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At least 361 records · Page 20Linked to original sources
PubMed1998

Systematic mutation screening of the estrogen receptor beta gene in probands of different weight extremes: identification of several genetic variants.

Estrogens are known to have an inhibitory effect on food intake in rodents and primates. Decreased estrogen levels that are found for instance in menopausal woman and in ovarectomized rodents result in body weight gain. Estrogen can act both in the periphery and in the central nervous system via at least two different estrogen receptors (alpha and beta). We systematically screened the coding region and part of the 5' and 3'regions of the estrogen receptor beta gene (ER beta) in 96 extremely obese children and adolescents, 50 patients with anorexia nervosa (AN), 28 patients with bulimia nervosa (BN), and 25 healthy underweight individuals. We detected five different sequence variants in the ER beta: a) A 21 bp deletion (codons 238 to 244) was detected in two obese probands and an underweight individual. b) An 846G-->A transition leading to a nonconservative amino acid substitution (G-250-S) was found in two obese male probands. Both a) and b) were located within the flexible hinge region between DNA and ligand binding domain. c) For a 1082G-->A polymorphism we found suggestive evidence for an association between the more common 1082G-allele and anorexia nervosa (nominal p=0.04). d) One silent mutation (1421T-->C) was found solely in two obese probands. e) A common variant is located in the 3' nontranslated region at position 1730(A-->G). We did not detect association of this polymorphism to any of the analyzed phenotypes. We conclude that the ER beta harbors several different mutations and polymorphisms, none of which can readily be associated with the phenotypes under study.

Adolescent↗
PubMed1998

Identification of new sequence variants in the leptin gene.

The leptin gene (LEP) has been linked to extreme obesity. However, no common obesity-related gene variants have been found to exist in the LEP. The present study was designed to investigate the LEP for variants by screening both the putative promoter and the coding region of this gene in obese Finnish subjects (n = 200; body mass index, > 27 kg/m2). PCR-amplified DNA samples were subjected to single strand conformation analysis. A G144A substitution in codon 48 and a G328A substitution in codon 110 were identified in two obese subjects, both of whom had very low serum leptin levels. A rare silent C538T polymorphism was detected 33 bp downstream of the translation stop codon (TGA). A common polymorphism A19G was identified in the untranslated exon 1. This polymorphism was not associated with traits of obesity; in agreement, the allele frequencies were similar between 64 normal weight and 141 obese Finns. In summary, this study failed to find a common gene variant in the LEP associated with obesity, but introduces 2 rare mutations associated with very low serum leptin concentrations in 2 obese subjects.

Adult↗
PubMed2002

Regulation of corticotropin-releasing hormone type 2 receptors by multiple promoters and alternative splicing: identification of multiple splice variants.

We demonstrate that multiple promoters and alternate splicing regulate expression of the human CRH receptor type 2 (CRHR2) gene. We show that flanking regions to the first exons drive promoter activity in both endogenously and nonendogenously expressing cell lines. Putative promoter elements have been identified that are conserved between species, including the comparison of CRHR2gamma in nonhuman primates that was previously known only in humans, which may be responsible for subtype tissue specific regulation. We have identified novel transcripts produced by alternate splicing of the first exon of CRHR2beta (beta1a) with various combinations of the 5' exons including a novel exon (beta1c) spliced to the common exons. The 5' structure of the gene permits many other combinations of alternate splicing that may arise as part of a regulatory mechanism controlling functional receptor expression. The 5'-untranslated region of the first exons has been extended; and 3' acceptor sites identified within the 5' untranslated region of CRHR2gamma and CRHR2alpha are used during alternate splicing of CRHR2beta upstream exons. This has important implications because various reports on the expression of CRHR2gamma and CRHR2alpha have been unable to discriminate between the functional receptor and CRHR2beta alternate splice variants. Only the described sequences upstream of the 3' splice site are unique to CRHR2gamma and CRHR2alpha.

5' Untranslated Regions↗
PubMed1992

Expression of messenger RNA for kit-ligand in human placenta: localization by in situ hybridization and identification of alternatively spliced variants.

Kit-ligand is a novel polypeptide growth factor which binds and activates the c-kit protooncogene, a receptor tyrosine kinase. We used the technique of reverse transcription-polymerase chain reaction to demonstrate the expression of this growth factor in human placenta. In situ hybridization showed that kit-ligand mRNA is expressed in cytotrophoblast and syncytiotrophoblast cells in the placenta, and in fetally derived extravillous trophoblast cells which have invaded the maternal endometrium. Five species of mRNA encoding variants of kit-ligand were identified by nested reverse transcription-polymerase chain reaction. Cloning and sequencing indicate that these variants arise by alternative splicing of the kit-ligand transcript. One of these species, KL486, uses a novel splice site in exon 8. There is a different pattern of expression of the variants in amnion, chorion, trophoblast, and placenta, indicating tissue-specific control of splicing.

