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At least 937 records · Page 52Linked to original sources
PubMed1994

Transcriptional activity in 3T3, F9, and PCC4 embryonal carcinoma cells: a systematic deletion and linker-scanning study of the polyomavirus enhancer.

The polyomavirus (PyV) genome is not expressed in undifferentiated embryonal carcinoma (EC) cells such as PCC4 or F9 EC cells. All the viral mutants that have been selected for their expression in these cells harbor mutations or rearrangements within a region which is important for early and late transcription (as transcriptional enhancer) as well as for viral DNA replication. We have studied the role of the different parts of this enhancer on the transcription driven by early PyV promoter. Two series of constructions containing progressive deletions starting from the ends of the region and one series containing linker-scanning mutations were tested in a luciferase assay in three cell lines: 3T3, F9, or PCC4. The results revealed that some regions that have not yet been shown to bind transcription factors are nevertheless important for transcriptional activity. Two subregions between nucleotides 5179 and 5187 and between 5220 and 5227 were found to be inhibitory for the activity of the enhancer in EC cells. The PEA1/AP1 binding site was also unexpectedly shown to be important in F9 EC cells.

3T3 Cells↗
PubMed2005

Systematic mutation analysis of KIAA0767 and KIAA1646 in chromosome 22q-linked periodic catatonia.

BACKGROUND: Periodic catatonia is a familial subtype of schizophrenia characterized by hyperkinetic and akinetic episodes, followed by a catatonic residual syndrome. The phenotype has been evaluated in two independent genome-wide linkage scans with evidence for a major locus on chromosome 15q15, and a second independent locus on chromosome 22qtel. METHODS: In the positional and brain-expressed candidate genes KIAA0767 and KIAA1646, we searched for variants in the complete exons and adjacent splice-junctions as well as in parts of the 5'- and 3'-untranslated regions by means of a systematic mutation screening in individuals from chromosome 22q-linked pedigrees. RESULTS: The mutation scan revealed 24 single nucleotide polymorphisms, among them two rare codon variants (KIAA0767: S159I; KIAA1646: V338G). However, both were neither found segregating with the disease in the respective pedigree nor found at a significant frequency in a case-control association sample. CONCLUSION: Starting from linkage signals at chromosome22qtel in periodic catatonia, we screened two positional brain-expressed candidate genes for genetic variation. Our study excludes genetic variations in the coding and putative promoter regions of KIAA0767 and KIAA1646 as causative factors for periodic catatonia.

Case-Control Studies↗
PubMed2001

Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection.

SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large number of DNA samples is screened for specific mutations. Here we describe a novel combined SSCP/duplex analysis adapted to the modern capillary electrophoresis (CE) system, which takes advantage of multicolor labeling of DNA fragments and laser-induced fluorescence detection. In developing this method, we first established the optimum conditions for homoduplex and heteroduplex analysis by CE. These were determined based on comprehensive analysis of representative Tamra-500 markers and BRCA1 fragments at different concentrations of sieving polymer and temperatures in the presence or absence of glycerol. The intrinsic features of DNA duplex structures are discussed in detail to explain differences in the migration rates between various types of duplexes. When combined SSCP/duplex analysis was carried out in single conditions, those found to be optimal for analysis of duplexes, all 31 BRCA1 and BRCA2 mutations, polymorphisms and variants tested were detected. It is worth noting that the panel of analyzed sequence variants was enriched in base substitutions, which are usually more difficult to detect. The sensitivity of mutation detection in the SSCP portion alone was 90%, and that in the duplex portion was 81% in the single conditions of electrophoresis. As is also shown here, the proposed combined SSCP/duplex analysis by CE has the potential of being applied to the analysis of pooled genomic DNA samples, and to multiplex analysis of amplicons from different gene fragments. These modifications may further reduce the costs of analysis, making the method attractive for large scale application in SNP scanning and screening.

BRCA1 Protein↗
PubMed2001

Fast transient cytokine-receptor interactions monitored in real time by reflectometric interference spectroscopy.

