Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural variants”

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 1,297 records · Page 72Linked to original sources
PubMed1984

Use of a synthetic oligonucleotide to identify a chromosomal gene for chloramphenicol acetyltransferase in a plasmid-bearing Flavobacterium.

A micro-organism previously designated Flavobacterium sp. CB60 is resistant to chloramphenicol as a consequence of antibiotic acetylation by the enzyme chloramphenicol acetyltransferase and subsequent degradation of the acetylated product by co-metabolism. Although a 15.6 kb plasmid (pCB60) was demonstrated in this Flavobacterium strain, it did not appear to play a role in chloramphenicol acetylation. DNA hybridization was used to identify a fragment of DNA presumptively carrying the cat gene. The sequence of the synthetic probe was based upon known nucleotide sequences corresponding to the highly-conserved active site region of several chloramphenicol acetyltransferase variants. The structural gene for the enzyme in strain CB60 appeared to be chromosomal since the radioactive probe hybridized with a unique restriction fragment from chromosomal DNA but failed to do so with the DNA of plasmid pCB60.

Acetyltransferases↗
PubMed1988

Stability of plasmid sequences in an acute Q-fever strain of Coxiella burnetii.

The rickettsial pathogen Coxiella burnetii undergoes a variation in which virulent isolates (phase 1) become avirulent (phase 2) after repeated passage in a non-immunologically competent host. Biochemically, this variation is associated with a lipopolysaccharide modification and possibly other factors. Genetically, the regions of DNA responsible for phase variation have not been identified. We have sought to determine whether the plasmid identified in acute disease isolates, QpH1, which represents approximately 5% of the coding capacity of this organism is involved in phase variation. Plasmids from phase 1 and phase 2 variants (designated QpH1 and QpH2, respectively) were compared by restriction endonuclease digestion and Southern blot hybridization to determine whether sequence changes in the phase 2 plasmid might account for changes in the virulence of phase 2 organisms compared with that of phase 1 cells. Using over 20 different restriction enzymes, no changes in DNA restriction fragment patterns were detected regardless of whether the phase change occurred during egg or tissue culture passage. The plasmid-specific mRNAs produced from metabolically active, purified cells were identical for each phase type. Using QpH1 or QpH2 DNA as a template, the mRNA produced by an E. coli extract was also identical. Finally, the proteins encoded by either plasmid in an in vitro transcription/translation reaction were identical. These data indicate that within the limits of our analysis, the plasmid DNA from C. burnetii phase variants is structurally and functionally the same and is therefore unlikely to be involved in phase variation.

Base Sequence↗
PubMed2003

The Arabidopsis basic/helix-loop-helix transcription factor family.

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.

Amino Acid Sequence↗
PubMed1994

Cross-reactivity and neutralizing ability of monoclonal antibodies against microcystins.

Monoclonal antibodies (MAbs) against the microcystin-leucine-arginine variant (MCYST-LR), a cyclic peptide toxin of the freshwater cyanobacterium Microcystis aeruginosa, were prepared from cloned hybridoma cell lines. The specificity of the MAbs and their ability to neutralize the toxin were investigated by an indirect enzyme-linked immunosorbent assay (ELISA) and by a neutralizing test in mice, respectively. All MAbs reacted with MCYST-LR and also with the microcystin-arginine-arginine variant (MCYST-RR), 3,7-didesmethylmicrocystin (MCYST-3, 7-dDMLR) and 7-desmethylmicrocystin (MCYST-7-DMLR). Furthermore, the antibodies reacted with cell-extracts of toxic and non-toxic M. aeruginosa strains. The MAbs can apparently recognize the common configuration, but not the variant-specific structure, in the microcystin molecules. The non-toxic strains apparently contain some substance(s) related antigenically to microcystin. The in vivo toxin-neutralizing ability of MAbs was minimal.

Animals↗
PubMed2004

Molecular diagnosis of haemoglobin disorders.

The haemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassaemias) or the synthesis of a structurally abnormal haemoglobin (Hb). In prevalent regions, the thalassaemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and haematological phenotypes. An appreciation of these phenotypes is needed to facilitate the definitive diagnosis of the causative mutations to inform management and counselling. Haematological and biochemical investigations, and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. With the exception of a few rare deletions and rearrangements, the molecular lesions causing haemoglobinopathies are all identifiable by PCR-based techniques. Although a full spectrum of >1000 mutations causing haemoglobinopathies has been documented, in practice only a limited number are associated with disease states and clinical significance. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassaemia mutations. Prior identification of the ethnic origin is thus an important part of the diagnostic strategy which becomes less reliable in the UK because of the large ethnic mix. Although the current approach using a combination of different PCR-based techniques seems to work in most laboratories, practice pressures with the imminent implementation of universal antenatal screening for clinically significant Hb disorders in the UK will require a higher throughput approach for DNA diagnostics in the near future. The complex mutational spectrum and the compactness of the globin genes places them in an ideal position for the different non-gel based analytical platforms.

Anemia, Sickle Cell↗
PubMed1978

Forssman glycolipid variants of dog gastric mucosa. Structure of a branched ceramide octasaccharide.

A fucose-containing ceramide octasaccharide exhibiting Forssman antigenic activity, and reacting in human H anti-H and anti-A systems, was isolated from water-soluble glycolipids of dog gastric mucosa. Defucosylation of the glycolipid resulted in the loss of H-activity, but had no effect on its Forssman nor blood-group A antigenic activity. The branched structure of glycolipid was identified by partial acid hydrolysis, sequential degradation with specific glycosidases and comparison of the permethylation products of the native and enzyme-degraded compound. The structure of this glycolipid is proposed to be: formula.

Animals↗
PubMed1996

No association of the structural dopamine D2 receptor (DRD2) variant 311Cys with alcoholism.

The human dopamine D2 receptor (DRD2) has been implied in the vulnerability for alcoholism and/or the modification of its severity. This is supported through animal experimental and pharmacological data. We analyzed the DRD2 311Ser/Cys polymorphism in 312 German alcoholics and 131 ethnically matched controls to investigate the association of genetic DRD2 variants with alcoholism or clinical characteristics of homogeneous subgroups of alcoholics. We observed no association between the 311Cys variant and alcoholism, and none of the clinical characteristics evaluated was significantly associated with 311Cys. The allele frequencies of the 311Cys variant were 0.026 and 0.031 in the alcoholics and controls, respectively. These are the highest reported 311Cys frequencies in Caucasians. The DRD2 TaqI A1/A2 restriction fragment length polymorphism was analyzed simultaneously in our samples. In most cases, the 311Cys allele is associated with the TaqI A2-allele. Data do not suggest a clinical relevance of the 311Cys variant in alcoholism. However, the relevance of this variant in other diseases or the existence of other DRD2 variants with altered receptor function or expression cannot be excluded.

Adult↗
PubMed1998

Identification and recombinant expression of a Mycobacterium avium rhamnosyltransferase gene (rtfA) involved in glycopeptidolipid biosynthesis.

The Mycobacterium avium complex is a source of disseminated infections in patients with advanced AIDS. This group of mycobacteria is distinguished by the presence of highly antigenic, surface-exposed glycopeptidolipids, and these glycolipids possess variant oligosaccharide structures that are the chemical basis of the 28 distinct serovars of the M. avium complex. We previously described the ser2 gene cluster, encoding the synthesis of the haptenic oligosaccharide (2, 3-dimethylfucose-rhamnose-6-deoxytalose-) of the serovar 2-specific glycopeptidolipid, and revealed a locus (ser2A) encoding a putative rhamnosyltransferase. Sequencing of the ser2A locus demonstrated the presence of three open reading frames, two of which yielded significant homology to several glycosyltransferases, and the deduced amino acid sequences of these two putative glycosyltransferases had 63% identity. These two genes were expressed in Mycobacterium smegmatis, and the resulting recombinant glycopeptidolipids were characterized by thin-layer chromatography and gas chromatography-mass spectrometry. These analyses demonstrated that only one of these genes, termed rtfA, encoded the rhamnosyltransferase responsible for the transfer of rhamnose to 6-deoxytalose. The identification of rtfA will permit further evaluation of glycopeptidolipid biosynthesis and the construction of isogenic mutants of multiple M. avium complex serovars. Moreover, such mutants will help define the role of glycopeptidolipids in the intracellular survival of these bacteria.

Bacterial Proteins↗
PubMed1981

Epstein-Barr virus membrane antigens: characterization, distribution, and strain differences.