Alternative Splicing↗
PubMed1997

Smoothelin expression characteristics: development of a smooth muscle cell in vitro system and identification of a vascular variant.

Recently we described a protein, smoothelin, that has been exclusively found in smooth muscle cells (SMC). The human cDNA has been cloned from a colon cDNA library and the putative protein sequence was deduced. Smoothelin does not belong to a known protein family but shows a partial homology with members of the spectrin family. Transfection studies revealed that smoothelin has an affinity for actin and is either capable of forming filamentous structures or colocalizes with such structures. The protein is expressed in visceral as well as vascular tissues of all vertebrate classes. A study on the distribution of smoothelin in the vascular and placental system showed that smoothelin expression was largely restricted to the muscular pulsating blood vessels. Therefore, we hypothesized that smoothelin is expressed in contractile SMC only (36, 37). No expression of smoothelin was observed in established cell lines of SMC. In tissue explants smoothelin mRNA concentration decreases to undetectable levels within 12 hours after dissection as was in general the case in primary cell cultures. Here we report on continued smoothelin expression for several passages observed in a human prostate primary cell culture system. Smoothelin was demonstrated to colocalize with actin stress fibers but not with desmin filaments. This culture system offers opportunities to study the cytological localization of smoothelin, interactions with other proteins and should provide a system to test the promoter of the smoothelin gene. On immunoblots the molecular weight of smoothelin differed between visceral and vascular smooth muscle tissue with apparent molecular weights of respectively 59 kDa and 94 kDa. There is no evidence for the existence of another gene coding for the 94 kDa smoothelin. Thus, posttranslational modification, alternative splicing and dual promoter control are the alternatives for the expression of two isoforms of smoothelin.

Adult↗
PubMed2025

Identification of novel PfEMP1 variants containing domain cassettes 11, 15 and 8 that mediate the Plasmodium falciparum virulence-associated rosetting phenotype.

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a diverse family of variant surface antigens, encoded by var genes, that mediates binding of infected erythrocytes to human cells and plays a key role in parasite immune evasion and malaria pathology. The increased availability of parasite genome sequence data has revolutionised the study of PfEMP1 diversity across multiple P. falciparum isolates. However, making functional sense of genomic data relies on the ability to infer binding phenotype from var gene sequence. For P. falciparum rosetting, the binding of infected erythrocytes to uninfected erythrocytes, the analysis of var gene/PfEMP1 sequences encoding the phenotype is limited, with only eight rosette-mediating PfEMP1 variants described to date. These known rosetting PfEMP1 variants fall into two types, characterised by N-terminal domains known as "domain cassette" 11 (DC11) and DC16. Here we test the hypothesis that DC11 and DC16 are the only PfEMP1 types in the P. falciparum genome that mediate rosetting, by examining a set of thirteen recent culture-adapted Kenyan parasite lines. We first analysed the var gene/PfEMP1 repertoires of the Kenyan lines and identified an average of three DC11 or DC16 PfEMP1 variants per genotype. In vitro rosette selection of the parasite lines yielded four with a high rosette frequency, and analysis of their var gene transcription, infected erythrocyte PfEMP1 surface expression, rosette disruption and erythrocyte binding function identified four novel rosette-mediating PfEMP1 variants. Two of these were of the predicted DC11 type (one showing the dual rosetting/IgM-Fc-binding phenotype), whereas two contained DC15 (DBLα1.2-CIDRα1.5b) a PfEMP1 type not previously associated with rosetting. We also showed that a Thai parasite line expressing a DC8-like PfEMP1 binds to erythrocytes to form rosettes. Hence, these data expand current knowledge of rosetting mechanisms and emphasize that the PfEMP1 types mediating rosetting are more diverse than previously recognised.

Plasmodium falciparum↗
PubMed2004

Identification of CYP2B6 sequence variants by use of multiplex PCR with allele-specific genotyping.