Investigating protein-protein interactions by mutational analysis requires practical techniques for quantifying rate constants and equilibrium constants over several orders of magnitude with reasonably high sample throughput. We have employed spectroscopic interferometry for label-free monitoring of the interaction between the cytokine interferon alpha2 (IFNalpha2) and the extracellular domain of its receptor ifnar2 (ifnar2-EC). We implemented a versatile surface chemistry for the glass substrate of this transducer for covalent immobilization of proteins. Affinity capturing with a monoclonal anti-ifnar2-EC antibody (mAb) followed by crosslinking with a second, noncompetitive mAb provided stable, but still reversible, immobilization of ifnar2-EC. We measured kinetics and affinity of numerous of mutants of IFNalpha2 and ifnar2-EC. Dissociation rate constants up to 0.3 s(-1) and association rate constants up to 3 x 10(6) M(-)1 s(-1) were resolved by the system. Dissociation constants down to 200 microM were measured with protein concentrations up to 50 microM without no background signal or nonspecific binding. The instrument detection limit is approximately 10 pm without the need for temperature stabilization or referencing channels. The system proved effective for large-scale mutational analysis involving alanine scanning mutagenesis and double mutant cycles.

Antibodies, Monoclonal↗
PubMed1996

Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene.

In order to search for mutations in the multicopy RBM genes that might be associated with male infertility, we have used sequence data from the reported cDNA clone to determine the intron exon boundaries of the YRRM 1 gene. This gene has 12 exons, three of which encode the putative RNA binding domain of the protein. Different copies of the gene contain sequence variations and, additionally, give rise to transcripts with different numbers of copies of the repeated SRGY motif. Since mutations in the RNA binding domain would seem likely to have an effect on the activity of the protein, we have scanned these exons for mutations by SSCP on DNA from normal and infertile men. Sequence differences in the exon encoding the N-terminal part of the RNA binding domain account for at least four different classes of the gene and give rise to different SSCP conformers. Sequence analysis shows that one of these classes is a pseudogene and that the members of another class are nonfunctional. RT-PCR shows that all classes are transcribed and that the A class is most abundant. We have found a point mutation that alters the highly conserved RNP2 motif in one infertile patient. This mutation is also found in his father. We have used PCR followed by SSCP analysis to map RBM on a Y Chromosome (Chr) YAC contig and have demonstrated a distribution that spans a major part of this chromosome's euchromatin.

Amino Acid Sequence↗
PubMed2005

High-throughput scanning of breast tumor surgical specimens for low-level mutations.

Large numbers of mutations are postulated to occur as early events in carcinogenesis. For certain types of human tumors (mutator phenotypes) these mutations can be a driving force in generating clonogenic, causative genetic changes leading to multistage carcinogenesis. These low-level mutational events are highly significant due to their potential use as molecular markers for early identification of genomic instability that can lead to cancer and to their potential influence on the ability of tumors to resist drug treatment and/or metastasize. Detecting the presence and diversity of such genetic changes in human tumors is desirable due to their potential prognostic value. However, identification of these low-frequency genetic changes is difficult, since most mutations exist at mutant/wild-type ratios of <10(-3). We recently developed inverse PCR-based amplified restriction fragment-length polymorphism (iFLP), a new technology that combines inverse PCR, RFLP, and denaturing HPLC to allow scanning of the genome at several thousand positions per experiment for low-level point mutations. Using iFLP we previously demonstrated low-level mutations (mutation frequency <10(-3)) in human colon cancer cells that harbor mismatch repair deficiency and in sporadic colon cancer surgical specimens. In the present work we investigated whether low-level mutations are also present in sporadic breast cancer surgical specimens. Using iFLP we identified widespread low-level mutations in two out of ten surgical specimens examined (20%). Examination of the microsatellite instability status of these samples demonstrated that the samples are stable (MSI-S). We conclude that low-level mutations are less frequent in breast cancer than in colon cancer; however, single nucleotide instability that generates such mutations may still be present in a fraction of breast cancers.

Base Sequence↗
PubMed2001

Single nucleotide polymorphism (D68D, T to C) in the syntaxin 1A gene correlates to age at onset and insulin requirement in Type II diabetic patients.

