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Results for “Heterogeneity Mapping”

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PubMed2000

A refined physical and transcriptional map of the SPG9 locus on 10q23.3-q24.2.

Hereditary spastic paraplegia (HSP) is a genetically heterogeneous disorder characterised by progressive spasticity of the lower limbs. Beside 'pure' forms of HSP, 'complicated' forms are reported, where spasticity occurs associated with additional symptoms. We recently described an Italian family with a complicated dominant form of HSP (SPG9) and we mapped the gene responsible to 10q23.3-q24.2, in a 12cM interval between markers D10S564 and D10S603. The phenotypic manifestations in our family are reminiscent of those already described in a smaller British pedigree. We typed individuals from this British family using markers located in the SPG9 critical interval and haplotype reconstruction showed the disorder co-segregating with SPG9. To characterise the SPG9 region better, we constructed a contig of 22 YACs, assigned it to 18 polymorphic markers and positioned 54 ESTs. Furthermore, we searched for ESTs containing a trinucleotide repeat sequence, since anticipation of symptoms was reported in both families. Finally, analysis of a muscle biopsy specimen from one patient was normal, suggesting that, contrary to SPG7, mitochondrial disturbance could not be a primary feature of SPG9.

Biopsy↗

PubMed2005

Mapping of a novel autosomal recessive nonsyndromic deafness locus (DFNB46) to chromosome 18p11.32-p11.31.

Hereditary nonsyndromic deafness (NSD) is extremely heterogeneous. Autosomal recessive (AR) forms account for approximately 75% of genetic cases. To date, over 40 ARNSD loci have been mapped. A novel locus (DFNB46) for ARNSD was mapped to chromosome 18p11.32-p11.31 in a five-generation Pakistani family. A 10 cM genome-wide scan and fine mapping was carried out using microsatellite markers. A maximum multipoint LOD score of 3.8 was obtained at two markers, D18S481 and D18S1370. The three-unit support interval is flanked by markers D18S59 and D18S391, corresponds to a 17.6 cM region according to the deCode genetic map and spans 5.8 Mb on the sequence-based physical map.

Chromosome Mapping↗

PubMed1996

Geographical mapping of childhood diabetes in the northern English county of Yorkshire.

This study aimed to highlight geographical differences in childhood Type 1 (insulin dependent) diabetes mellitus (IDDM) by mapping incidence at 3 different geographical scales, within the northern English county of Yorkshire. Mapping techniques are applied to incident cases from a population-based regional register of childhood IDDM. The Yorkshire Children's Diabetes Register (YCDR) comprises 1310 children (0-14 years) diagnosed with IDDM from 1978-1990. Age standardized incidence rates (cases/100000/year) are given for administrative county, standardized incidence ratios (SIRs) are mapped by local government district and electoral ward. Heterogeneity between areas was assessed by a chi 2 test. At county level, incidence is 25% higher in Humberside (16.82 per 100000 per year) compared to West Yorkshire (12.21 per 100000 per year) (p < 0.001). SIRs for the 22 districts display significant heterogeneity (p < 0.001) with deficits in the urban areas of Kirklees (70 95% CI 57-85) and Bradford (81 95% CI 68-95) and significant excesses in the rural districts of Ryedale (147 95% CI 106-198), Beverley (149 95% CI 113-193), Holderness (166 95% CI 112-237) and Boothferry (186 95% CI 134-250). At the smallest scale, variation between wards is significant (p < 0.001) and low incidence in urban areas is notable. Geographical variation in the incidence of childhood IDDM may provide strong clues to its aetiology. Within Yorkshire, geographical distribution shows significant heterogeneity at three different scales. The magnitude of the variation is not explained by ethnic or genetic differences in the population and underlines the important influence of environmental factors in disease aetiology.

Adolescent↗

PubMed1991

Waardenburg I syndrome: a clinical and genetic study of two large Brazilian kindreds, and literature review.

Two large kindreds with Waardenburg I syndrome are described. The total number of affected individuals is 73. The major manifestations are telecanthus (the only constant anomaly in all cases), prominent nasal root, round or square tip of nose, hypoplastic alae, smooth philtrum, bushy eyebrows with synophrys, sensorineural deafness, heterochromia or hypoisochromia iridis, hypopigmented ocular fundus, white forelock, premature greying, and hypopigmented skin lesions. These and other aspects of the syndrome, associated findings, frequency, genetic heterogeneity, pathogenesis, animal models, and gene linkage and mapping are reviewed briefly.

