome analysis across 26 maize inbred lines identified 13 Zm4CL genes (nine core and four near-core) classified into three evolutionary clades.2.Structural variations (SVs) are significantly associated with the expression and altered conserved protein domains of key Zm4CL genes.3.Zm4CL genes exhibit distinct tissue-specific expression patterns and dynamic enzymatic and transcriptional responses to stresses, particularly cold and drought.4-Coumarate:CoA ligase (4CL) is a key enzyme in the phenylpropanoid pathway and plays important roles in plant growth, development, and responses to environmental stresses. However, a comprehensive pan-genome analysis of the 4CL gene family in maize is still lacking. In this study, 13 Zm4CL genes were identified from a maize pan-genome comprising 26 diverse inbred lines, including nine core genes and four near-core genes. Phylogenetic analysis classified these genes into three evolutionary clades, while Ka/Ks analysis indicated that most members have been maintained under purifying selection, although several genes exhibited greater evolutionary divergence and relatively relaxed evolutionary constraints. Structural variation (SV) analysis revealed significant associations between SVs and the expression of Zm4CL2 and Zm4CL3, while sequence comparisons suggested that SVs were also associated with alterations in conserved protein domains in some genotypes. Transcriptome analyses revealed distinct tissue-specific expression patterns and diverse transcriptional responses to abiotic and biotic stresses. Enzyme activity assays showed that cold stress significantly increased 4CL activity at 12 h, whereas heat, salt, and alkali stresses caused an initial decrease followed by recovery, while drought had no significant effect. Time-course RT-qPCR further validated dynamic expression changes of representative Zm4CL genes under cold and drought stresses. Overall, this study provides a comprehensive pan-genome framework for understanding the evolutionary conservation, regulatory diversification, and stress-responsive characteristics of the maize Zm4CL gene family, providing valuable resources for future functional studies and the genetic improvement of stress tolerance in maize.

Zea mays↗

PubMed1993

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.

Complexes of five peptides (from HIV-1, influenza A virus, HTLV-1, and hepatitis B virus proteins) bound to the human class I MHC molecule HLA-A2 have been studied by X-ray crystallography. While the peptide termini and their second and C-terminal anchor side chains are bound similarly in all five cases, the main chain and side chain conformations of each peptide are strikingly different in the center of the binding site, and these differences are accessible to direct TCR recognition. Each of the central peptide residues is seen to point up for some bound peptides, but down or sideways for others. Thus, although fixed at its ends, the structure of an MHC-bound peptide appears to be a highly complex function of its entire sequence, potentially sensitive to even small sequence differences. In contrast, MHC structural variation is relatively limited. These results offer a structural framework for understanding the role of nonanchor peptide side chains in both peptide-MHC binding affinity and TCR recognition.

Amino Acid Sequence↗

PubMed2005

Differentiation of a passive vaccine and the humoral immune response toward infection: analysis of phage displayed peptides.

Antibody-genes undergo molecular events that produce unique binding-sites that recognize specific epitopes, thus, leading to B-cell clonal variation. As a result, different binding-site structures (paratope internal images) are produced even when two distinct B-cells bind one and the same epitope. Paratope structural variation can be exploited to enable one to evaluate antibody-diversity in a single polyclonal serum sample. This is accomplished through the selection of antibody-specific peptides isolated from combinatorial phage displayed peptide libraries. As an example, we demonstrate the analysis of macaque sera containing passively administered antibodies, given as a therapeutic vaccine and antibodies actively produced by the virus-infected monkeys.

Animals↗

PubMed2005

Growth of silicon nanowires on H-terminated Si {111} surface templates studied by transmission electron microscopy.

We have studied the growth of silicon nanowires (SiNWs) by means of transmission electron microscopy. SiNWs are grown from nanocatalysts via the Vapor-Liquid-Solid (VLS) mechanism using silane (SiH4) gas as a source gas. The nanocatalysts are prepared on a hydrogen (H)-terminated Si surface. We have examined the formation mechanism of nanocatalysts on H-terminated surface and have observed several structural variants of SiNWs. According to the study we have suggested that many structural variations of SiNWs are possible, which modify the structural properties of SiNWs to great extents.

Journal Article↗

PubMed2003

Structure of a constitutively activated RhoA mutant (Q63L) at 1.55 A resolution.