AIM/HYPOTHESIS: Syntaxin 1A is a candidate gene for Type II (non-insulin-dependent) diabetes mellitus, because it plays an important role in insulin secretion from the islet beta cells. We aimed to scan this gene for mutations or genetic markers that correlate with Type II diabetes. METHODS: We identified and characterized coding exons of the syntaxin 1A gene and scanned the newly identified 10 exons using direct sequencing. RESULTS: In the single nucleotide polymorphism (SNP) of exon 3 (D68D, T to C) among three newly identified SNPs, genotype frequency of the homozygote of C allele (CC) occurred more frequently in a Type II diabetic group than in a non-diabetic group (16.48 %, n = 182, vs 11.05 %, n = 181, p = 0.0499). Among the diabetic patients, age of onset in patients with CC genotype was lower than that in patients with the TT and TC genotypes [40.10 +/- 1.50 years old (means +/- SEM) vs 44.20 +/- 0.58, p = 0.005]. Patients with the CC genotype had a higher frequency of insulin treatment (78.30 % vs 46.80 %, p = 0.006) with a duration equal to, or longer than, 10 years. Multiple regression analysis confirmed that the genotype was significantly and independently associated with age at onset and mode of treatment, respectively. CONCLUSION/INTERPRETATION: These data indicate that the SNP in the syntaxin 1A gene (D68D, T to C) correlates to the age of onset and insulin requirements of Type II diabetic Japanese patients.

Age of Onset↗
PubMed1998

Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays.

Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-oligonucleotide probes, 25 nucleotides in length, were designed to screen for all possible heterozygous germ-line mutations in the 9.17-kb coding region of the ATM gene. A strategy for rapidly developing multiexon PCR amplification protocols in DNA chip-based hybridization analysis was devised and implemented in preparing target for the 62 ATM coding exons. Improved algorithms for interpreting data from two-color experiments, where reference and test samples are cohybridized to the arrays, were developed. In a blinded study, 17 of 18 distinct heterozygous and 8 of 8 distinct homozygous sequence variants in the assayed region were detected accurately along with five false-positive calls while scanning >200 kb in 22 genomic DNA samples. Of eight heterozygous sequence changes found in more than one sample, six were detected in all cases. Five previously unreported sequence changes, not found by other mutational scanning methodologies on these same samples, were detected that led to either amino acid changes or premature truncation of the ATM protein. DNA chip-based assays should play a valuable role in high throughput sequence analysis of complex genes.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2003

Comparison of the CFTR mutation spectrum in three cohorts of patients of Celtic origin from Brittany (France) and Ireland.

This study aims to compare the spectrum of the mutations identified in the gene responsible for cystic fibrosis in three cohorts of patients of Celtic origin from Brittany and Ireland. It included 389 patients from Brittany, 631 from Dublin and 139 from Cork. The CFTR gene analysis relied on the detection of the most common mutations, followed by a complete gene scanning using DGGE or D-HPLC. High mutation detection rates were obtained in each cohort: 99.6%, 96.8%, and 96.0% respectively. A high frequency of the c.1652_1655 del3 mutation (F508del: 74.8% to 81.3%) and of the "Celtic" mutation (c.1784G>A (G551D): 3.7% to 9.7%) was observed in each population. Apart from this, the mutation spectrums differed. In Brittany, the most common abnormalities were: c.1078delT (3.6%), c.4041C>G (N1303K: 1.4%), c.2670G>A (W846X(2): 1.0%) and c.1717-1G>A (1.0%), whereas in the cohort of Dublin, the main mutations were: c.482G>A (R117H: 3.0%), c.1811G>C (R560T: 2.4%) and c.621+1G>T (1.7%). Finally, in the Cork area, only the c.482G>A mutation (R117H) reached a frequency of 1%. Two previously-unreported mutations were identified in the Dublin cohort: c.2623-2A>G and c.3446T>G (M1105R). This collaborative study highlights the similarities of the CFTR alleles in the Breton and Irish populations, but also the disparities that exist between these populations, despite their common origin. Each population has its own history, with its mixture of founder effects and genetic drifts, which are at the origin of the current mutation distribution. The molecular study of the CFTR gene provides new tools for retracing European populations' histories.