Aged↗

PubMed2003

Evaluation of multiplex capillary heteroduplex analysis: a rapid and sensitive mutation screening technique.

Bardet-Biedl syndrome (BBS) is a heterogeneous disease; to date seven loci have been mapped and five identified (BBS1, BBS2, BBS4, BBS6, and BBS7). Inheritance in some families is complex with multiallelic participation making linkage analysis difficult. Previous mutation screens have been carried out by direct sequencing but with an increasing number of patients to be screened for five relatively large genes, a more rapid and cost-effective mutation assay for BBS was required. We have adapted the technique of heteroduplex analysis for use on the MegaBACE 1000, a capillary-based DNA fragment analyser, to improve the resolution and sensitivity of the system. Twelve known alterations (insertions, deletions, missenses, and SNPs) in BBS1, BBS2, BBS4, and BBS6 were used to test the sensitivity of the assay and subsequently used to screen new patients for mutations. We achieved a 100% detection rate while dramatically increasing the sample throughput by virtue of multiplexing up to six PCR products in each capillary. In addition, four novel variants were identified: two in BBS2 [c.522T>A (p.D174E) and c.805-20A>G] and two in BBS4 [c.332+27_28insA and c.1414A>G (p.M472V)]. Compared with sequencing and alternative screening methods, multiplex capillary heteroduplex analysis (MCHA) is extremely cost effective. Hum Mutat 22:151-157, 2003.

Bardet-Biedl Syndrome↗

PubMed2006

AUF-1 mediates inhibition by nitric oxide of lipopolysaccharide-induced matrix metalloproteinase-9 expression in cultured astrocytes.

Neuroinflammatory diseases are associated with increased production of matrix metalloproteinase-9 (MMP-9) and excessive generation of nitric oxide (NO). NO has been reported to have variable effects on MMP-9 gene expression and activation in various cell types. In the present study, we investigated the effect of NOon MMP-9 expression in primary cortical astrocytes. Zymography and real-time PCR showed that lipopolysaccharide (LPS) dramatically increased latent MMP-9 gelatinolytic activity and MMP-9 mRNA expression. By using the NO donor DETA NONOate, we observed a dose-dependent inhibition of MMP-9 induction by LPS. Active forms of MMP-9 were not found by zymography after NO treatment. The MEK1/2 inhibitor U0126 completely inhibited LPS-induced MMP-9, which was partially inhibited by the p38 MAPK inhibitor SB203580. NO had no effect on LPS-stimulated ERK1/2 and p38 MAPK activation, suggesting that the inhibitory action of NO occurs downstream of MAPK cascades. Real-time PCR analysis showed that NO accelerated the degradation of MMP-9 mRNA after LPS induction. Western blotting and pull-down assay demonstrated that NO increased AUF-1 expression as well as its specific binding to the MMP-9 gene 3'-untranslated region. Knockdown of AUF-1 with siRNA partially reversed the inhibitory action of NO on LPS-stimulated MMP-9 induction. We conclude that NO does not activate MMP-9 in astrocyte cultures but reduces LPS-induced MMP-9 expression via accelerating MMP-9 mRNA degradation, which is partially mediated by AUF-1. Our results suggest that elevated NO concentrations may suppress MMP-9 and restrict the inflammatory response in neurodegenerative diseases.

Animals↗

PubMed1995

Disulfide bonds in a recombinant protein modeled after a core repeat in an aquatic insect's silk protein.

We constructed a gene encoding rCAS, recombinant constant and subrepeat protein, modeled after tandem repeats found in the major silk proteins synthesized by aquatic larvae of the midge, Chironomus tentans. Bacterially synthesized rCAS was purified to near homogeneity and characterized by several biochemical and biophysical methods including amino-terminal sequencing, amino acid compositional analysis, sedimentation equilibrium ultracentrifugation, and mass spectrometry. Complementing these techniques with quantitative sulfhydryl assays, we discovered that the four cysteines present in rCAS form two intramolecular disulfide bonds. Mapping studies revealed that the disulfide bonds are heterogeneous. When reduced and denatured rCAS was allowed to refold and its disulfide bonding state monitored, it again adopted a conformation with two intramolecular disulfide bonds. The inherent ability of rCAS to quantitatively form two intramolecular disulfide bonds may reflect a previously unknown feature of the in vivo silk proteins from which it is derived.

