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At least 19 recordsLinked to original sources
PubMed1992

Structural variations in the crystal structures of two homologous DL-Leu and delta-Leu containing peptides.

The similar conformations and interaction modes of Ac-DL-Leu-NMe2 and Ac-delta-Leu-NMe2 molecules in the solid state allow the comparison of their geometrical parameters. The most evident variations are essentially restricted to the alpha, beta-unsaturated side-chain which adopts the Z-disposition. The dimensions of the peptide backbone are much less sensitive to alpha, beta-unsaturation, with a small shortening by 0.04 A and 0.02 A of the N--C alpha and C alpha--C' bonds, respectively, and an increase by 6 degrees of the N--C alpha--C' bond angle. The ethylenic and amide groups in the delta-Leu derivative are far from coplanarity, and a significant electronic conjugation of the pi-orbital is likely to be rejected.

Crystallization↗
PubMed2025

Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.

Structural variation makes an important contribution to canine evolution and phenotypic differences. Although recent advances in long-read sequencing have enabled the generation of multiple canine genome assemblies, most prior analyses of structural variation have relied on short-read sequencing. To offer a more complete assessment of structural variation in canines, we performed an integrative analysis of structural variants present in 12 canine samples with available long-read and short-read sequencing data along with genome assemblies. Use of long-reads permits the discovery of heterozygous variation that is absent in existing haploid assembly representations while offering a marked increase in the ability to identify insertion variants relative to short-read approaches. Examination of the size spectrum of structural variants shows that dimorphic LINE-1 and SINE variants account for over 45% of all deletions and identified 1,410 LINE-1s with intact open reading frames that show presence-absence dimorphism. Using a graph-based approach, we genotype newly discovered structural variants in an existing collection of 1,879 resequenced dogs and wolves, generating a variant catalog containing a 56.5% increase in the number of deletions and 705% increase in the number of insertions previously found in the analyzed samples. Examination of allele frequencies across admixture components present across breed clades identified 283 structural variants evolving with a signature of selection.

Animals↗
PubMed1995

[The stria vascularis of the inner ear and its normal structural variations].

The ultrastructural effects of gentamicin on the stria vascularis of the inner ear of guinea pigs were studied by transmission electron microscopy. In a single specimen of an isolated, inner ear we found an unexpected variation in the structure of the stria vascularis in a normal, pigmented, guinea pig not treated with ototoxic drugs. There were prominent, wide protrusions from the apical surfaces of marginal cells into the endolymphatic space. This finding has not been previously reported and was seen in only 1 of 7 animals studied. It may be considered a normal structural variation, and is not pathological change in the stria vascularis due to ototoxic drugs.

Animals↗
PubMed1985

Localization of structural variations distinguishing I-Ak-related molecules to the alpha 1 and beta 1 domains.

The structural variations that distinguish the A molecules encoded by wild-derived H-2 complexes which express Ak-related molecules have been localized into the alpha 1 and beta 1 domains by radiochemical sequence analyses of tryptic peptides. The A alpha subunits of B10.STC90 (Akv1) and W12A (Akv2) differ from those of B10.BR (Ak) in two adjacent tryptic peptides spanning positions 43 to 71 in the alpha 1 domain. The A beta subunit of W12A differs from that of B10.BR in two peptides spanning positions 26 to 29 and 95 to 106. Isoleucine and leucine residues present at positions 28 and 95, respectively, in the B10.BR A beta subunit are not found in the corresponding positions in W12A A beta subunits. Both of these A beta sequence variations are in the beta 1 domain. B10.STC90 A beta subunits are identical to those of W12A except for a structural variation in the beta 1 domain affecting the HPLC retention time of a peptide spanning positions 49 to 63. These results suggest that these A molecules are encoded by closely related class II gene alleles which have diversified by the accumulation of discrete mutations within the exons encoding the alpha 1 and beta 1 domains of the A molecule. Our previous functional analyses of these minor variant A molecules have demonstrated that they are readily distinguished with A molecule-specific alloreactive T lymphocytes. Together, these findings suggest that minor structural variations in the alpha 1 and beta 1 domains of the A molecule can dramatically modify the allodeterminants recognized by alloreactive T lymphocytes.