Alleles↗
PubMed1990

Direct detection of a missense mutation causing severe hemophilia A by PCR amplification and fluorescence scanning.

The amplification of Factor VIII gene-specific sequences, obtained by polymerase chain reaction, was used for hemophilia A carrier detection. Exon 24 sequences were employed in the carrier status determination of a missense mutation causing severe hemophilia A in two unrelated patients. After agarose gel electrophoresis, the digested DNA was subjected to quantitative determination of fluorescence. This technique significantly improves the digest analysis.

Base Sequence↗
PubMed1999

Two different mutations in the same codon of a type II hair keratin (hHb6) in patients with monilethrix.

Monilethrix is an autosomal dominant hair disorder characterized by a beaded appearance of the hair due to periodic thinning of the shaft. The phenotype shows variable penetrance and results in hair fragility and patchy dystrophic alopecia. Mutations of the helix-encoding region in two hair-specific keratins (hHb1 and hHb6) have been identified. We have now investigated two unrelated monilethrix patients and identified two different novel heterozygous point mutations of the same codon in exon 7 of the hHb6 gene. Dystrophic hair samples obtained from both patients showed the typical beaded appearance by scanning electron microscopy. Both mutations affected the first base of codon 402 (glutamic acid). In patient A, a G to C transition occurred causing a glutamine substitution (GAG to CAG: E402Q) whereas in patient B, the transition was G to A yielding a lysine substitution (GAG to AAG: E402K). The sequence of the 1A helical regions of hHb1 and hHb6 as well as the 2B helical region of hHb1, were normal. Unaffected relatives did not have the hHb6 mutation and this codon was found to be highly conserved showing no alteration in the normal population (100 alleles examined). Both mutations disrupted a Taq I restriction site and restriction fragment length polymorphism analysis showed that a diagnostic 361 bp fragment could confirm the mutation. Thus, two new point mutations of the hair-specific keratin gene hHb6 have been identified in this genetic disease.

Alopecia↗
PubMed1999

DNA diagnostics: goals and challenges.

The exponential increase in the discovery of human disease genes over the past 10 years has transformed DNA diagnostics from a minor research-based activity to a major professional operation. Mutation testing and linkage analysis are now used to provide prenatal or postnatal diagnosis for a wide range of monogenic disorders, but robust automated procedures for scanning disease genes for mutations are not yet available. The discovery of genes which confer susceptibility to common disorders is likely to create demand for high throughput testing for specific mutations or clinically relevant polymorphisms. Widespread genetic testing must be supported by adequate genetic counselling and by education of healthcare professionals in order to ensure the appropriate application of this information for the benefit of patients and their families.

Chromosome Mapping↗
PubMed2004

Molecular genetic diagnosis of familial tumors.

Recent advances in molecular biology have identified the responsible genes for many hereditary cancer syndromes (familial tumors). Therefore, now, the final diagnosis of familial tumors can be done by molecular methods to detect the genetic alteration in the disease-causing responsible gene(s) in the patient. So-called "genetic testing" is now available, not only as the diagnosis in the proband but also as the pre-symptomatic carrier diagnosis for unaffected family members. However, a number of issues, including legal, ethical, social, psychological, economic, and technical ones, surround and inhibit the clinical application of this testing, especially in Japan. As for molecular analysis to detect possible mutation in clinical specimens, highly sensitive scanning and detection methods are indispensable for screening nucleotide substitutions, including point mutations and single-nucleotide polymorphisms (SNPs). Also, several methods have been developed to screen and confirm the genetic alterations in familial tumors. These analytical techniques for detecting genetic alterations are categorized into four types, involving (1) scanning of nucleotide substitutions, (2) detection of defined mutations or SNPs, (3) size determination, and (4) DNA sequencing. Each technique has its advantages and disadvantages, and the technique in each case should be selected according to the purpose of the analysis. In this article, the concept of molecular diagnosis in familial tumors and the related molecular methods are described.

Genetic Predisposition to Disease↗
PubMed2000

Mizuo phenomenon observed by scanning laser ophthalmoscopy in a patient with Oguchi disease.

