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Results for “Heterogeneity Mapping”

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PubMed1989

A tandem repeat sequence found in a heterogeneous fragment of UL of herpes simplex virus type 1.

We found a tandem repeat sequence in the region (designated BS7) in which restriction fragments BamHI D and SalI B overlap each other, near the centre of the unique long sequence (UL) of the herpes simplex virus type 1 (HSV-1) strain F genome. The SmaI physical map of BS7 was constructed, and the position of a heterogeneous SmaI subfragment from HSV-1 isolates and plaque-purified clones from a single strain was defined on the map. The maximum size difference in the SmaI subfragment was estimated to be 600 bp between these isolates and 100 bp between the clones. The 0.23 kb SmaI subfragment recloned from BS7 was sequenced, and was shown to contain a tandem repeat sequence consisting of 15 units of 12 bp, 5' TTGGGGCTGGGG 3'. These results suggest that the fragment length heterogeneity in the UL of HSV-1 isolates and clones is attributable to copy number variation of the tandem repeat sequence.

Base Sequence↗

PubMed1995

Localisation of a gene for chondrocalcinosis to chromosome 5p.

Chondrocalcinosis is a common disorder which may associate with acute and chronic arthritis. A familial form, inherited as an autosomal dominant trait, has been mapped in a large family in which affected members also suffer recurrent fits in childhood. The gene which causes this disease shows linkage with several polymorphic markers on chromosome 5p with a maximum multipoint lod score of 4.6 between D5S810 and D5S416. Mapping a locus for chondrocalcinosis will allow the heterogeneity of the disorder to be assessed and may also be relevant to understanding the aetiology of osteoarthritis with which it commonly associates.

Child↗

PubMed1998

The syndromes of Sotos and Weaver: reports and review.

The syndromes of Sotos and Weaver are paradigmatic of the daily nosologic difficulties faced by clinical geneticists attempting to diagnose and counsel, and to give accurate prognoses in cases of extensive phenotypic overlap between molecularly undefined entities. Vertebrate development is constrained into only very few final or common developmental paths; therefore, no developmental anomaly seen in humans is unique to ("pathognomonic" of) one syndrome. Thus, it is not surprising that prenatal overgrowth occurs in several syndromes, including the Sotos and Weaver syndromes. Are they sufficiently different in other respects to allow the postulation of locus (rather than allele) heterogeneity? Phenotypic data in both conditions are biased because of ascertainment of propositi, and the apparent differences between them may be entirely artificial as they were between the G and BBB syndromes. On the other hand, the Sotos syndrome may be a cancer syndrome, the Weaver syndrome not (though a neuroblastoma was reported in the latter); in the former there is also remarkably advanced dental maturation rarely commented on in the latter. In Weaver syndrome there are more conspicuous contractures and a facial appearance that experts find convincingly different from that of Sotos individuals. Nevertheless, the hypothesis of locus heterogeneity is testable; at the moment we are inclined to favor the hypothesis of allele heterogeneity. An international effort is required to map, isolate, and sequence the causal gene or genes.

Brain↗

PubMed1983

Characterization of ploidy level in bladder tumors and selected site specimens by flow cytometry.

The histopathological grade of atypia was compared with the ploidy level in biopsy specimens from bladder tumors and six grossly normal areas (selected sites). The study included investigation of 303 specimens from 45 patients. The results demonstrated a high correlation between the grade of atypia and the occurrence of aneuploid cell populations. The selected site specimens were diploid in patients with low grade malignant tumors, while high grade malignant tumors were associated with aneuploid selected site specimens in 20% of the cases. The divergence of ploidy level in the tumor and selected site specimens found in some cases clearly demonstrated that the carcinogenic process in the bladder may lead to clonal heterogeneity. Flow cytometric analysis seems suited for mapping of the ploidy levels in different parts of the bladder. The possible importance of the additional information is discussed.

Aneuploidy↗

PubMed1993

Oligosaccharide composition of heparin and low-molecular-weight heparins by capillary electrophoresis.