Mutants of the small G protein RhoA that are deficient in GTPase activity and thereby exhibit constitutive molecular signaling activity are commonly used to discover its cellular functions. In particular, two such mutants, Gly14-->Val (G14V) and Gln63-->Leu (Q63L), are often used interchangeably for such studies. However, while their in vitro rates of GTP hydrolysis are very similar, differences are observed in their other functional properties. The structure of G14V-RhoA is known; in order to assess whether structural variations are responsible for functional differences, the crystal structure of a Q63L-RhoA bound to the GTP-analog 5'-guanylylimidodiphosphate (GMPPNP) was determined at 1.5 A resolution. Overall, the structure is very similar to that of G14V-RhoA, but the significantly higher resolution data permit an improved basis for structural analysis and comparison. The data support the notion that differences observed between the mutants in vivo are likely to arise from altered affinities for RhoGDI and not from direct structural differences.

Amino Acid Substitution↗

PubMed2002

Risedronate preserves trabecular architecture and increases bone strength in vertebra of ovariectomized minipigs as measured by three-dimensional microcomputed tomography.

Risedronate reduces the risk of new vertebral fractures up to 70% within 1 year of treatment in patients with osteoporosis. Both increases in bone mass and preservation of bone architecture are thought to contribute to antifracture effects. Our objectives were to determine the effects of risedronate on trabecular bone mass and architecture and to determine the relative contributions of mass and architecture to strength in the vertebra of ovariectomized (OVX) minipigs. The minipigs were OVX at 18 months of age and were treated daily for 18 months with either vehicle or risedronate at doses of 0.5 mg/kg per day or 2.5 mg/kg per day. The three-dimensional (3D) bone architecture of the L4 vertebral cores of Sinclair S1 minipigs was evaluated by 3D microcomputed tomography (muCT). Compared with the OVX control, the vertebral bone volume (bone volume/tissue volume [BV/TV]) was higher in both treated groups (p < 0.05). The architectural changes were more significant at the 2.5-mg/kg dose and were more prevalent at the cranial-caudal ends compared with the midsection. At the higher dose, the trabecular thickness (Tb.Th), trabecular number (Tb.N), and connectivity were higher, and marrow star volume (Ma.St.V) and trabecular separation (Tb.Sp) were lower (p < 0.05). The trabecular separation variation index (TSVI), a new measure to approximate structural variations, was smaller in the 2.5-mg/kg-treated group (p < 0.05). In this group, a significant preservation of trabeculae orthogonal to the cranial-caudal axis was confirmed by a decrease in the degree of anisotropy (DA) and an increase in the percent Cross-strut (% Cross-strut; p < 0.05). Both normalized maximum load (strength) and normalized stiffness of the same vertebral cores were higher in the 2.5-mg/kg risedronate group compared with the OVX group (p < 0.05). BV/TV alone could explain 76% of the variability of the bone strength. The combination of bone volume and architectural variables explained >90% of the strength. The study showed that risedronate preserved trabecular architecture in the vertebra of OVX minipigs, and that bone strength is tightly coupled to bone mass and architecture.

Animals↗

PubMed1993

Relationship between colony morphology and the life cycle of Haemophilus influenzae: the contribution of lipopolysaccharide phase variation to pathogenesis.

Colonies of Haemophilus influenzae are heterogeneous in appearance because of phase variation in opacity. The only cell surface component found to have structural variation correlating with differences in opacity was the lipopolysaccharide (LPS). Changes in LPS structure, seen as migration patterns on tricine-SDS-PAGE, appeared to be independent of a previously described mechanism for generating LPS phase variation. The more transparent variants expressing a higher-molecular-weight LPS were serum sensitive and could efficiently colonize the infant rat nasopharynx after intranasal inoculation. In contrast, the fully opaque variant expressing a smaller-molecular-weight LPS was serum resistant, unable to colonize the nasopharynx, and more virulent when intraperitoneally administered. Organisms disseminating into the blood-stream from the nasopharynx changed phenotype from transparent to opaque. These findings demonstrate the potential importance of LPS structures that determine opacity in pathogenesis and colonization of mucosal surfaces.

Animals↗

PubMed2005

Microfocus X-ray scattering investigations of eggshell nanotexture.