PURPOSE: To elucidate the origin of the abnormal fundus reflex in Oguchi disease. METHODS: The ocular fundus of a 63-year-old woman who showed a homozygous arrestin 1147delA mutation was observed by scanning laser ophthalmoscopy with the use of an argon blue laser (wavelength, 488 nm), a helium-neon laser (633 nm), and an infrared laser (780 nm). RESULTS: Diffuse, fine, white particles, which do not exist in normal subjects, were clearly demonstrated only with the helium-neon laser. After 4-hour dark adaptation, the abnormal particles disappeared, but then they reappeared gradually during 30 minutes of light adaptation, in accordance with the golden metallic reflex. CONCLUSION: The white particles found by helium-neon laser could be the origin of the abnormal fundus reflex in Oguchi disease.

Arrestin↗
PubMed2005

[A novel mutation of WFS1 gene in Chinese patients with Wolfram syndrome].

OBJECTIVE: Wolfram syndrome is an autosomal recessive disorder characterized by early-onset diabetes mellitus, diabetes insipidus, optic atrophy and deafness. The aim of this study was to scan the WFS1 gene mutations in a Chinese Wolfram syndrome pedigree. METHODS: Eight exons and flanking introns of WFS1 gene were screened using PCR-DNA direct sequencing. Effects of the mutation on the structure and function of the WFS1 gene product, Wolframin, were evaluated by bioinformatics. RESULTS: A novel mutation, F417del, in the WFS1 gene was identified. The patient was homozygous of this mutation and the consanguineous parents were heterozygous. The mutation causes the lose of a non-polar amino acid, which was located in the transmembrane domain of the protein product. Bioinformatics predicted that the mutation altered the secondary structure of the transmembrane domain and decreased the hydrophobicity of F417del protein. CONCLUSIONS: This study identified a novel mutation of WFS1 gene and represented the first cause of molecular characterization of Chinese Wolfram syndrome patients.

Adult↗
PubMed1995

Identification of 15 different candidate causal point mutations and three polymorphisms in 19 patients with protein S deficiency using a scanning method for the analysis of the protein S active gene.

To screen for point mutations causing protein S deficiency, we used a sequence of techniques specifically for the study of the protein S active gene, PS alpha. This strategy comprises amplification of exons and intron/exon junctions by means of the polymerase chain reaction (PCR) and electrophoresis of the amplified fragments in polyacrylamide gel containing a gradient of denaturing agents (denaturing gradient gel electrophoresis). Only fragments with altered melting behavior are sequenced after asymmetric PCR. Beside the frequent polymorphism already described on Pro 626, we detected 18 different sequence variations by studying exons II, IV, V, VIII, X, and XV in 19 of 100 consecutive patients with protein S deficiency. Fifteen were candidate causal mutations, 4 of which were associated with a qualitative deficiency (type IIa or IIb). The remaining three sequence variations were probably polymorphisms.

Base Sequence↗
PubMed1997

Induction of leaves directly from leaves in the maize mutant Lax midrib1-O.

One of the several phenes specified by the maize dominant mutation Lax midrib1-O (Lxm1-O on 3L) is the proliferation of leaf "flaps" usually paired around veins on the abaxial leaf surface. Using histology and scanning electron microscopy, we show these flaps to be authentic leaf structures; in rare instances, complete ectopic leaves are found. The first divisions preceding flap emergence occur between plastochrons 4 and 7, stages when the course of leaf differentiation is well under way. No sign of meristem or any small, densely cytoplasmic primordium-like cells were seen at the sites of flap initiation. In addition, the sites of ectopic leaf initiation do not express KNOX (Knotted-like homeobox) proteins, a molecular marker for shoot apical meristem cell identity. Thus, the cells that proliferate into ectopic leaves do not arise from a meristem or a primordium. A similar phenomenon has been described in several dicots, but in no other monocots. The details of flap morphology compared to the morphology of the leaf proper suggest a model whereby cells in regions of the leaf proper maintain the competence they acquired in the meristem. These cells then respond properly, in a regulated manner, to a delayed signal emanating from veins denoting "make the organ you are competent to make."

Meristem↗