Amino Acid Sequence↗
PubMed2025

Structural variation detection and association analysis of whole-genome-sequence data from 16,543 Alzheimer's disease sequencing project subjects.

INTRODUCTION: The role of structural variations (SVs) in Alzheimer's disease (AD) remains understudied. METHODS: We analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (N&#xa0;=&#xa0;16,543) and identified 400,234 (168,223 high-quality) SVs. Laboratory validation yielded a sensitivity of 82% (85% for high-quality). RESULTS: We found a burden of singletons (odds ratio [OR]&#xa0;=&#xa0;1.07, p&#xa0;=&#xa0;0.0017) and homozygous deletions (OR&#xa0;=&#xa0;1.14, p&#xa0;<&#xa0;0.0001) in cases. On AD genes, we observed the ultra-rare SVs associated with the disease, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1. Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, exemplified by a 5k deletion in LD (R2&#xa0;=&#xa0;0.99) with rs143080277 in NCK2. We identified a rare deletion near RNA5SP293 associated with AD (OR&#xa0;=&#xa0;1.99, p&#xa0;=&#xa0;1.3&#xa0;&#xd7;&#xa0;10-5), which was replicated using an independent dataset. DISCUSSION: This study highlights the pivotal role of SVs in AD genetics. HIGHLIGHTS: Observed a significant burden of singletons and homozygous deletions in Alzheimer's disease (AD) patients. Identified rare protein-altering structural variations (SVs) in ABCA7, APP, PLCG2, and SORL1. Established linkages between SVs and AD risk-associated single nucleotide variants (SNVs). Discovered a novel deletion near RNA5SP293 linked to AD, replicated independently. Uncovered over-representation of SVs in neuronal function pathways.

Humans↗
PubMed2026

Comparative genomics reveals lineage-associated structural variation and diversification in a barley fungal pathogen.

Leaf rust, caused by Puccinia hordei, is a major barley disease worldwide. Despite repeated shifts in virulence, contrasting reproductive histories, and emerging fungicide insensitivity, the genomic basis of its diversification and adaptation remains poorly understood. In this study, we generated haplotype-resolved, chromosome-level genome assemblies for two isolates with contrasting virulence and analyzed 41 Australian isolates collected over 54&#x2009;yr (1966-2020), integrating comparative and population genomics, mating-type gene phylogenies, chromosome-specific k-mer profiling, genome-wide copy-number variation (CNV) analysis, and gene-expression analysis. We identified a structurally dynamic chromosome characterized by repeat-associated rearrangements, structural variation, and lineage-associated CNV, representing the first evidence in a rust fungus of chromosome-scale structural diversification of this extent. Population analyses distinguished clonally expanded lineages from recombination-associated lineages, with mating-type gene phylogenies providing further support for lineage differentiation. More recently collected isolates showed increased duplication-associated variation, and CNV boundaries were associated with structural-variant breakpoints. We also identified lineage-associated amplification of Cyp51, with increased copy number associated with higher transcript abundance, supporting a potential role in fungicide adaptation. Overall, our findings highlight structural variation, contrasting reproductive histories, and lineage-associated CNV as important contributors to diversification in P. hordei, providing insights for future rust pathogen surveillance and management strategies.

Cyp51 gene↗
PubMedDate not supplied

The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence-specific DNA structure variations.

Curved DNA fragments have a reduced electrophoretic mobility in polyacrylamide gels. The retardation in gels is extremely sensitive to small structural variations which influence the DNA helix axis. This gel assay can also be used to detect very small structural variations in DNA sequences which are not curved: The noncurved sequences of interest can be combined with curved stretches in phase with the helix turn. Using such sequence constructions, even subtle influences on the DNA helix axis can be detected. Experiments of this kind allow the determination of a relative order of sequence-specific DNA twist and wedge angles.