The application of capillary electrophoresis to total compositional analysis of heparin and low-molecular-weight heparin samples has been studied. Optimum resolution of 17 defined oligosaccharides was obtained with the buffer system composed of 10 mM sodium borate and 50 mM sodium dodecyl sulfate at pH 8.81 and at a constant voltage of 20 kV. The ratio of oligosaccharide charge to the number of saccharide residues correlated with the migration time. For oligosaccharides having the same charge to saccharide ratio, the larger of the oligosaccharides eluted earlier. A hexasaccharide having a 3-O-sulfated glucosamine residue at the reducing end and arising from heparin's antithrombin III binding site, migrated in an unusual fashion. The limit of oligosaccharide detection was from 600 fmol to 1 pmol. Quantitative analysis could conveniently be performed on 10 pmol of an oligosaccharide sample. Oligosaccharide composition using capillary electrophoresis was obtained by nearly complete depolymerization of heparins with a mixture of heparin lyase I, II, and III. The analysis resulted in 95% mass balance for both heparin and low-molecular-weight heparin. Capillary electropherograms of heparin and different low-molecular-weight heparins depolymerized with heparin lyase I alone showed a high level of structural heterogeneity in the products formed. The oligosaccharide maps thus obtained might find use in fingerprinting the heparin and low-molecular-weight samples.

Carbohydrate Sequence↗

PubMed2004

DFNA54, a third locus for low-frequency hearing loss.

Nonsyndromic hereditary hearing impairment (NSHHI) is a highly heterogeneous disorder with more than 90 loci mapped, of which nearly one-half of the responsible genes are identified. In dominant NSSHI hearing loss is typically biased towards the high frequencies while low-frequency hearing loss is unusual. Only two NSHHI loci, DFNA1 and DFNA6/14/38, are associated with predominantly low-frequency loss. We mapped the loci harboring the gene responsible for autosomal dominant low-frequency hearing loss in a multigenerational family. The pedigree of a Swiss family with low-frequency hearing loss was established. Using genomic DNA, DFNA1 and DFNA6/14/38 were excluded by linkage analysis or by direct sequencing of the responsible gene. Genome-wide linkage analysis was performed using commercially available microsatellite markers. Two-point linkage analysis demonstrated linkage to chromosome 5q31, the locus for DFNA15, with a lod score of 6.32 at recombination fraction theta=0 for marker D5S436. Critical recombinations were seen at markers D5S1972 and D5S410. Sequencing of the corresponding gene POU4F3 yielded no pathogenic mutation segregating with the affected members. In addition to Wolfram syndrome gene 1 (DFNA6/14/38) and diaphanous (DFNA1) there is evidence for a third gene involved in low-frequency hearing loss located at DFNA15. Because of the differences in auditory phenotype and the absence of pathogenic mutation in the coding region of POU4F3 it is likely that there is a second gene in 5q31, designated DFNA54, associated with NSHHI.

Adolescent↗

PubMed2004

Uncertainty assessment for management of soil contaminants with sparse data.

In order for soil resources to be sustainably managed, it is necessary to have reliable, valid data on the spatial distribution of their environmental impact. However, in practice, one often has to cope with spatial interpolation achieved from few data that show a skewed distribution and uncertain information about soil contamination. We present a case study with 76 soil samples taken from a site of 15 square km in order to assess the usability of information gleaned from sparse data. The soil was contaminated with cadmium predominantly as a result of airborne emissions from a metal smelter. The spatial interpolation applies lognormal anisotropic kriging and conditional simulation for log-transformed data. The uncertainty of cadmium concentration acquired through data sampling, sample preparation, analytical measurement, and interpolation is factor 2 within 68.3 % confidence. Uncertainty predominantly results from the spatial interpolation necessitated by low sampling density and spatial heterogeneity. The interpolation data are shown in maps presenting likelihoods of exceeding threshold values as a result of a lognormal probability distribution. Although the results are not deterministic, this procedure yields a quantified and transparent estimation of the contamination, which can be used to delineate areas for soil improvement, remediation, or restricted area use, based on the decision-makers' probability safety requirement.

Data Collection↗

PubMed2002

Gene dosage of the spermidine/spermine N(1)-acetyltransferase ( SSAT) gene with putrescine accumulation in a patient with a Xp21.1p22.12 duplication and keratosis follicularis spinulosa decalvans (KFSD).