The avian eggshell is a highly ordered calcitic bioceramic composite, with both inorganic and organic constituents. The interactions between the inorganic and organic components within the structure are poorly understood but are likely to occur at the nanometre level. Thus structural variation at this level may impinge on the overall structural integrity and mechanical performance of the eggshell, and therefore analysis at this level is fundamental in fully understanding this ordered structure. In this study, structural changes in the mineral crystallites were investigated by microfocus small-angle X-ray scattering (microSAXS) using synchrotron radiation. Small-angle X-ray scattering (SAXS) can be used to investigate structures on the nanometre scale such as size, shape, arrangement and internal porosity. A microfocused X-ray beam, 1.5 microm vertically by 7 microm, was used to produce vertical linear scans of the eggshell section. SAXS patterns were taken from the eggshell membrane (inner surface of the eggshell) to the cuticle (outer surface of the eggshell). This allowed textural variations within the eggshell to be mapped. The scattering intensity profile was then used to derive the dimension of scattering objects that define the nanotexture. The nanotexture observed may result from the presence of the organic matrix, which is embedded as intracrystalline particles producing voids within the calcified framework of large (>1 microm) calcite crystals. Porod analysis revealed the average size of a scattering interface to be approximately 4.5 nm with small changes that had a depth-dependent variation. These were largest at the mammillary layer/membrane boundary. The palisade layer displayed a small upward trend in size of scattering object. Parallel scans showed that the textural variations observed within the palisade layer are significant and indicate local subtextures. In addition, many of the patterns exhibit diffuse scattering streaks that could result from reflectivity from the larger crystallite interfaces. Changes in the orientation of diffuse streaks were observed within the different layers, the membranes, mammillary layer, palisade layer, vertical crystal layer and cuticle, indicating certain preferred orientations of the crystallites within the layers. The nanotextural variations that are apparent could have implications at the macroscopic level of the resulting eggshell.

Animals↗

PubMed2000

Coadaptation of male aedeagal filaments and female spermathecal ducts of the old world phlebotomine sand flies (Diptera: Psychodidae).

The morphology of insect genitalia is often highly species-specific, and its variation has been suggested as an important impetus for evolution. Structural variation of the male genitalia and the female spermathecae in Phlebotomine sand flies is unique among the blood sucking Diptera. We describe the fine structures involved in mating for Phlebotomus papatasi (Scopoli). Relationships among the length of the spermathecal duct and aedeagal filament were studied in 26 species of Old World phelebotomine sand flies comprising 12 subgenera. In most taxa the aedeagal filaments were very long allowing direct insemination into the spermathecae, indicating that intrasexual competition among males occurs as sperm precedence. There was a positive correlation between the lengths of the spermathecal ducts and aedeagal filaments, indicating that an evolutionary "arms race" occurs between males and females over the control of fertilization. The pattern of genitalia variation in phlebotomine sand flies also indicated that differences in the lengths of the spermathecal ducts and aedeagal filaments are distributed unevenly among closely related species. Genital differences do not seem to occur in populations of the Phlebotomus argentipes Annandale & Brunetti complex, whereas differences showed strongly in closely related Phlebotomus papatasi and P. bergeroti Parrot, and in sympatric Phlebotomus martini Parrot and P. celiae Minter.

Animals↗

PubMed1999

Almost pure I(alpha) cellulose in the cell wall of Glaucocystis.

Crystalline features of cellulose microfibrils in the cell walls of Glaucocystis (Glaucophyta) were studied by combined spectroscopy and diffraction techniques, and the results were compared with those of Oocystis (Chlorophyta). Although these algae are grouped into two different classes, by the composition of their chloroplasts for instance, their cell walls are quite similar in size and morphology. The most striking features of their cellulose crystallites are that they have the highest cellulose I(alpha) contents reported to date. In particular, the I(alpha) fraction of cellulose from Glaucocystis was found to be as high as 90% from (13)C NMR analysis. The mode of preferential orientation of cellulose crystallites in their cell walls is also interesting; equatorial 0.53-nm lattice planes were oriented parallel to the cell surface in the case of Glaucocystis, while the 0.62-nm planes were parallel to the Oocystis cell surface. Such a structural variation provides another link to the evolution of cellulose structure, biosynthesis, and its biocrystallization mechanism.

Cell Wall↗

PubMed2004

Truncated structural variants of lipoarabinomannan in Mycobacterium leprae and an ethambutol-resistant strain of Mycobacterium tuberculosis.

