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PubMed1979

Cis-active control of mouse beta-galactosidase biosynthesis by a systemic regulatory locus.

Several higher organisms have been reported in which enzyme levels are determined genetically by sites located in close proximity to the corresponding structural genes. In several cases, these sites have been shown to act by controlling the rates of enzyme synthesis. Cis compared with trans action has been tested for those proximate regulatory sites controlling enzymes for which appropriate structural variants exist. The rate of synthesis of beta-galactosidase in mouse tissues is under the control of a regulatory locus; Bgl-s, that is tightly linked to the enzyme structural gene; we have tested the cis/trans nature of Bgl-s action by analysis of the electrophoretic mobility of the enzyme from animals heterozygous for the appropriate regulatory and structural alleles. Our results indicate that Bgl-s acts cis, controlling the expression of the structural gene located on the same chromosome.

Animals↗
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 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↗
PubMed2003

Structural studies on the lipopolysaccharide core of Proteus OX strains used in Weil-Felix test: a mass spectrometric approach.

The core region of the lipopolysaccharides of Proteus group OX bacteria, which are used as antigens in Weil-Felix test for serodiagnosis of rickettsiosis, were studied by chemical degradations in combination with ESI FTMS, including infrared multi-photon dissociation (IRMPD) MS/MS and capillary skimmer dissociation. Structural variants of the inner core region were found to be the same as in Proteus non-OX strains that have been studied earlier. The outer core region has essentially the same structure in Proteus vulgaris OX19 (serogroup O1) and OX2 (serogroup O2) and a different structure in Proteus mirabilis OXK (serogroup O3). A fragmentation due to the rupture of the linkage between GlcN or GalN and GalA was observed in IRMPD-MS/MS of core oligosaccharides and found to be useful for screening of Proteus strains to assign structures of the relatively conserved inner core region and to select for further studies strains with distinct structures of a more variable outer core region.

Carbohydrate Sequence↗
PubMed1998

Complex serology and immune response of mice to variant high-molecular-weight O polysaccharides isolated from Pseudomonas aeruginosa serogroup O2 strains.

The O antigen of the Pseudomonas aeruginosa lipopolysaccharide is the optimal target for protective antibodies, but the unusual and complex nature of their sugar substituents has made it difficult to define the range of these structures needed in an effective vaccine. Most clinical isolates of P. aeruginosa can be classified into 10 O-antigen serogroups, but slight chemical differences among O polysaccharides within a serogroup give rise to subtype epitopes. These epitopes could impact the reactivity of O-antigen-specific antibodies, as well as the susceptibility of a target strain to protective, opsonic antibodies. To define parameters of serogroup and subtype-epitope immunogenicity, antigenicity, and surface expression on P. aeruginosa cells, we prepared high-molecular-weight O-polysaccharide vaccines from strains of P. aeruginosa serogroup O2, for which eight structurally variant O antigens expressing six defined subtype epitopes (O2a to O2f) have been identified. A complex pattern of immune responses to these antigens was observed following vaccination of mice. The high-molecular-weight O polysaccharides were generally more immunogenic at low doses (1 and 10 microg) than at a high dose (50 microg) and usually elicited antibodies that opsonized the homologous strain for phagocytic killing. Some of the individual polysaccharides elicited cross-opsonic antibodies to a variable number of strains that express all of the defined serogroup O2 subtype epitopes. Combination into one vaccine of two antigens that individually elicited cross-reactive opsonic antibodies to most members of the O2 serogroup inhibited, instead of enhanced, the production of antibodies broadly reactive with most serogroup O2 subtype strains. Thus, immune responses to P. aeruginosa O antigens may be restricted to a limited range of epitopes on structurally complex O antigens, and combining multiple related antigens into a single vaccine formulation may inhibit the production of those antibodies best able to protect against most P. aeruginosa strains within a given O-antigen serogroup.

Animals↗
PubMed2024

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.

The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.

Humans↗
PubMed1996

Variant TCR ligands: new insights into the molecular basis of antigen-dependent signal transduction and T-cell activation.