Keratosis follicularis spinulosa decalvans (KFSD) or Siemens-1 syndrome is a rare X-linked disease of unknown etiology affecting the skin and the eye. Although most affected families are compatible with X-linked inheritance, KFSD appears to be clinically and genetically heterogeneous. So far, the gene has been mapped to Xp22.13p22.2 in two extended KFSD families. Analysis of additional recombination events in the first Dutch pedigree located the gene to an interval covering approximately 1 Mb between markers DXS7163 and DXS7593/DXS7105, whereas haplotype reconstruction in the second German family positioned the gene outside the previously identified region, proximal to marker DXS274. We report here the molecular characterization of an Xp21.1p22.12 duplication present in a patient affected with dosage-sensitive sex reversal (DSS) and KFSD. The duplicated region includes both the DAX1 gene (previously demonstrated to be responsible for DSS) and the KFSD interval, in which the gene encoding spermidine/spermine N(1)-acetyltransferase ( SSAT) is located. This enzyme catalyzes the N(1)-acetylation of spermidine and spermine and, by the successive activity of polyamine oxidase, the spermine can be converted to spermidine and the spermidine to putrescine. Overexpression of the SSAT enzyme in a mouse model results in putrescine accumulation and a phenotype with skin and hair abnormalities reminiscent of human KFSD. Analysis of polyamine metabolism in the cells of the patient indicated that the levels of metabolites such as putrescine, spermidine and spermine were consistent with the overexpression of the SSAT gene as in the murine model. Thus, we propose that overexpression of SSAT and the consequent putrescine accumulation are involved in the KFSD phenotype, at least in our propositus.

Acetyltransferases↗

PubMed1989

Multipartite structure of mitochondrial DNA in a fungal longlife mutant.

Rearrangements in the mitochondrial genome of the longlife mutant ex1 of the ascomycete Podospora anserina have led to a heterogeneous population of subgenomic molecules. The restriction maps of individual subcircles were established using overlapping recombinant lambda phages isolated from an ex 1 mtDNA/EMBL3 library. The formation of the subcircles and the resulting multipartite organization of the ex1 mtDNA are discussed.

Ascomycota↗

PubMed1984

Long interspersed repeated sequences of the mouse genome.

Long interspersed repeated sequences of the mouse genome can be prepared by digesting reassociated DNA with single-strand nuclease. Length resolution reveals many discrete bands that can be assigned to 15 kbp and 6 kbp groups. The reassociated 6 kbp group (which we identify with the MIF-1 family) possesses significant sequence heterogeneity, evidenced by the production of several smaller fragments upon single-strand nuclease digestion of heteroduplexes. The sites of sequence heterogeneity are relatively few and can be mapped using additional restriction endonuclease cuts. We have mapped additional restriction sites into this group, particularly within a cloned HindIII 400 bp fragment, and have also clearly mapped one end of this relatively homogeneous long interspersed repeated sequence.

Animals↗

PubMed2005

Germline mutations of the paired-like homeobox 2B (PHOX2B) gene in neuroblastoma.

Hereditary predisposition to neuroblastoma accounts for less than 5% of neuroblastomas and is probably heterogeneous. Recently, a predisposition gene has been mapped to 16p12-p13, but has not yet been identified. Occurrence of neuroblastoma in association with congenital central hypoventilation and Hirschsprung's disease suggests that genes, involved in the development of neural-crest-derived cells, may be altered in these conditions. The recent identification of PHOX2B as the major disease-causing gene in congenital central hypoventilation prompted us to test it as a candidate gene in familial neuroblastoma. We report a family with three first-degree relatives with neuroblastic tumours (namely two ganglioneuromas and one neuroblastoma) in one branch and two siblings with Hirschsprung's disease in another branch. A constitutional R100L PHOX2B mutation was identified in all three patients affected with tumours. We also report a germline PHOX2B mutation in one patient treated for Hirschsprung's disease who subsequently developed a multifocal neuroblastoma in infancy. Both mutations disrupt the homeodomain of the PHOX2B protein. No loss of heterozygosity at the PHOX2B locus was observed in the tumour, suggesting that haplo-insufficiency, gain of function or dominant negative effects may account for the oncogenic effects of these mutations. These observations identify PHOX2B as the first predisposing gene to hereditary neuroblastic tumours.

Adult↗

PubMed2006

A characterization study of some aspects of the adsorption of aqueous Co2+ ions on a natural bentonite clay.

The natural bentonite used in this study contained montmorillonite in addition to low cristobalite. The uptake of aqueous Co(2+) ions was investigated as a function of time, concentration, and temperature. In addition, the change in the interlayer space of montmorillonite was analyzed using XRPD, and the distribution of fixed Co(2+) ions on the heterogeneous clay surface was recorded using EDS mapping. The sorbed amount of Co(2+) appeared to closely follow Freundlich isotherm, with the sorption process showing apparent endothermic behavior. The relevance of the apparent DeltaH(o) values is briefly discussed. Analysis of the Co-sorbed bentonite samples using SEM/EDS showed that the montmorillonite fraction in the mineral was more effective in Co(2+) fixation than the cristobalite fraction. XRPD analysis demonstrated that the interlayer space of montmorillonite was slightly modified at the end of sorption.

