Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genomic Structural 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.

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

At least 1,711 records · Page 95Linked to original sources
PubMed1987

Theoretical mechanisms for synthesis of carcinogen-induced embryonic proteins: XVIII. Biomethylation and differentiation.

Many reports have appeared describing a direct relationship between hypomethylated states of genes and gene activity. Even after the introduction of viral genomes, these new genes appear to be controlled by specific DNA methylations. A variety of other studies have shown chromatin structural changes being implicated in the activities of certain gene loci. Modifications of chromatin domains may also be initiated or under the control of methylation reactions. Embryonic genes may be controlled by particular methylations by virtue of a differential (hyper-) sensitivity to concentrations of active methyl groups, on a variety of chromatin domains thereby explaining the variation in S-adenosyl-L-methionine synthesis required in developing liver tissue. Also our finding of the ability to manipulate experimentally the activity of the alpha-fetoprotein gene by methyl group availability indicates some methyl-sensitive mechanism is operating with respect to embryonic genes.

Animals↗
PubMed2006

The Immunoglobulin G Heavy Chain (IGHG) genes of the Atlantic bottlenose dolphin, Tursiops truncatus.

Dolphin Immunoglobulin G Heavy Chain (IGHG) sequences were obtained by PCR amplification of cDNA from peripheral blood leukocytes using degenerate primers. Analysis of full-length sequences indicated the presence of two expressed isotypes, IGHG1 and IGHG2 that differ mainly in the hinge region of the molecule. Genomic Southern blot analysis indicated that the IGHG1 and IGHG2 genes are most likely present in single copies. The inferred amino acid sequences show greatest similarity between the dolphin and other closely related artiodactyl species. The genetic structure of the IGHG genes were deduced through genomic PCR and revealed that the hinge regions of both IGHG1 and IGHG2 are encoded by a single exon. The transmembrane region of the dolphin IGHG chain shows similarity to the transmembrane region of other mammalian IGHG chains with a canonical CART motif. This is in contrast to the unusual Ser to Gly substitution previously found in the dolphin IGHM transmembrane region, and the functional significance of this variation for B cell antigen-receptor dimer activation remains unknown.

Amino Acid Sequence↗
PubMed2002

Solution structure of CopC: a cupredoxin-like protein involved in copper homeostasis.

The structure of the metal-free form of CopC, a protein involved in copper homeostasis, has been obtained. The fold is a Greek key beta barrel similar to that of functionally unrelated blue copper proteins but with important structural variations. The protein binds one equivalent of copper (II) with relatively high affinity and contains a cluster of conserved residues (His1, Glu27, Asp89, and His91) which could form a water-accessible metal binding site. The structure also reveals a loop containing the M(X)(n)M motif which is present in a number of proteins also involved in copper homeostasis. The present structure represents a link between copper-trafficking proteins and cupredoxins. Within a structural and genomic analysis, the role of CopC in copper trafficking is discussed.

Amino Acid Sequence↗
PubMed2000

High-throughput sequencing in the population analysis of bacterial pathogens of humans.

High-throughput nucleotide sequence determination technologies present new opportunities for studies of bacterial pathogens by enabling the accumulation of large volumes of biodiversity information from isolate collections. Population studies, which combine these data with epidemiological, phylogenetic, and evolutionary concepts, provide insights into the behaviour of pathogens that are unavailable from other approaches as they address questions of relevance to pathogenesis from the perspective of the infectious organism rather from that of the host. Hypothesis-driven analyses applied to these data permit the determination of microbial population diversity and structure, the identification of the mechanisms of genetic change in bacterial populations, and the generation of models of pathogen evolution. The nucleotide sequence-based population studies performed to date demonstrate a spectrum of nucleotide sequence diversity, population structure, and evolutionary mechanisms among pathogenic bacteria. The rapid development of nucleotide sequence determination and analysis techniques provides the tools necessary for the prosecution of population studies on an increasing number of bacterial pathogens.

Bacteria↗
PubMed2004

Chicken genomics charts a path to the genome sequence.