Recent studies have identified peptide-MHC molecule ligands of alpha beta T-cell receptors with properties apparently distinct from classical agonists. These complexes, which are slight structural variants of the immunizing peptide or original presenting MHC molecule, have several novel properties. They can act as partial agonists able to induce only some and not other effector activities of the T cell, as antagonists able to inhibit T-cell functions stimulated by agonist ligand, or as mixed partial agonists/antagonists. Here we discuss the existing data suggesting that a simple receptor occupancy model does not account for the properties of these TCR ligands and review emerging data on qualitative differences in signal transduction following TCR engagement by priming versus variant complexes. We propose several non-exclusive models to explain both the biochemical and biological properties of variant ligands with partial agonist or antagonist properties.

Animals↗
PubMed1999

Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana.

Linker histones (e.g. H1, H5, H1 degrees ) are thought to exert control on chromatin function by restricting nucleosomal dynamics. All higher eukaryotes possess a diverse family of linker histones, which may exhibit functional specialization. Arabidopsis thaliana apparently contains a minimal complement of linker histone structural variants and therefore is an ideal model for investigating functional differentiation among linker histones. Histones H1-1 and H1-2 are relatively similar proteins that are expressed in a wide variety of tissues and make up the majority of linker histone while H1-3 is a highly divergent minor variant protein that is induced by drought stress. We are interested in determining whether the in vivo distribution of each of these proteins also differs. To this end, we have produced subtype-specific antibodies and have localized each of the three proteins at the intranuclear and DNA sequence levels by indirect immunofluorescence and immunoprecipitation, respectively. Antibodies against linker histones H1-1 and H1-2 decorate nuclei in patterns very similar to 4',6-diamidino-2-phenylindole (DAPI) staining, but different than the staining pattern of total histones. In contrast, antibodies made against two regions of H1-3 bind to chromatin in a diffuse pattern distinct from the DAPI-staining pattern. We also describe a technique to determine the localization of plant linker histone variants along regions of chromatin, employing in vivo chemical DNA-protein cross-linking to preserve native associations followed by immunoprecipitation with subtype-specific antibodies. We use this technique to demonstrate that, in contrast to the major linker histones, H1-3 does not bind the repetitive sequences pAL1 and 5S rDNA. In addition, we show that linker histones are bound to the compacted nucleosomal arrays at the telomere but with reduced stoichiometry. Taken together, our results suggest that plants, as has been shown for animals, possess a variant linker histone that is differentially localized.

Antibody Specificity↗
PubMed2005

Targeting carbohydrate antigens in HIV vaccine development.

Peptide mimotopes provide a strategy to augment human immunodeficiency virus 1 (HIV-1) specific carbohydrate reactive immune responses. Their antigenic and immunological properties will depend on the optimization of motif clustering and multimerization. We observe that structural variants of the same mimetic motif, linear versus cyclic, can be used to tune the properties of the antibodies elicited. The expansion of the database of mimotope sequence motifs can be increased by analyzing structures that bind to HIV directed monoclonal antibody 2G12 and the lectin Concanavalin A (Con A), fostering new mimotope designs. Such analysis indicates that these reagents bind to subsets of mannosyl antigens on the envelope (env) protein.

AIDS Vaccines↗
PubMed1987

Evolution of antibody variable region structure during the immune response.

The results reviewed above reveal that during the anti-Ars immune response of strain A mice a somatic process that results in the evolution of V region structure occurs. This process involves both the selection of V regions encoded by particular gene segment combinations as well as the selection of structural variants of these V regions produced by somatic mutation as the immune response progresses. As a result, both quantitative and qualitative changes in the V region population initially elicited by immunization take place. The structural and functional character of the immune V region repertoire appears to be largely determined by this process of "somatic evolution" occurring in the primary response.

Animals↗
PubMed2003

The karyotypic structure of cell populations in vitro as an integral system.