Amino Acid Sequence↗

PubMed1997

A matrix-assisted laser desorption ionization time-of-flight mass spectrometry approach to identify the origin of the glycan heterogeneity of diptericin, an O-glycosylated antibacterial peptide from insects.

In a previous study, electrospray ionization mass spectrometry was used to analyze the structure of the O-glycopeptide diptericin, an antibacterial peptide from the fleshfly Phormia terranovae. Several glycoforms of diptericin differing in the length of their oligosaccharide chains were present at the final stage of purification. In order to determine the origin of this glycan heterogeneity, we analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) the relative abundance of the different diptericin glycoforms in fractions obtained after each purification step, and directly in the hemolymph and in the fat body which produces diptericin. MALDI-MS clearly shows that the purification procedure had no effect on the O-linked oligosaccharide chains of diptericin, suggesting that diptericin is synthesized as a family of heterogeneous glycopeptides. In addition, in these experiments, differential mapping by MALDI-MS of the hemolymph and fat body tissue from bacteria-challenged and naive larvae allowed us to detect induced or repressed molecules which may be involved in the immune response of P. terranovae.

Amino Acid Sequence↗

PubMed2002

Autoimmune antibodies to hnRNPG protein in dogs with systemic lupus erythematosus: epitope mapping of the antigen.

We previously reported the presence of circulating autoantibodies to hnRNPG protein in dogs with systemic lupus erythematosus (Soulard et al. 1993, 1994). These antibodies appeared to be specifically limited to German shepherd dog species. In the present report, we have analysed the nature of the hnRNPG epitopes responsible for autoantibody specificity. By using a set of 11 dog sera selected for their strong reactivity to hnRNPG protein, we have found that these sera had the ability to recognize two epitopes: (1) within a stretch of 33 amino acids located around the central part of protein, that is readily detected by immunoblotting; (2) a N-terminal conformation of the protein close to the RNA binding domain (RBD), that is revealed by immunoprecipitation. Our data strongly support the notion that the dog autoimmune response against hnRNPG protein is antigen-driven.

Amino Acid Sequence↗

PubMed1997

Familial amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis is sporadic in ninety percent of cases and familial (FALS) in ten percent. Both forms of FALS whether transmitted as an autosomal dominant (DFALS) or as an autosomal recessive (RFALS) trait is genetically heterogeneous. The locus for one form of RFALS maps to chromosome 2q33. Fifteen percent of DFALS families have mutations in the gene for Cu, Zn superoxide dismutase (SOD1) gene which is coded on chromosome 21. These mutations result in decreased SOD1 activity and shortened half-life of the protein in most instances. Transgenic mice overexpressing mutated SOD1 protein develop an ALS-like disease which suggests that the degeneration of motor neurons in DFALS is caused by the gain of a novel toxic function by mutated SOD1 rather than by the decrease of SOD1 activity. Possible mechanisms of the novel neurotoxic function of mutated SOD1 are discussed.

Amyotrophic Lateral Sclerosis↗

PubMed1990

Transcription of two divergently transcribed yeast genes initiates at a common oligo(dA-dT) tract.

Oligo(dA-dT) tracts are frequently found in the intergenic regions of the yeast Saccharomyces cerevisiae and have been proposed to act as upstream promoter elements for constitutive transcription. An oligo(dA-dT) tract of 23 bp is also found as a characteristic sequence motif in the centre of the 230 bp segment which separates the open reading frames of the CBS2 gene and its 5'-flanking gene on chromosome IV. Recently we have reported that transcription of CBS2 is initiated immediately adjacent to this oligo(dA-dT) tract (michaelis et al. 1988). Here we report that the flanking gene of unknown function is divergently transcribed into an RNA with heterogeneous 5' ends. Two of these 5' ends map within the oligo(dA-dT) stretch, while the third is located upstream, leading to an RNA species which is partially complementary to the CBS2 transcript. Gel shift assays show that the oligo(dA-dT) stretch is specifically recognized by (a) binding factor(s) in nuclear extracts. We discuss these results with respect to the role of oligo(dA-dT) stretches in gene expression in yeast.