BACKGROUND: Cytochrome P450 2B6 (CYP2B6) has a role in the metabolism of many clinically important substances, but the variation within the CYP2B6 gene has not been fully characterized. The aim of the present study was to develop a reliable and robust assay for determining genotypic variants. METHODS: We used a two-stage procedure. An initial multiplex PCR reaction amplified the relevant gene fragments in exonic and regulatory regions to ensure isolation of CYP2B6 from its similar pseudogene (CYP2B7). This product was then genotyped by allele-specific PCR. RESULTS: The assay detected the following published single-nucleotide polymorphisms: C64T (Arg22Cys), C78T, G216C, G516T (Gln172His), C777A (Ser259Arg), A785G (Lys262Arg), and C1459T (Arg487Cys), as well as additional loci found within the single-nucleotide polymorphism (SNP) databases: A1190G, C1268A, C1330T, A1382G, A1402T, and an A/T SNP in intron 2 (A12917T). This approach detected all common, previously reported alleles and identified a new allele (CYP2B6*4C) present in 2.2% of a Caucasian population. Genotypic frequencies obtained were consistent with previously published results. CONCLUSIONS: This method is simple, reliable, rapid, and amenable to automation and could facilitate the large-scale genotypic analysis of CYP2B6.

Alleles↗
PubMed1991

The usefulness of sequence analysis of amplified DNA for the identification of delta chain variants.

A method of identifying delta chain variants using relatively small volumes of blood is described. The procedure consists of the amplification of two segments of genomic DNA with two sets of delta chain specific primers and sequencing of the three exons (exons 1, 2, and 3) which are part of the amplified DNA segments. Data for three delta chain variants present in seven adult heterozygotes are presented.

Adult↗
PubMed1993

Allele-specific amplification for the identification of several hemoglobin variants.

Eight known abnormal hemoglobins in more than 40 patients have been identified with an allele-specific amplification procedure. These are mutants of the A gamma (Hb F-Sardinia), the delta (Hb B2), the alpha (Hb G-Philadelphia), and the beta (Hbs S, C, E, D-Los Angeles, O-Arab) globin genes. Adjustment to an unusually high annealing temperature improves the procedure greatly, allowing excellent discrimination between normal and mutant alleles, irrespective of the particular mismatch. The discrimination includes the Hbs C and E in the same reaction mixture-multiplex allele-specific amplification. The procedure can successively use primers with 3'-penultimate critical nucleotides, degenerative ends, and potentially dimerizing properties.

Alleles↗
PubMed1995

Identification of CD44 splice variant in Korean colorectal cancers and cell lines.

CD44 is a glycoprotein expressed in a wide variety of cell types. Recently expression of some alternatively-spliced variants of CD44 transcripts (CD44v) has been suggested to play a potential role in tumor metastasis and the detection of CD44v containing exon 6 to 11 may be helpful for the diagnosis of cancers. Expressions of CD44v containing exon 6 to 11 were investigated in 20 human colorectal cancer samples, peripheral blood leukocytes isolated from colorectal cancer patients, and 4 colorectal cancer cell lines using reverse transcription-polymerase chain reaction and Southern blot analysis. The standard form of CD44 transcripts was expressed in all samples tested. CD44v containing exon 6 to 11 was expressed in 18 cases of colorectal cancers (sensitivity = 90%), 3 out of 4 cell lines, and one normal tissue (specificity = 95%). These results suggest that the expression of CD44v containing exon 6 to 11 can be regarded as tumor specific and that this marker may be helpful for the early diagnosis of colon cancers, if specimens from the early stage are available.

Adenocarcinoma↗
PubMed1996

Identification of two apolipoprotein variants, A-I Kaho (Asp 51-->Val) and A-I Lys 107 deletion.

We have identified two apolipoprotein (apo) A-I variants using isoelectric focusing gel electrophoresis: apo A-I Kaho which has a relative charge of +1 compared to normal apo A-I4, and apo A-I Nanakuma2 which has a relative charge of -1. Sequence analysis of PCR-amplified DNA from the proband of apo A-I Kaho revealed a single substitution of aspartic acid (GAC) for valine (GTC) at residue 51. Sequence analysis of PCR-amplified DNA from the proband of apo A-I Nanakuma2 revealed a three-base (AAG or AGA) deletion between bases 186 and 193 from the 5' end of exon 4 that leads to deletion of Lys 106 or 107. This mutation may be the same as that of apo A-I Marburg or A-I Munster-2 reported by Rall et al. (Rall SC Jr, Weisgraber KH, Mahley RW, Ogawa Y, Fielding CJ, Utermann G, Haas J, Steinmetz A, Menzel HJ, and Assmann G, J Biol Chem, 259: 10063-10070, 1984). Because of its unique sequence between 185 and 193 from the 5' end of exon 4 of apo A-I gene, we could not define whether AAG or AGA is deleted by DNA sequencing.

Adult↗
PubMed1999

Identification of JC virus variants in multiple tissues of pediatric and adult PML patients.