This review describes regularities of karyotypic variability maintaining karyotypic stabilization of continuous cell lines. Statistical analysis of individual karyotypes of "marker" and "markerless" cell lines show that survival of cell population in vitro is maintained by a certain ratio of cells with different structural variants of karyotype (SVK). Characteristic feature of karyotypic variability in the "markerless" cell lines during long-term cultivation under various conditions is dicentric formation due to telomeric associations. These dicentrics seem to form genetical structures providing adaptation to conditions in vitro of the cell population as an autonomous system. Correlations between the numerical variability reflecting in SVK, and structural variability (dicentric formation) are manifestations of an integral cell-populational function. Experimental data allow to suggest that integrity of the karyotypic structure of cell populations is maintained not only by selection of random variations, but also by programmed (adaptive) changes of karyotype. As a whole, in the cell population the state is realized that can be called karyotypic homeostasis; the observed phenomena characterize processes maintaining such homeostasis.

Adaptation, Physiological↗
PubMed1998

Structural and molecular studies of human chorionic gonadotropin and its receptor.

Human chorionic gonadotropin (hCG) is a placental hormone that stimulates secretion of the pregnancy-sustaining steroid progesterone. It and other glycoprotein hormones are disulfide-rich heterodimers that share a common alpha chain and distinctive beta chains specific to their particular G protein-linked receptors. We determined the structure of partially deglycosylated hCG at 2.6 A resolution from multiwavelength anomalous diffraction (MAD) measurements of a selenomethionyl hCG crystal. We have also begun three- and four-dimensional structural studies on the biologically active hormone and have determined the structure of the carbohydrate attached to the alpha-subunit. Despite little sequence similarity limited to 10% identity, the alpha and beta subunits of hCG maintain strikingly similar tertiary folds, with cystine-knot motifs at cores of extended hairpin loops. Structural and sequence comparisons indicate an evolutionary homology between the glycoprotein hormone chains and other cystine-knot proteins, notably PDGF, TGF-beta, and NGF. This structural similarity has led us to speculate that early hCG secretion has a broader role than solely the stimulation of the corpus luteum; indeed, levels of hCG, which rise rapidly in the circulation after implantation, are greater than the levels necessary for corpus luteum function. One such role of hCG or its subunits could be as a growth factor that facilitates endometrial receptivity. Our studies of hCG have also identified structural variants, notably in the carbohydrate moiety, that are distinctive for patients with a variety of disorders of pregnancy, including hydatidiform mole and choriocarcinoma. We have also focused our efforts on using information gleaned from the structure of hCG for the design of drug-like molecules that might serve as either agonists or antagonists of hCG. To facilitate these experiments, we have designed a rapid screen for the identification of molecules that might bind the hCG receptor by identifying compounds that disrupt binding of hCG to its receptor. This screen employs a filamentous phage that displays the extracellular domain of the hCG receptor on its surface. Thus far, we have identified a few compounds that disrupt binding of hCG with its receptor at a concentration of approximately 1 micromolar. These "lead" molecules are currently being modified in an attempt to identify a molecule that can disrupt binding of hCG at nanomolar concentrations.

Amino Acid Sequence↗
PubMed2026

A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.

Structural variants (SVs) are increasingly recognized as key contributors to adaptive evolution, yet they remain underexplored compared with single-nucleotide variation. To understand how large-scale genomic changes shape repeated evolution, we leveraged multiple levels of sequence data across the powerful evolutionary model system of the Mexican tetra fish (Astyanax mexicanus). We constructed one of the first pangenome graphs from a naturally evolving vertebrate, enabling comprehensive discovery of SVs among 120 fish from 11 populations. We discover substantial amounts of structural variation and explore the roles of genomic biases and selection in shaping the distribution of these variants. More than 2400 high-confidence cave-specific deletions are enriched in biological pathways involved in vision, metabolism, and behavior and cluster nonrandomly in quantitative trait loci linked to cavefish traits. Additionally, 67 genes harbor unique deletions between independent cavefish lineages. These reused genes show evidence of population-specific selection (99% contain selective sweeps compared with 8%-15% in genes lacking SVs), indicating that deletions likely rose in frequency through repeated positive selection rather than drift. Together, these results reveal that recurrent deletion events have repeatedly contributed to the evolution of cave-adapted phenotypes and highlight deletions as underexplored contributors of adaptive evolution in extreme environments.