Adsorption↗

PubMed2005

Expression profiling of adrenocortical neoplasms suggests a molecular signature of malignancy.

BACKGROUND: Distinguishing between adrenocortical adenomas and carcinomas is often difficult. Our aim was to investigate the differences in transcriptional profiles between benign and malignant adrenocortical neoplasms using complementary DNA microarray techniques. METHODS: We studied 7 patients with adrenocortical carcinomas and 13 with adenomas. Histopathology was reviewed in all patients; clinical follow-up was at least 1 year. Hybridizations were performed in duplicate against RNA reference. Expression levels were analyzed in the R environment for statistical computing with the use of aroma, limma, statistics, and class packages. RESULTS: Transcriptional profiles were homogeneous among adenomas, while carcinomas were much more heterogeneous. Hierarchical clustering and self-organizing maps could separate clearly carcinomas from adenomas. Among genes that were most significantly upregulated in carcinomas were 2 ubiquitin-related genes (USP4 and UFD1L) and several insulinlike growth factor-related genes (IGF2, IGF2R, IGFBP3 and IGFBP6). Among genes that were most significantly downregulated in carcinomas were a cytokine gene (CXCL10), several genes related to cell metabolism (RARRES2, ALDH1A1, CYBRD1 and GSTA4), and the cadherin 2 gene (CDH2). CONCLUSIONS: Through the use of cDNA arrays, adrenocortical adenomas and carcinomas appear to be clearly distinguishable on the basis of their specific molecular signature. The biologic importance of the up- and downregulated genes is yet to be determined.

Adrenal Cortex Neoplasms↗

PubMed2002

Characterization of antibody affinities using an AGE-modified dipeptide spot library.

Recent immunological approaches have greatly helped understanding the significance of advanced glycation end products (AGEs) in age-related diseases. However, immunohistochemical localization of AGEs in tissues or their quantitative determination in biological fluids sometimes yields inconsistent results among different investigators. Since these differences might be caused by the heterogeneity of the AGE antibodies, a systematic mapping of their epitope recognition pattern would help in the evaluation of these different results. For this purpose, an N-terminally acetylated combinatorial dipeptide library with 400 positionally defined dipeptides was modified by glucose to yield AGEs, which are thought to be present on the protein side chains. Using this library, we have characterized six different AGE antibodies in respect to their immunoreactivity towards AGE-modified dipeptides. All antibodies predominantly recognized only one AGE-modified amino acid side chain (and not a particular dipeptide). In most cases, arginine- and lysine- derived AGEs, but also some epitopes on asparagine and on heterocyclic amino acids were recognized. Very interestingly, the immunization of different animals with the same antigen produced AGE antibodies with a totally different epitope recognition pattern. Defining the antigen recognition pattern with this method might help in the quality control of polyclonal AGE antibodies for immunodetection. In addition, defined AGE antibodies (as neutralizing antibodies) could also help to define "signal-active" AGEs in terms of specific AGE-mediated cellular responses.

Antibody Affinity↗

PubMed1997

Regional tumor oxygen dynamics: 19F PBSR EPI of hexafluorobenzene.

We demonstrate a novel approach to measuring regional tumor oxygen tension using 19F pulse burst saturation recovery echo planar imaging (EPI) relaxometry of hexafluorobenzene. Hexafluorobenzene offers exceptional sensitivity to changes in oxygen tension, and has a single resonance making it ideal for imaging studies. By combining a pulse burst saturation recovery preparation sequence with EPI, the relaxation experiments were performed in approximately 20 min facilitating measurements of dynamic changes in pO2 accompanying interventions. Direct intratumoral administration of hexafluorobenzene permitted labeling of specific regions of interest, and imaging provided maps of pO2, confirming distinct intra tumoral heterogeneity. For a group of three Dunning prostate adenocarcinoma R3327-AT1 tumors interrogation of the central tumor region showed skewed pO2 distributions with considerable radiobiological hypoxia (approximately 90% voxels had pO2 < 15 torr) when rats breathed 33% O2. Altering the inspired gas to pure oxygen caused distributions to shift towards increased pO2 with significant increases in mean oxygen tension (p < 0.05) in two cases. Interrogation of both central and peripheral regions in a fourth tumor showed bimodal distribution for tumor oxygenation including approximately 75% voxels with pO2 > 15 torr. EPI allows the fate of individual voxels to be traced: upon altering the inspired gas to pure oxygen those voxels with baseline pO2 > 30 torr showed significant changes (p < 0.05), whereas those with pO2 < 16 torr showed minimal response. The precision of the measurements, together with the ability to simultaneously examine dynamic changes in multiple regions should provide a useful technique for investigating tumor hypoxia with respect to therapy.