The transcriptional control region (TCR) of JC virus (JCV), the causative agent of progressive multifocal leukoencephalopathy (PML), undergoes rearrangement during replication of the virus in its human host. The mechanism by which viral promoter/enhancer sequences are deleted and duplicated within the TCR of the archetype form of JCV is not understood, but it is hypothesized that the generation of JCV variants with rearranged TCRs contributes to the virus's pathogenic potential. In a recent study of a pediatric PML patient, we detected extensive rearrangement of the JCV TCR in multiple tissues, and the archetype TCR was amplified from sites other than the kidney. These findings differed from those of previous studies that had examined tissues from adult PML patients. Since exposure to JCV usually occurs early in life, it is likely that some pediatric cases of PML arise as the result of a primary infection, whereas adult cases of PML are thought to result from the reactivation of an infection suffered as an immunocompetent child. To investigate further whether rearrangement of the JCV TCR is affected by the host's age and immune status at the time of exposure, a second pediatric patient and two adult PML patients were examined. As in our first study, multiple tissues were found to contain JCV DNA; however, fewer rearranged variants were detected. In one adult patient, related rearranged variants were detected in the brain, while archetype JCV was found in the other tissues. Based on differences in their VP1 sequences, these two forms represented different JCV genotypes, indicating that this patient had suffered a dual infection. The relevance of these findings to the rearrangement process that alters the JCV TCR is discussed.

Capsid↗
PubMed1998

Identification of two rare variants (G-->A at nucleotide 721; C-->T at nucleotide 5200) in the rhodopsin gene. Mutations in brief no. 187. Online.

The authors report two new rare DNA sequence variants in the Rhodopsin gene. This gene is involved in the pathogenesis of some retinal hereditary disorders as Retinitis Pigmentosa. These rare variants are G-->A at nucleotide 721 of the non-coding region and C-->T at nucleotide 5200 within codon 323 which does not alter the aminoacid cysteine. Therefore, they are not implicated in the development of the Retinitis Pigmentosa disease.

Adenine↗
PubMed2000

[Isolation and cytological identification of a desynaptic variant in rice].

A sterile variant was found from the population of a japonica rice variety Lunhui 422. Cytological investigation was conducted in meiosis. It is showed that the sterility was caused by desynapsis. As there were 8.69 bivalents in average occurred to be desynaptic, moreover, the most number of the desynaptic bivalents reached 12 at post diakinsis. It can be considered that the desynaptic variation is a complete desynapsis found in rice so far.

Mutation↗
PubMed2003

Identification of DYS385 allele variants by using shorter amplicons and Northern Thai haplotype data.

Primers currently used for amplification of locus DYS385 on the Y chromosome give quite long amplicons that are difficult to resolve on native polyacrylamide gels. We therefore designed new primers that give much shorter products for easy separation. With this system, two allele variants that were characterized by sequencing as 14.1 (GAAA --> GAAAA) and 14.2 (GA insertion), were identified in two unrelated Northern Thai men due to their decreased mobility. Interestingly, initial capillary electrophoresis mistyped the 14.1 variant amplified with the traditional primers as allele 14. Forty different haplotypes were found in 147 Northern Thais with a haplotype diversity of 0.9430. Haplotype 13-18 (frequency 0.136) is the most frequent one: for comparison: haplotype 14-18 (frequency 0.074) was found to be the most common in a population from Bangkok (n = 95) in an earlier study. This striking difference within Thailand's population probably results from genetic differences in the founding populations.

Alleles↗
PubMed2004

[Identification of G6PD gene variants from Hakka population in Guangdong province].

OBJECTIVE: Studying on G6PD polymorphism from Hakka population in Guangdong province. METHODS: Identifying the variants of G6PD gene and determining the frequencies respectively with the use of amplified refractory mutation system(ARMS), polymerase chain reaction-single strand conformation polymorphism(PCR-SSCP) and ABI 3100 DNA sequencing technologies. RESULTS: Mutations of G6PD gene in cDNA 1388 (G-->A), 1376 (G-->T), 95 (A-->G), 392 (G-->T), 1024 (C-->T), 1311 (C-->T) have been found. CONCLUSION: G6PD cDNA 1388 (G-->A), 1376 (G-->T), 95(A--> G), 392 (G-->T), 1024 (C-->T) and 1311 (C-->T) accompanied with intron 11 (93 T-->C) are the common mutations in Chinese population. cDNA 1388 (G-->A), cDNA 1376 (G-->T) are the most popular G6PD gene variants in Hakka population. In this study, no new type of G6PD gene mutation was found in the Hakkas of Guangdong.

Asian People↗