Base Sequence↗

PubMed1993

Pleotrophic action of interferon gamma in human orbital fibroblasts.

Analysis of the two-dimensional electrophoretic patterns of total radiolabeled cellular proteins derived from human orbital fibroblast cultures revealed that interferon gamma (100 U/ml) elicited significant quantitative changes in 42% of 86 randomly-selected proteins relative to untreated cultures. The most substantial up-regulation involved a protein with pI/mw map coordinates of 5.9/54,000 and a heterogenous 5 isoform protein cluster (pIs = 6.1-5.6) of approximately 47- to 50-kDa. These proteins were identified as the previously described 54-kDa protein inducible in interferon gamma-sensitive cell types and type-1 plasminogen activator inhibitor (PAI-1), respectively. Definition of PAI-1 as an interferon gamma-responsive protein in orbital fibroblasts was confirmed by immunoprecipitation using PAI-1-specific antibodies. Induction of PAI-1 and the 54-kDa protein in orbital fibroblasts, moreover, was relatively specific for interferon gamma since interferon alpha failed to initiate a similar inductive response. The synthesis of a 170 kDa protein, tentatively identified as a collagen, was decreased by approximately 80%. Analysis of the labeled proteins secreted into the culture medium revealed that interferon gamma increased the medium content of fibronectin and decreased the secretion of collagen. It would appear from these data that the inflammatory cytokine can exert regulatory effects on the synthesis of many specific proteins in orbital fibroblasts.

Cells, Cultured↗

PubMed2001

Dimension reduction and source identification for multispecies groundwater contamination.

Assessment of chemical contamination at large industrial complexes with long and sometimes unknown histories of operation represents a challenging environmental problem. The spatial and temporal complexity of the contaminant may be due to changes in production processes, differences in the chemical transport, and the physical heterogeneity of the soil and aquifer materials. Traditional mapping techniques are of limited value for sites where dozens of chemicals with diverse transport characteristics may be scattered over large spatial areas without documentation of disposal histories. In this context, a site with a long and largely undocumented disposal history of shallow groundwater contamination is examined using principal component analysis (PCA). The dominant chemical groups and chemical "modes" at the site were identified. PCA results indicate that five primary and three transition chemical groups can be identified in the space of the first three eigenvectors of the correlation matrix, which account for 61% of the total variance of the data. These groups represent a significant reduction in the dimension of the original data (116 chemicals). It is shown that each group represents a class of chemicals with similar chemo-dynamic properties and/or environmental response. Finally, the groups are mapped back onto the site map to infer delineation of contaminant source areas for each class of compounds. The approach serves as a preliminary step in subsurface characterization, and a data reduction strategy for source identification, subsurface modeling and remediation planning.

Environmental Monitoring↗

PubMed1998

Red cell membrane fatty acids, cytosolic phospholipase-A2 and schizophrenia.

Forty subjects with schizophrenia and 40 age- and sex-matched controls were recruited, and blood samples were obtained for analysis of red cell membrane fatty acid composition by capillary gas chromatography. A blood sample was also taken from the same population to test for allelic association between schizophrenia and a polymorphism close to the promoter site of the cytosolic phospholipase-A2 gene which is mapped to chromosome 1q25. The schizophrenic population was heterogeneous with regards age, symptoms severity and treatment. A significantly higher percentage concentration of dihomogamma-linolenic acid (DGLA) was found in the red cell membranes of schizophrenics compared to matched controls. All other fatty acids examined showed no difference from the normal population. No correlation was found between any demographic factor, treatment variable, diet, drug use, alcohol or tobacco consumption which could explain the biochemical findings. A negative correlation was found between the concentration of DGLA in red blood cell (RBC) membranes and severity of symptoms of schizophrenia. In particular, there was a significant correlation (r = -0.41, p = 0.009) between DGLA percentage concentrations and 'disorganised' symptoms. No association was found between schizophrenia and alleles of the polymorphism near the phospholipase-A2 gene or between fatty acid concentrations and the presence of any particular alleles. This study therefore finds support for membrane phospholipid abnormalities in patients with schizophrenia and particular symptom clusters, but does not replicate a previous report of an allelic association between a polymorphism close to the site of the cytosolic phospholipase-A2 gene and schizophrenia.

Adult↗

PubMed1998

Rates and patterns of chromosome evolution in enteric bacteria.