In this paper, the current status of chicken genomics is reviewed. This is timely given the current intense activity centred on sequencing the complete genome of this model species. The genome project is based on a decade of map building by genetic linkage and cytogenetic methods, which are now being replaced by high-resolution radiation hybrid and bacterial artificial chromosome (BAC) contig maps. Markers for map building have generally depended on labour-intensive screening procedures, but in recent years this has changed with the availability of almost 500,000 chicken expressed sequence tags (ESTs). These resources and tools will be critical in the coming months when the chicken genome sequence is being assembled (eg cross-checked with other maps) and annotated (eg gene structures based on ESTs). The future for chicken genome and biological research is an exciting one, through the integration of these resources. For example, through the proposed chicken Ensembl database, it will be possible to solve challenging scientific questions by exploiting the power of a chicken model. One area of interest is the study of developmental mechanisms and the discovery of regulatory networks throughout the genome. Another is the study of the molecular nature of quantitative genetic variation. No other animal species have been phenotyped and selected so intensively as agricultural animals and thus there is much to be learned in basic and medical biology from this research.

Animals↗
PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗
PubMed1991

Comparison of proteins of simian herpesvirus aotus type 2 and bovine herpesvirus type 4.

Genomes of herpesvirus aotus type 2 (HVA-2) and bovine herpesvirus type 4 (BHV-4) have previously been shown to be closely similar. Moreover, preliminary serological data indicated that HVA-2 is antigenically related to BHV-4. To extend this study, structural components of four BHV-4 strains and HVA-2 were compared by SDS-PAGE, radioimmunoprecipitation and Western blotting. The overall pattern of structural proteins was the same for HVA-2 and BHV-4 but variations were observed in electrophoretic profiles of glycoproteins, mainly of the two major ones (gp6/gp10/gp17 and gp11/VP24). Variations between HVA-2 and BHV-4 glycoproteins were greater than those observed among BHV-4 strains.

Animals↗
PubMed2005

Protein structures forming the shell of primitive bacterial organelles.

Bacterial microcompartments are primitive organelles composed entirely of protein subunits. Genomic sequence databases reveal the widespread occurrence of microcompartments across diverse microbes. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. We report three-dimensional crystal structures of multiple carboxysome shell proteins, revealing a hexameric unit as the basic microcompartment building block and showing how these hexamers assemble to form flat facets of the polyhedral shell. The structures suggest how molecular transport across the shell may be controlled and how structural variations might govern the assembly and architecture of these subcellular compartments.

Amino Acid Sequence↗
PubMed2026

The emergence of putative epistatic mutations and iSNVs in SARS-CoV-2 XBB.1.16 variants linked with alteration in immunogenic determinants.

The SARS-CoV-2 XBB variants have been proposed to evolve towards immune evasion against vaccination or natural infection, which may contribute to higher transmissibility. The XBB.1.16 independently emerged due to accumulation of two important substitutions, E180V and T478R in the spike protein. Its pseudoviral infectivity and evasion of humoral immunity were similar to XBB.1 and XBB.1.5. In March 2023, XBB.1.16 had outcompeted other dominant XBB variants in India, which indicate a potential growth advantage. Here, intra-host single nucleotide variations (iSNV) and mutations were screened in SARS-CoV-2 genomes in closely related individuals at two time points: at symptoms onset, and during recovery. The prominence of putative epistatic iSNVs (E180V, G184V, G252V, D253G, and P521S/T) in XBB.1.16 variants were detected during the recovery phase. E180V exhibits mutational constellations with the G252V and P521T in a subset of samples, and this pattern was also detected in contemporary SARS-CoV-2 genomes. Higher order protein structural predictions suggested that the putative epistatic interactions among E180V, G184V, and G252V, D253G may be associated with S protein folding and structural stability. This study involving genomics and computational analyses highlights the potential role of these putative epistatic interactions in immune evasion, which may have contributed to dominance of XBB variants.

Humans↗
PubMed1992

The human loricrin gene.