The Epstein-Barr virus (EBV)-associated membrane antigen polypeptides (350,000, 220,000, 140,000, and 85,000 daltons) are recognized by a rabbit anti-EBV serum and are present on the plasma membranes of producer cell lines, as we demonstrated previously. In this report, we show that these polypeptides are present on intact virus particles. Subcellular fractionation revealed that these antigens are distributed throughout the cell, except for the 85,000-dalton protein, which was poorly represented in the nuclear fraction. In addition, an EBV-associated protein of 160,000 daltons, which comigrates with a major component of the viral capsid, was detected in the cytoplasmic and nuclear fractions. The immunoprecipitation patterns of 13 different EBV isolates were similar, with two exceptions. First, the 350,000- and 220,000-dalton polypeptides from marmoset cell lines had slightly larger molecular sizes than the corresponding polypeptides from human cell lines. Second, B95-8 virus and B95-8-derived human and marmoset cell lines contained little of the 220,000-dalton protein; however, 883L, the human parent line of B95-8, has a normal amount of the 220,000-dalton protein. Thus, the B95-8 strain of EBV appears to be a structurally defective variant. We have not observed any variation in protein patterns associated with different EBV disease states. The 350,000-, 220,000-, and 85,000-dalton polypeptides were shown to be glycoproteins by incorporation of [3H]mannose and [3H]glucosamine and to contain N-asparagine-linked glycosyl groups by their sensitivity to tunicamycin. To simplify future work, the following nomenclature for these EBV-associated polypeptides is suggested: 350,000 (gp350), 220,000 (gp220), 160,000 (p160), 140,000 (p140), and 85,000 (gp85).

Animals↗
PubMed1987

Computer-assisted analysis of envelope protein sequences of seven human immunodeficiency virus isolates: prediction of antigenic epitopes in conserved and variable regions.

Independent isolates of human immunodeficiency virus (HIV) exhibit a striking genomic diversity, most of which is located in the viral envelope gene. Since this property of the HIV group of viruses may play an important role in the pathobiology of the virus, we analyzed the predicted amino acid sequences of the envelope proteins of seven different HIV strains, three of which represent sequential isolates from a single patient. By using a computer program that predicts the secondary protein structure and superimposes values for hydrophilicity, surface probability, and flexibility, we identified several potential antigenic epitopes in the envelope proteins of the seven different viruses. Interestingly, the majority of the predicted epitopes in the exterior envelope protein (gp120) were found in regions of high sequence variability which are interspersed with highly conserved regions among the independent viral isolates. A comparison of the sequential viral isolates revealed that changes concerning the secondary structure of the protein occurred only in regions which were predicted to be antigenic, predominantly in highly variable regions. The membrane-associated protein gp41 contains no highly variable regions; about 80% of the amino acids were found to be conserved, and only one hydrophilic area was identified as likely to be accessible to antibody recognition. These findings give insight into the secondary and possible tertiary structure of variant HIV envelope proteins and should facilitate experimental approaches directed toward the identification and fine mapping of HIV envelope proteins.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Tyrosine phosphorylation of a 120-kilodalton pp60src substrate upon epidermal growth factor and platelet-derived growth factor receptor stimulation and in polyomavirus middle-T-antigen-transformed cells.

The monoclonal antibody 2B12 is directed toward p120, a 120-kDa cellular protein originally identified as a protein tyrosine kinase substrate in cells expressing membrane-associated oncogenic variants of pp60src. In this report, we show that p120 was tyrosine phosphorylated in avian cells expressing membrane-associated, enzymatically activated variants of c-src, including variants having structural alterations in the src homology regions 2 and 3. In contrast, p120 was not tyrosine phosphorylated in cells expressing enzymatically activated, nonmyristylated pp60src. Furthermore, p120 was tyrosine phosphorylated in avian cells expressing middle T antigen, the transforming protein of polyomavirus, as well as in rodent cells stimulated with either epidermal growth factor (EGF) or platelet-derived growth factor. Analysis of the time course of p120 tyrosine phosphorylation in EGF-stimulated cells revealed a rapid onset of tyrosine phosphorylation. In addition, both the extent and duration of p120 phosphorylation increased when cells overexpressing the EGF receptor were stimulated with EGF. Biochemical analysis showed that p120 (in both normal and src-transformed cells) was membrane associated, was myristylated, and was phosphorylated on serine and threonine residues. Hence, p120 appears to be a substrate of both nonreceptor- and ligand-activated transmembrane receptor tyrosine kinases and of serine/threonine kinases and is perhaps a component of both mitogen-stimulated and tyrosine kinase oncogene-induced signaling pathways.

Animals↗
PubMedDate not supplied

T1 signal hyperintensity in the sellar region: spectrum of findings.