Current knowledge on the structure of lipoarabinomannan (LAM) has resulted primarily from detailed studies on a few selected laboratory strains of Mycobacterium tuberculosis, Mycobacterium bovis BCG, and Mycobacterium smegmatis. Our previous work was the first to report on the salient structural features of M. tuberculosis clinical isolates and demonstrated significant structural variations. A prime effort is to correlate a particular structural characteristic with observed differences in eliciting an immunobiological response, especially in the context of CD1-restricted presentation of LAM to T cells. T cell clones derived from the cutaneous lesions of leprosy patients have been shown to recognize specifically LAM from Mycobacterium leprae and not from M. tuberculosis Erdman or H37Rv. Herein we provide further fine structural data on LAM from M. leprae (LepLAM) and a tuberculosis clinical isolate, CSU20 (CSU20LAM), which was unexpectedly recognized by the supposedly LepLAM-specific CD1-restricted T cell clones. In comparison with the de facto laboratory LAM standard from M. tuberculosis H37Rv (RvLAM), LepLAM derived from in vivo grown M. leprae is apparently simpler in its arabinan architecture with a high degree of exposed, non-mannose-capped termini. On the other hand, CSU20, an ethambutol-resistant clinical isolate, makes a vastly heterogeneous population of LAM ranging from rather small and non-mannose-capped to full-length and fully capped variants. LepLAM and CSU20LAM contain a higher level of succinylation than RvLAM, which, in the context of truncated or less elaborated arabinan, may contribute to selective recognition by T cells. LAM from all species could be resolved into discrete forms by isoelectric focusing based apparently on their arabinan heterogeneity. In the light of our current and more recent findings, we reason that all immunobiological data should be cautiously interpreted and that the actual LAM variants that may be present in vivo during infection and pathogenesis need to be taken into consideration.

Blotting, Western↗

PubMed2000

Identification and functional expression of four isoforms of ATPase II, the putative aminophospholipid translocase. Effect of isoform variation on the ATPase activity and phospholipid specificity.

ATPase II, a vanadate-sensitive and phosphatidylserine-dependent Mg(2+)-ATPase, is a member of a subfamily of P-type ATPase and is presumably responsible for aminophospholipid translocation activity in eukaryotic cells. The aminophospholipid translocation activity plays an important physiological role in the maintenance of membrane phospholipid asymmetry that is observed in the plasma membrane as well as the membranes of certain cellular organelles. While the preparations of ATPase II from different sources share common fundamental properties, such as substrate specificity, inhibitor spectrum, and phospholipid dependence, they are divergent in several characteristics. These include specific ATPase activity and phospholipid selectivity. We report here the identification of four isoforms of ATPase II in bovine brain. These isoforms are formed by a combination of two major variations in their primary sequences and show that the structural variation of these isoforms has functional significance in both ATPase activity and phosholipid selectivity. Furthermore, studies with the phosphoenzyme intermediate of ATPase II and its recombinant isoforms revealed that phosphatidylserine is essential for the dephosphorylation of the intermediate. Without phosphatidylserine, ATPase II would be accumulated as phosphoenzyme in the presence of ATP, resulting in the interruption of its catalytic cycle.

Amino Acid Sequence↗

PubMed1992

Geographic patterns of chromosomal variation in South American marsh rats, Holochilus brasiliensis and H. vulpinus.

Karyotypes were prepared from 146 individuals, representing nine populations evenly spaced along a 2,000-km north-south transect in Paraguay and Argentina, to determine the nature, extent, and pattern of chromosomal variation in Holochilus brasiliensis chacarius and H. vulpinus. Two distinct patterns of chromosomal variation characterized these two species. In H. brasiliensis, the diploid number (2n) ranged from 48 to 56 and the nombre fondamental (NF) from 57 to 63. Four classes of chromosomal variation were found in populations of H. brasiliensis: whole-arm Robertsonian (Rb) translocations, including Rb changes with monobrachial homology, variation in the number and kind of supernumerary (B) chromosomes, centromeric rearrangements (putative pericentric inversions), and variation in the amount of euchromatin. The amount of structural variation was uniformly high in all populations of H. brasiliensis sampled, and all rearrangements appeared to be in Hardy-Weinberg proportions, corroborating the hypothesis that chromosomal rearrangements are not strongly underdominant in this species. In H. vulpinus, 2n ranged from 35 to 39 and NF from 57 to 61. Two classes of variation were found in this species: variation in the number, but not the kind, of supernumerary chromosomes and variation in the amount of euchromatin.

Animals↗

PubMed1995

Molecular mechanisms and implications for infection of lipopolysaccharide variation in Neisseria.

The lipopolysaccharides of the pathogenic Neisseria species are subject to structural variation owing to a combination of intrinsic changes in lipopolysaccharide (LPS) biosynthesis and external modification of the LPS molecule with sialic acid. This variation appears to control bacterial behaviour by altering their ability to interact with human cells and to evade host immune defences. This interconversion of LPS phenotypes, which is also observed during the natural infection, is probably due to environmental regulation of LPS biosynthesis superimposed on spontaneous changes in the DNA of distinct LPS loci. LPS variation may be a common strategy of mucosal pathogens to colonize and persist within the human host.

Carbohydrate Conformation↗