Loricrin is the major protein component of the cornified cell envelope of terminally differentiated mammalian epidermal (stratum corneum) cells. Using a specific human cDNA clone, we have isolated and characterized the human loricrin gene. We show that it has a very simple structure of a single intron of 1188 base pairs (bp) in the 5'-untranslated region; there are no introns in coding sequences. By use of rodent-human somatic cell hybrids, followed by in situ hybridization with a biotin-labeled genomic DNA clone, the single-copy gene maps to chromosome location 1q21. Polymerase chain reaction analyses of genomic DNAs from different individuals show that human loricrin consists of two allelic size variants, due to sequence variations in its second glycine loop domain, and these variants segregate in the human population by normal Mendelian mechanisms. Furthermore, there are multiple sequence variants within these two size class alleles due to various deletions of 12 bp (4 amino acids) in the major loop of this glycine loop domain. By use of a specific loricrin antibody, we show by immunogold electron microscopy that loricrin initially appears in the granular layer of human epidermis and forms composite keratohyalin granules with profilaggrin, but localizes to the cell periphery (cell envelope) of fully differentiated stratum corneum cells.

Amino Acid Sequence↗
PubMed2003

[Efficient production of wheat alien translocation lines and characterization by molecular cytogenetics].

The Triticum aestivum-Leymus mollis and T. aestivum-Thinopyrum intermedium translocation lines were induced by gametocidal chromosome 3C derived from Aegilops triuncialis and gamma-ray irradiated pollens of a T. aestivum-Th. intermedium addition line TAI-14 with a lower dosage (10Gy), respectively. By genomic in situ hybridization (GISH) analysis, three T. aestivum-L. mollis translocation lines (WM-10, WM-43 and WM-47) and three deletion lines (WM-18, WM-43 and WM-44) were selected from 59 F2 plants derived from a cross combination of T. aestivum-L. mollis substitution line M8724-8-13 x T. aestivum-Ae. triunicalis 3C chromosome addition line. The frequency of translocation lines produced and total frequency of chromosome structural variation occurred were 5.08% and 8.47%, respectively. Two of the three translocation lines, WM-10 and WM-43 all were heterozygous translocation lines carrying one T. aestivum-L. mollis Robertsonian translocation chromosome, but the translocation chromosome in the two lines were different in morphology. The other one, WM-47 was a double heterozygous translocation with two different translocation chromosomes. By the C-banding, one of the three translocation lines was identified, the translocation chromosome consisted of 7DL of wheat and a chromosome arm of L. mollis. In addition, wheat chromosome deletions were observed in some plants. In another cross combination involved in common wheat and T. aestivum-Th. intermedium addition line, two alien terminal non-Robertsonian translocation lines (WI-21 and WI-68) were identified from 69 F2 plants by C-banding and GISH, and the percentage of translocation line was 2.90%. By C-banding analysis, the translocation chromosomes involved in wheat chromosomes 3A and 4A in the two lines, respectively. These results indicate that inducing wheat alien translocation line by gametocidal chromosome and irradiated pollens all are efficient methods.

Chromosome Banding↗
PubMed1997

[Inhibition of hepatitis C virus by antisense oligodeoxynucleotide in vitro].

OBJECTIVE: To study inhibitory effect of antisense oligodeoxynucleotide (asODN) on HCV in vitro. METHODS: The H9 cells transfected by pCD-HCV, a recombinant HCV containing total HCV structural gene, were treated with two 15-mers phosphorothioate (PS) ODNs complementary (PS-ASON) and homologous (PS-ODN) to HCV core genomic region, which were labeled with digoxin (DIG). Spot blot hybridization was carried out. Treated by the two ODNs, rPS-ODN (a 15-mers PS ODN of random sequence) or PS-ASON were modified with two liposomes (DOTAP and Lipofectin) and calcium phosphate precipitation respectively. With a half-ration, the variation of level of HCV mRNA and HCV antigen expression was observed by RT-PCR and dot ELISA. 3H-TdR adding test was done to observe PS-ASON cytotoxicity. RESULTS: PS-ODN and PS-ASON were detected in the H9 cells. The target gene was hybridized to PS-ASON and PS-ODN labeled with DIG. PS-ASON cut down level of HCV mRNA and HCV antigen expression obviously. However, PS-ODN and rPS-ODN did not influence the level of the both. The time-dependent and dose-dependent inhibition of PS-ASON was observed. In contrast to free PS-ASON, both of liposomal PS-ASON showed more highly effective inhibition, but calcium phosphate precipitation-PS-ASON complex did not. The results showed PS-ASON did not influence the H9 cells growth at 10 mumol/L. CONCLUSION: PS-ASON complementary to HCV core gene is asODN and exerts antisense-inhibitory effect on the level of HCV translation obviously, but not on the level of HCV replication and transcription.