Although several types of large-scale alterations potentially affect the structure and organization of bacterial genomes, recent analyses of physical maps and complete genomic sequences reveal that chromosome heterogeneity in enteric bacteria has resulted from the acquisition and deletion of large segments of DNA. These acquired sequences can provide novel functions immediately upon their introduction and play a significant role in the diversification of bacterial species.

Biological Evolution↗

PubMed2004

Genetic evaluation of inherited motor/sensory neuropathy.

Inherited disorders of peripheral nerves represent a common group of neurologic diseases. Charcot-Marie-Tooth neuropathy type 1 (CMT1) is a genetically heterogeneous group of chronic demyelinating polyneuropathies with loci mapping to chromosome 17 (CMT1A), chromosome 1 (CMT1B), chromosome 16 (CMT1C) and chromosome 10 (CMT1D). CMT1A is most often associated with a tandem 1.5-megabase (Mb) duplication in chromosome 17p11.2-p12. In rare patients it may result from a point mutation in the peripheral myelin protein-22 (PMP22) gene. CMT1B is associated with point mutations in the myelin protein zero (Po or MPZ) gene. Mutations in the SIMPLE gene cause CMT1C, and CMT1D is the result of mutations in the early response 2 (ERG2 or Krox-20) gene. An X-linked form of CMT1 (CMT1X) maps to Xq13 and is associated with mutations in the connexin32 (Cx32) gene. Charcot-Marie-Tooth neuropathy type 2 (CMT2) is an axonal neuropathy that maps to chromosome 1p35-p36 (CMT2A), chromosome 3q13-q22 (CMT2B), chromosome 7p14 (CMT2D), chromosome 8p21 (CMT2E), chromosome 1q22-q23 (CMT2F) or chromosome 3q13 (CMT2G). Two X-linked forms of CMT2 have been reported (CMT2XA and CMT2XB), but the genes remain unidentified. An area that has recently expanded is the identification of autosomal recessive forms of CMT type 1 and 2. Of the eight recessive forms of CMT1 that have been identified to date, only two have been fully characterized at the molecular level (CMT1 AR B 1 and CMT1 AR D). Point mutations were found in the myotubularin-related protein-2 (MTM2) gene for CMT1 AR B1. CMT1 AR D is the result of point mutations in the N-myc downstream-regulated gene 1 (NDRG1). Dejerine-Sottas disease (DSD), also called hereditary motor and sensory neuropathy type III (HMSNIII), is a severe, infantile-onset demyelinating polyneuropathy syndrome that may be associated with point mutations in either the PMP22 gene, PO gene, EGR2 gene or the PRX gene (for the recessive form). It shares considerable clinical and pathological features with CMT1. Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant disorder that results in a recurrent, episodic demyelinating neuropathy. HNPP is associated with a 1.5-Mb deletion in chromosome 17p11.2-p12 that results in reduced expression of the PMP22 gene. CMT1A and HNPP are reciprocal duplication/deletion syndromes that originate from unequal crossover during germ cell meiosis. Other rare forms of demyelinating peripheral neuropathies map to chromosome 8q, 10q and 11q.

Animals↗

PubMed1998

Nonsyndromic hearing impairment is associated with a mutation in DFNA5.

Nonsyndromic hearing impairment is one of the most heterogeneous hereditary conditions, with more than 40 loci mapped on the human genome, however, only a limited number of genes implicated in hearing loss have been identified. We previously reported linkage to chromosome 7p15 for autosomal dominant hearing impairment segregating in an extended Dutch family (DFNA5). Here, we report a further refinement of the DFNA5 candidate region and the isolation of a gene from this region that is expressed in the cochlea. In intron 7 of this gene, we identified an insertion/deletion mutation that does not affect intron-exon boundaries, but deletes five G-triplets at the 3' end of the intron. The mutation co-segregated with deafness in the family and causes skipping of exon 8, resulting in premature termination of the open reading frame. As no physiological function could be assigned, the gene was designated DFNA5.

Adolescent↗

PubMed2000

Different site, different splice.

The MKK3/6-p38 pathway has been found to induce the relocalization of premessenger-RNA splicing factors from the nucleus to the cytoplasm. This represents the first physiological mechanism that alters the nuclear ratios of splicing factors and modulates alternative splice-site choice in vivo.

Alternative Splicing↗