Animals↗
PubMed2002

A novel CD28 mRNA variant and simultaneous presence of various CD28 mRNA isoforms in human T lymphocytes.

The primary transcript of the human CD28 gene in T lymphocytes, encoding for a costimulatory molecule, is known to undergo alternative splicing, and different small sets of variant isoforms have been reported. This report presents the novel simultaneous presence of eight different mRNA isoforms, all observed together in normal human T cells; this is an interesting finding in the study of CD28 mRNA structural variants. A similar pattern was found in a total of four individuals. In addition, we also report the occurence and sequence of a new CD28 mRNA isoform, one of the above eight, which is a novel variant generated by the use of a new combination of splice donor and acceptor sites.

Alternative Splicing↗
PubMed2026

Architectural logic of the 3D genome: mechanisms of dysregulation and emerging cancer therapeutics.

The three-dimensional (3D) genome provides an essential layer of organization that shapes genome function in space and time. Chromatin compartments and topologically associating domains (TADs) arise from the interplay between intrinsic properties of chromatin and architectural factors, including cohesin and CTCF. Despite substantial progress in defining these structural features, whether 3D genome architecture plays a causal role in regulating processes such as transcription, DNA replication, and DNA repair, or instead reflects underlying regulatory activity, remains unresolved. Here, we use the distinction between chromatin-intrinsic features and architectural factors as a framework to evaluate evidence for causality in genome structure-function relationships. We extend this framework to cancer, where both intrinsic alterations (including noncoding mutations, structural variants, and changes in chromatin state) and architectural factor perturbations (such as mutations in architectural proteins and dysregulation of transcriptional machinery) disrupt genome organization and contribute to disease progression. These findings suggest that alterations in genome structure can, in some contexts, actively reshape oncogenic programs. A major limitation in applying 3D genome insights to cancer biology is the cost and complexity of omics assays. Recent advances in artificial intelligence (AI) and machine learning (ML) enable inference and prediction of 3D genome organization from sequence and epigenomic features, providing insight into the extent to which genome folding is encoded intrinsically versus dynamically regulated in architectural factors. This perspective provides a unified view of how genome structure is established, how it relates to function, and how its disruption contributes to tumorigenesis.

3D genome↗
PubMed2026

Idiopathic neonatal arterial ischaemic stroke: a trio-based whole-exome sequencing study.

OBJECTIVE: To assess the contribution of rare coding genetic variants to idiopathic neonatal arterial ischaemic stroke (NAIS). DESIGN: Observational genetic study using trio-based whole-exome sequencing (WES). SETTING: Multicentre study. PATIENTS: 23 newborns diagnosed with idiopathic NAIS and their biological parents. INTERVENTIONS: WES-trio with a customised workflow for filtering and interpreting variants in de novo autosomal dominant and recessive inheritance models. MAIN OUTCOME MEASURES: Identification of pathogenic (P) or likely pathogenic (LP) variants potentially associated with NAIS. RESULTS: We identified 28 unique rare de novo variants in 28 genes across 23 newborns with NAIS. Under the autosomal recessive model, no candidate genes were identified. No common P/LP variant across the 23 newborns was detected. In-silico predictors and comprehensive knowledge-driven analysis highlighted PIK3CD (p.Gln431Arg) as a candidate gene in one patient with perforant stroke. However, no more cases were identified with PIK3CD variants, and functional studies are warranted to assess its pathogenicity impact. CONCLUSIONS: Trio-based WES did not identify a monogenic cause for idiopathic NAIS. Coding variants therefore appear unlikely to explain the underlying genetic base of the disease. Furthermore, PIK3CD (p.Gln431Arg) may contribute to perforant stroke, although it requires further association evidence. As the potential role of non-coding or structural variants in NAIS remains possible, genome-wide long-read sequencing approaches may provide further insights into the genetic architecture of this condition.