T1 signal hyperintensity is a common finding at magnetic resonance imaging of the sellar region. However, this signal intensity pattern has different sources, and its significance depends on the clinical context. Normal variations in sellar T1 signal hyperintensity are related to vasopressin storage in the neurohypophysis, the presence of bone marrow in normal and variant anatomic structures, hyperactive hormone secretion in the anterior pituitary lobe (eg, in newborns and pregnant or lactating women), and flow artifacts and magnetic susceptibility effects. Pathologic variations in T1 signal hyperintensity may be related to clotting of blood (in hemorrhagic pituitary adenoma, pituitary apoplexy, Sheehan syndrome, or thrombosed aneurysm) or the presence of a high concentration of protein (Rathke cleft cyst, craniopharyngioma, or mucocele), fat (lipoma, dermoid cyst, lipomatous meningioma), calcification (craniopharyngioma, chondroma, chordoma), or a paramagnetic substance (manganese, melanin). After treatment, T1 signal hyperintensity may result from the presence of materials used for surgical packing (gelatin sponge, fat); from compression of the cavernous sinus and reduction of the venous flow, caused by overpacking of the operative bed; or from hormone hypersecretion by a remnant of normal tissue in the anterior lobe of the pituitary gland.

Adolescent↗
PubMed1987

Structure and function of a new hemoglobin variant, Hb meilahti (alpha 2 beta 2 36(C2)Pro----Thr), characterized by mass spectrometry.

An abnormal hemoglobin was found by isoelectric focusing in the blood of a Finnish woman with erythrocytosis. Oxygen equilibrium curves of the patient's hemolysate indicated the presence of a variant with a very high oxygen affinity. Structural analysis was carried out by mass spectrometry. In the spectrum of the tryptic digest, an abnormal peptide was found at m/z1278 which corresponded to the mass number of the protonated molecular ion of beta T4 with 36Pro----Thr substitution. The structure was confirmed by the mass spectrum of the chymotryptic digest.

Genetic Variation↗
PubMed2026

Integrating Optical Genome Mapping into the Genetic Diagnostic Algorithm: Clinical Utility in Unresolved Autosomal Recessive Disorders from a Large Cohort.

INTRODUCTION: The identification of precise genetic etiologies is indispensable for the clinical management of monogenic disorders. However, conventional diagnostic methods and exome sequencing (ES) frequently fail to identify complex structural variations (SVs), leaving the genetic basis unexplained in approximately 30-60% of suspected cases. Optical genome mapping (OGM) emerges as a high-resolution technology capable of detecting cryptic SVs inaccessible to standard methodologies. METHODS: In this study, we evaluated the clinical utility of integrating OGM into the diagnostic algorithm for unresolved monogenic diseases. Following negative or inconclusive results from standard ES pipelines, OGM was applied to a targeted subset of patients (n = 7) selected from a comprehensive clinical cohort of 1,257 individuals with suspected genetic disorders. RESULTS: The integration of OGM identified candidate SVs that may represent the second allelic alteration in two distinct cases; however, confirmation through parental segregation analysis remains pending. Specifically, OGM identified an intronic insertion in the TTLL5 gene and a deletion in a putative regulatory region approximately 400 kb upstream of the NMNAT1 gene, both of which were missed by prior diagnostic testing. CONCLUSION: Our findings suggest that OGM has potential value in investigating the missing heritability of autosomal recessive disorders. By detecting candidate SVs invisible to conventional methods, OGM may warrant consideration as a complementary diagnostic approach following inconclusive ES; however, larger cohorts and confirmatory functional studies are needed to establish its clinical utility.

Autosomal recessive disorders↗
PubMed2005

A functional mutation in the terminal exon of elastin in severe, early-onset chronic obstructive pulmonary disease.

We describe a novel variant in the terminal exon of human elastin, c.2318 G > A, resulting in an amino acid substitution of glycine 773 to aspartate (G773D) in a pedigree with severe early-onset chronic obstructive pulmonary disease (COPD). Transfection studies with elastin cDNAs demonstrate that the glycine to aspartate change compromises the ability of the mutant protein to undergo normal elastin assembly. Other functional consequences of this amino acid substitution include altered proteolytic susceptibility of the C-terminal region of elastin and reduced interaction of the exon 36 sequence with matrix receptors on cells. These results suggest that the G773D variant confers structural and functional consequences relevant to the pathogenesis of COPD.

Alternative Splicing↗