Base Composition↗
PubMed1992

The aesthetasc concept: structural variations of putative olfactory receptor cell complexes in Crustacea.

The structure of the aesthetascs has been investigated in the prawn Macrobrachium rosenbergii (larvae and juveniles), the opossum shrimp Neomysis integer, the euphausid Meganyctiphanes, and in the water-fleas Daphnia magna and D. longispina. The aesthetascs, that are thought to represent olfactory receptors, exhibit a considerable structural variation, ranging from the well known aesthetascs of higher crustaceans (lobster, crab, crayfish) to the corresponding sensilla found in the water-fleas and the males of opossum shrimps. The two following morphological characteristics of the aesthetascs are thought to indicate an olfactory function: the shape of the cuticular hair that is long and essentially hose-shaped, and the thin, loosely arranged cuticle of at least the outer part of the cuticular hair. The presence of other structural elements such as sensory cells, cilia, and enveloping cells are vital for the olfactory function, but the development is variable, which makes their use in the morphological definition of aesthetascs problematic.

Animals↗
PubMed2026

Charting host structural variations in cervical cancer by long-read sequencing pinpoints a functional deletion in PIAS1.

Host structural variations (SVs) are critical in cancer development but their landscape and interaction with HPV integration in cervical carcinogenesis remain unclear. In this study, we performed Nanopore long-read sequencing on five HPV-positive cervical cancer tissues and two cell lines to profile host SVs. We identified thousands of SVs and statistically demonstrated their significant enrichment in genomic windows &#xb1;25 to &#xb1;50&#xa0;kb from HPV integration sites. Cross-sample analysis revealed 60 shared SVs, including a recurrent deletion within the PIAS1 gene. Multi-omics integration (Hi-C, H3K27ac ChIP-seq, and TCGA data) showed that this deletion is associated with reduced PIAS1 expression, disruption of local topologically associating domains, advanced pathological tumor stage, and poorer overall survival. Functional assays confirmed that PIAS1 deficiency inhibits cervical cancer cell proliferation and migration. Our findings identify a PIAS1 deletion as a candidate driver event, and underscore the pivotal role of host genomic instability in HPV-associated oncogenesis.

Cervical cancer↗
PubMed1982

Haemaphysalis (Garnhamphysalis) mjoebergi: identity, structural variation and biosystematic implications, deer hosts, and distribution in Borneo and Sumatra (Ixodoidea: Ixodidae).

Haemaphysalis (Garnhamphysalis) mjoebergi Warburton was reported from four male specimens from Sarawak, Borneo. We redescribe herein the male, from three specimens from Sarawak and 24 from Lampung District, Sumatra, and describe the female from 24 specimens from Lampung. Male structural variation in the dental formula and development of the coxa IV spur and segments of legs III and IV is unusual or unique in the genus Haemaphysalis. "Atypical" males might easily be misidentified. This species provides an ideal model for experimental study of population genetics and evolutionary processes and of biological factors influencing body size and structural variation in the genus Haemaphysalis. The sambar deer, Cervus unicolor brookei Hose (Sarawak) and C. unicolor equinus Cuvier (Sumatra), appears to be the chief host in humid, marshy, lowland forests and secondary growth. Single collections were from a human and a domestic cow. The dynamics and vector potential of this tick should be investigated in environments being exploited for human settlement and cattle breeding.

Animals↗
PubMed1985

Structural variations in actins. Biochemical and immunological tools for probing the structure of rabbit skeletal-muscle and bovine aortic actins.

Structural differences between skeletal-muscle and aortic actins were studied by using biochemical and immunological approaches. By using proteinase digestion we found that three regions of actin show structural differences: (a) in the C-terminal part, (b) the region around residue 227 and (c) the region around residue 167. By using antibodies specific to particular actin conformations we can discriminate between monomeric and filamentous forms of the two actins. Our results show that the minor sequence variations of the N- and C-terminal regions induce structural change in these regions, but also some long-range structural variations in other regions.