Humans↗
PubMed2006

Transmission electron microscopy and theoretical analysis of AuCu nanoparticles: atomic distribution and dynamic behavior.

Though the application of bimetallic nanoparticles is becoming increasingly important, the local atomistic structure of such alloyed particles, which is critical for tailoring their properties, is not yet very clearly understood. In this work, we present detailed study on the atomistic structure of Au-Cu nanoparticles so as to determine their most stable configurations and the conditions for obtaining clusters of different structural variants. The dynamic behavior of these nanoparticles upon local heating is investigated. AuCu nanoparticles are characterized by high resolution transmission electron microscopy (HRTEM) and energy filtering elemental composition mapping (EFECM), which allowed us to study the internal structure and the elemental distribution in the particles. Quantum mechanical approaches and classic molecular dynamics methods are applied to model the structure and to determine the lowest energy configurations, the corresponding electronic structures, and understand structural transition of clusters upon heating, supported by experimental evidences. Our theoretical results demonstrate only the core/shell bimetallic structure have negative heat of formation, both for decahedra and octahedral, and energetically favoring core/shell structure is with Au covering the core of Cu, whose reverse core/shell structure is not stable and may transform back at a certain temperature. Experimental evidences corroborate these structures and their structural changes upon heating, demonstrating the possibility to manipulate the structure of such bimetallic nanoparticles using extra stimulating energy, which is in accordance with the calculated coherence energy proportions between the different configurations.

Alloys↗
PubMed1980

[Structure and biological properties of immunoglobulins and gamma-globulin preparations. I. Structure and function of immunoglobulins].

Antibodies serve two different functions: they bind antigens and mediate a series of other functions party as a consequence of antigen binding. These functions are usually termed effector functions. This functional dualism is reflected in the structural arrangement of the immunoglobulin molecules, the basic structure of which consists of 4 polypeptide chains: 2 identical light chains (molecular weight 22 000--23 000) and 2 identical heavy chains (molecular weight 50 000--70 000). These polypeptide chains may be divided into compact globular regions, which are called domains and have different biological functions. The domains which are involved in antigen binding consist of the 110--120 aminoterminal amino acid residues of heavy and light chains. The amino acid sequence within these domains differs from one immunoglobulin molecule to another, and for this reason they are designated variable domains. The remaining domains are of substantially the same structure within groups of immunoglobulins and are therefore called constant domains. The structural variants within the constant domains of the heavy chains are termed classes and subclasses, and those of the light chains, types. The constant domains of the heavy chains mediate the effector functions of the immunoglobulin molecules. This structural division into a variable and a constant part allows the combination of a great number of different antigen binding specifities with a series of different effector functions.

Humans↗
PubMed1998

A functionally deficient DRD2 variant [Ser311Cys] is not linked to alcoholism and substance abuse.

Association studies with the DRD2 Taq1A marker have been variable in implicating DRD2 as a "Reward Deficiency Syndrome Gene" for alcoholism and substance abuse. Given that the Taq1A marker is not functionally significant, second-generation studies on the DRD2 receptor to identify functional variants and evaluate their effect on the phenotype are the logical step towards confirming and extending the DRD2 hypothesis. This article discusses the implications and process of progress made in these directions. The new findings are the description of structural variants in the D2 receptor, the demonstration that one of these, Ser311Cys, largely prevents signal transduction following receptor activation and the use of Ser311Cys in a large association and sib-pair linkage anlysis in an American Indian isolate. In this particular population, the Cys311 variant is far more abundant (0.16) than in Caucasians (0.03). Genotyping of Ser311Cys, the DRD2 intron 2 STR, and the Taq1A marker in 459 subjects, including 373 sib-pairs and 15 Cys311/Cys311 homozygous individuals, revealed no association to alcoholism, substance use disorders, or schizophrenia. The implication is that a DRD2 variant that dramatically impairs receptor function was not sufficient to significantly alter alcoholism vulnerability in a relatively large and also genetically and environmentally homogeneous sample.

Alcoholism↗