Adenocarcinoma↗

PubMed2001

Identification of amplified genes from SV40 large T antigen-induced rat PNET cell lines by subtractive cDNA analysis and radiation hybrid mapping.

Primitive neuroectodermal tumors (PNETs) such as human medulloblastomas are genetically heterogeneous and therefore poorly understood. In a rat model the SV40 large T antigen was used to induce neoplasms with characteristic features of PNETs. Tumor development requires a latency period of 8-11 months implicating secondary genetic alterations. To identify such secondary alterations we performed comparative analyses of two phenotypically identical PNET-derived cell lines. Indeed, these cell lines displayed distinct high-level amplification sites. Using a combination of subtractive cDNA analysis and radiation hybrid mapping we have now identified genes in the amplicon regions of the two cell lines. Interestingly, one of these genes encodes the rat homolog of a cytosolic branched chain aminotransferase (BCAT(C)) previously shown to be amplified in a mouse teratocarcinoma cell line. We propose that this simple cloning strategy may serve as a powerful tool for the isolation of genes implicated in known chromosomal aberrations in primary tumors and tumor cell lines.

Amino Acid Sequence↗

PubMed2002

Is the transportation highway the right road for hereditary spastic paraplegia?

The term "hereditary spastic paraplegia" (HSP) refers to a genetically and clinically diverse group of disorders whose primary feature is progressive spasticity of the lower extremities. The condition arises because of degeneration of the longest motor and sensory axons on the spinal cord, which appear to be most sensitive to the underlying mutations. The marked genetic heterogeneity in HSP, with 20 loci chromosomally mapped and eight genes now identified, suggests that a number of defective cellular processes may be shown to result in the disease. Although previous studies have suggested a mitochondrial basis for at least one form of the disease, a mechanism common to a number of the other genes mutated in HSP has remained elusive until now. The identification of the most recent genes for the condition suggests that aberrant cellular-trafficking dynamics may be a common process responsible for the specific pattern of neurodegeneration seen in HSP.

Amino Acid Sequence↗

PubMed2002

Hereditary deafness and phenotyping in humans.

Hereditary deafness has proved to be extremely heterogeneous genetically with more than 40 genes mapped or cloned for non-syndromic dominant deafness and 30 for autosomal recessive non-syndromic deafness. In spite of significant advances in the understanding of the molecular basis of hearing loss, identifying the precise genetic cause in an individual remains difficult. Consequently, it is important to exclude syndromic causes of deafness by clinical and special investigation and to use all available phenotypic clues for diagnosis. A clinical approach to the aetiological investigation of individuals with hearing loss is suggested, which includes ophthalmology review, renal ultrasound scan and neuro-imaging of petrous temporal bone. Molecular screening of the GJB2 (Connexin 26) gene should be undertaken in all cases of non-syndromic deafness where the cause cannot be identified, since it is a common cause of recessive hearing impairment, the screening is straightforward, and the phenotype unremarkable. By the same token, mitochondrial inheritance of hearing loss should be considered in all multigeneration families, particularly if there is a history of exposure to aminoglycoside antibiotics, since genetic testing of specific mitochondrial genes is technically feasible. Most forms of non-syndromic autosomal recessive hearing impairment cause a prelingual hearing loss, which is generally severe to profound and not associated with abnormal radiology. Exceptions to this include DFNB2 (MYO7A), DFNB8/10 (TMPRSS3) and DFNB16 (STRC) where age of onset may sometimes be later on in childhood, DFNB4 (SLC26A4) where there may be dilated vestibular aqueducts and endolymphatic sacs, and DFNB9 (OTOF) where there may also be an associated auditory neuropathy. Unusual phenotypes in autosomal dominant forms of deafness, include low frequency hearing loss in DFNA1 (HDIA1) and DFNA6/14/38 (WFS1), mid-frequency hearing loss in DFNA8/12 (TECTA), DFNA13 (COL11A2) and vestibular symptoms and signs in DFNA9 (COCH) and sometimes in DFNA11 (MYO7A). Continued clinical evaluation of types and course of hearing loss and correlation with genotype is important for the intelligent application of molecular testing in the next few years.

Adolescent↗