Actins↗
PubMed2025

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.

For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing. Severus works with matching normal samples, supports unbalanced cancer karyotypes, can characterize complex multibreak SV patterns and produces haplotype-specific calls. On a comprehensive multitechnology cell line panel, Severus consistently outperforms other long-read and short-read methods in terms of SV detection F1 score (harmonic mean of the precision and recall). We also illustrate that compared to long-read methods, short-read sequencing systematically misses certain classes of somatic SVs, such as insertions or clustered rearrangements. We apply Severus to several clinical cases of pediatric leukemia/lymphoma, revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

Humans↗
PubMed1984

Antigenic and structural variation in the major nucleocapsid protein of respiratory syncytial virus.

Antigenic and structural variation in the major nucleocapsid protein, VPN41, from different strains of respiratory syncytial (RS) virus was observed using a combination of monoclonal antibodies and two-dimensional peptide mapping. Limited trypsin treatment of intact nucleocapsids produced two peptide fragments Mr 27K and Mr 14K. Two monoclonal antibodies, N1 and N2, reactive with primary sequence epitopes located on intact nucleocapsids also reacted with either the 27K fragment (N2) or the 14K fragment (N1). Competitive radioimmunoassay studies using N1 and N2 antibodies revealed two discrete antigenic groups among the seven human strains of RS virus examined. A bovine strain of RS virus, although antigenically similar to the human strain of RS virus, was placed in a separate group. Two-dimensional peptide mapping of 125I-labelled VPN41 purified by SDS-PAGE revealed extensive structural homology between all strains. However, several unique tryptic/chymotryptic peptides supported the grouping obtained with the monoclonal antibodies.

Animals↗
PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗
PubMed1989

Behavioral responses to novelty and structural variation of the hippocampus in mice. I. Quantitative-genetic analysis of behavior in the open-field.

As a first step towards a multivariate quantitative-genetic analysis of covariations between heritable variation in hippocampal structure and mouse behavior, a univariate analysis of the genetic architecture of behavioral responses to novelty is presented. For several components of exploratory behavior considerable amounts of genetic variation were found and an evolutionary history of stabilizing selection for intermediate levels of exploration was inferred. Comparison of these results with those from a previous study indicated that even a relatively small diallel cross, involving 4-5 inbred strains, may provide useful genetic information on a specific sample of animals. Larger numbers of strains are needed to provide precise estimates of genetic parameters in a population.

Animals↗
PubMed1992

Effects of structural variations on the rates of enzymatic and nonenzymatic hydrolysis of carbonate and carbamate esters.

The effect of structural variations on the rates of elastase-catalyzed hydrolysis of model carbonate and carbamate esters was studied using HPLC. It is shown that branching in the immediate vicinity of the carbonate or carbamate functionally results in decreased hydrolysis rates. Whereas aryl carbonates act as substrates for elastase, p-nitrophenyl butyl carbamate inhibits the enzyme. A novel method was developed for the entrapment and quantitation of 14CO2 produced upon hydrolysis of carbonyl-14C-labeled carbonate esters. This technique could be useful in studying the mechanism of enzymatic hydrolysis of this type of compound and has the potential of being adapted as a convenient method in the assessment of estrolytic activity of tissue homogenates.

Carbamates↗
PubMed1982

Structural variations in the surface zone of human tooth enamel observed by scanning electron microscopy.

The surface zone of human deciduous and permanent enamel was examined following sectioning, polishing and etching. Three main types of surface were where prisms reached the surface, where the prisms were not discernible and those formed by a complex of both types. The aprismatic layers were measured and the percentage of teeth with varying thicknesses at different sample sites was calculated. Thickness of surface aprismatic enamel varied between different tooth types, tooth surfaces and between deciduous and permanent teeth. It is likely that variations in the structure of surface enamel affect caries susceptibility and results of etching and bonding techniques.

Adolescent↗