CD4-Positive T-Lymphocytes↗
PubMed2026

EscaPRRS-ORF5: a structure-aware evolutionary framework for prioritizing immune escape-prone variants in porcine reproductive and respiratory syndrome virus.

MOTIVATION: Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a rapidly evolving RNA virus causing significant economic losses, posing a formidable challenge to vaccine efficacy due to its high mutational variability and immune escape. As the viral mutants evolve, their ability to sustain in population is driven by a range of host biology factors such as receptor binding, fusion, and uncoating. Existing tools that predict viral fitness and escape propensities rely heavily on extensive, up-to-date sequence data and lack integration of biochemical host interactions, limiting mechanistic understanding of the mutational landscape. We introduce Esca, a sequence-only toolchain framework that identifies immune escape-prone residues by exhaustively scanning each residue position for all amino acid substitutions using a Bayesian Variational Autoencoder (VAE) trained on protein language model embeddings. We demonstrate Esca on the GP5(ORF5) glycoprotein of PRRSV (EscaPRRS-ORF5) by training on ESM-2 embeddings of 32 146 GP5 sequences (2015-2022) spanning 140 sub-lineages. RESULTS: Despite being trained only on GP5 sequence data, EscaPRRS-ORF5 recovered 85.7% of the surface-exposed receptor binding interfaces as escape-prone regions. We use a mutation-sensitive fitness scoring scheme that goes beyond Hamming distances, to predict antibody escape tendencies, supporting surveillance of (re) emerging PRRSV variants. We do not claim that ORF5 alone captures PRRSV evolution or serves as a surveillance endpoint; rather, Esca offers a scalable path toward whole-genome, structure-aware surveillance. AVAILABILITY AND IMPLEMENTATION: EscaPRRS-ORF5 is freely available at https://doi.org/10.6084/m9.figshare.32661033 with an interactive Colab notebook at https://colab.research.google.com/drive/1TEgzAhPwvNAZ01VXeJbIFibfri2jnDA5? usp=sharing.

Porcine respiratory and reproductive syndrome viru↗
PubMed2005

Identification of inhibitors of the kinase activity of oncogenic V600E BRAF in an enzyme cascade high-throughput screen.

The Cancer Genome Project has identified several oncogenic mutations in BRAF that represent important opportunities for cancer drug discovery. The V600E BRAF mutation accounts for approximately 90% of the mutations identified. A strong case has emerged from molecular, cellular, and structural studies for the identification and development of inhibitors of this mutated BRAF protein. The authors have developed and run a high-throughput screen to find inhibitors of V600E BRAF using an enzyme cascade assay in which oncogenic BRAF activates MEK1, which in turn activates ERK2, which then phosphorylates the transcription factor ELK1. A phosphospecific antibody, Europium-labeled secondary antibody, and a time-resolved fluorescent readout were used to measure phosphorylation of ELK1. Overall assay variation was 12.4%. The assay was used to screen 64,000 compounds with an overall Z' factor of 0.58 +/- 0.12. A series of 3,5, di-substituted pyridines were identified as inhibitors of the cascade assay. These compounds did not inhibit a shortened activated MEK1 to ELK1 cascade but were active (0.5-27.9 microM) in a V600E BRAF assay and represent a potential starting point for future drug discovery and development.

Drug Evaluation, Preclinical↗
PubMed2003

Relationships in Ananas and other related genera using chloroplast DNA restriction site variation.

Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera. One hundred fifteen accessions representing the seven Ananas species and seven other Bromelioideae including the neighboring monospecific genus Pseudananas, two Pitcairnioideae, and one Tillandsioideae were included in the study. Eight primers designed from cpDNA were used for generating fragments. Restriction by 18 endonucleases generated 255 variable fragments. Dissimilarities were calculated from the resulting matrix using the Sokal and Michener index and the neighbor-joining method was used to reconstruct the diversity tree. Phylogenetic reconstruction was attempted using Wagner parsimony. Phenetic and cladistic analyses gave consistent results. They confirm the basal position of Bromelia in the Bromelioideae. Ananas and Pseudananas form a monophyletic group, with three strongly supported sub-groups, two of which are geographically consistent. The majority of Ananas parguazensis accessions constitute a northern group restricted to the Rio Negro and Orinoco basins in Brazil. The tetraploid Pseudananas sagenarius joins the diploid Ananas fritzmuelleri to constitute a southern group. The third and largest group, which includes all remaining species plus some accessions of A. parguazensis and intermediate phenotypes, is the most widespread and its distribution overlaps those of the northern and southern groups. Ananas ananassoides is dominant in this sub-group and highly variable. Its close relationship to all cultivated species supports the hypothesis that this species is the wild ancestor of the domesticated pineapple. The data indicate that gene flow is common within this group and scarcer with both the first and second groups. Comparison of cpDNA data with published genomic DNA data point to the hybrid origin of Ananas bracteatus and support the autopolyploidy of Pseudananas. The Ananas-Pseudananas group structure and distribution are consistent and we propose a scenario based on the refugia hypothesis to explain our data. These results and hypotheses bring some interesting points to consider in the current discussion on Ananas taxonomy.

Bromeliaceae↗
PubMed2002

Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana.

Higher plants possess a large set of the classical guaiacol peroxidases (class III peroxidases, E.C. 1.11.1.7). These enzymes have been implicated in a wide array of physiological processes such as H(2)O(2) detoxification, auxin catabolism and lignin biosynthesis and stress response (wounding, pathogen attack, etc.). During the last 10 years, molecular cloning has allowed the isolation and characterization of several genes encoding peroxidases in plants. The achievement of the large scale Arabidopsis genome sequencing, combined with the DNA complementary to RNA (cDNA) expressed sequence tags projects, provided the opportunity to draw up the first comprehensive list of peroxidases in a plant. By screening the available databases, we have identified 73 peroxidase genes throughout the Arabidopsis genome. The evolution of the peroxidase multigene family has been investigated by analyzing the gene structure (intron/exon) in correlation with the phylogenetic relationships between the isoperoxidases. An evolutionary pattern of extensive gene duplications can be inferred and is discussed. Using a cDNA array procedure, the expression pattern of 23 peroxidases was established in the different organs of the plant. All the tested peroxidases were expressed at various levels in roots, while several were also detected in stems, leaves and flowers. The specific functions of these genes remain to be determined.

Arabidopsis↗
PubMedDate not supplied

[Genomic study of the hereditary pathology and genetic diversity of the Siberian population].

The review considers the results of genome research on the Russian program Human Genome carried out in the Institute of Medical Genetics (Tomsk) from 1990. The three major fields were molecular cytogenetics and chromosomal disorders, genomics of Mendelian and high-incidence diseases, and ethnogenomics of the North Asian population. Several human genes were cytogenetically mapped, and numerical and structural abnormalities associated with human diseases studied by fluorescence hybridization. Procedures of DNA diagnostics were developed for 15 hereditary diseases. New data were obtained on genetic heterogeneity of idiopathic hypertrophic cardiomyopathy. The genetic bases of multifactorial (atopic bronchial asthma) and infectious (tuberculosis) diseases were analyzed. The North Eurasian population (41 local populations of 21 ethnic groups) was tested for genetic diversity with numerous genetic markers, including Y-chromosomal haplotypes, autosomal microsatellites, and polymorphic Alu insertions.

Ethnicity↗
PubMed1996

Analysis of the murine Dtk gene identifies conservation of genomic structure within a new receptor tyrosine kinase subfamily.

The receptor tyrosine kinase Dtk/Tyro 3/Sky/rse/brt/tif is a member of a new subfamily of receptors that also includes Axl/Ufo/Ark and Eyk/Mer. These receptors are characterized by the presence of two immunoglobulin-like loops and two fibronectin type III repeats in their extracellular domains. The structure of the murine Dtk gene has been determined. The gene consists of 21 exons that are distributed over 21 kb of genomic DNA. An isoform of Dtk is generated by differential splicing of exons from the 5' region of the gene. The overall genomic structure of Dtk is virtually identical to that determined for the human UFO gene. This particular genomic organization is likely to have been duplicated and closely maintained throughout evolution.

Alternative Splicing↗