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PubMed2000

Alleles from chromosomes 1 and 3 of NOD mice combine to influence Sjögren's syndrome-like autoimmune exocrinopathy.

OBJECTIVE: NOD mice exhibit at least 2 overlapping autoimmune diseases: autoimmune endocrinopathy (Type I, insulin dependent diabetes) and autoimmune exocrinopathy (Sjogren's syndrome, SS). To date, 18 chromosomal regions have been identified that contribute to development of diabetes in NOD mice; however, genetic mapping of similar susceptibility loci for autoimmune exocrinopathy is just beginning. We investigated if these 2 autoimmune diseases share a genetic predisposition. METHODS: Congenic partner strains of NOD and C57BL/6 mice containing defined genetic intervals influencing susceptibility to diabetes (Idd) were screened for histological and biochemical markers for their effect on the development of SS-like disease. Saliva flow rates, protein concentration, amylase activity, and cysteine protease activity were evaluated. RESULTS: In contrast to the nonsusceptible parental C57BL/6 strain, C57BL/6.NOD Idd5 congenic partner strain, containing a genetic region derived from chromosome 1 of the NOD mouse, exhibited pathophysiological characteristics of autoimmune exocrinopathy. Replacement of individual diabetes susceptibility intervals Idd3, Idd5, Idd13, Idd1, and Idd9, as well as a combination of the Idd3, Idd10, and Idd17 intervals, with resistance alleles had little effect on development of autoimmune exocrinopathy. Conversely, NOD mice, in which the chromosome regions containing both Idd5 and Idd3 have been replaced by intervals derived from C57BL mice, exhibit a reduced pathophysiology associated with SS-like autoimmune exocrinopathy. CONCLUSION: Alleles on chromosomes 1 (Idd5) and 3 (Idd3) in combination appear to greatly influence susceptibility and resistance to development of autoimmune exocrinopathy. The association with certain Idd, but not other Idd loci, indicate that genetic overlap is present but probably not inclusive.

Alleles↗
PubMed2006

A novel single step double positive double negative selection strategy for beta-globin gene replacement.

beta-Thalassemias are a heterogeneous group of autosomal recessive disorders, characterized by reduced or absence of the beta-globin chain production by the affected alleles. Transplantation of genetically corrected autologous hematopoietic stem cell (HSC) is an attractive approach for treatment of these disorders. Gene targeting (homologous recombination) has many desirable features for gene therapy due to its ability to target the mutant genes and restore their normal expression. In the present study, a specific gene construct for beta-globin gene replacement was constructed consisting of: two homologous stems including, upstream and downstream regions of beta-globin gene, beta-globin gene lying between hygromycin and neomycin resistant genes as positive selection markers and thymidine kinase expression cassettes at both termini as negative selection marker. All segments were subcloned into pBGGT vector. The final plasmid was checked by sequencing and named as pFBGGT. Mammalian cell line COS-7 was transfected with linear plasmid by lipofection followed by positive and negative selection. DNA of the selected cells was analyzed by PCR and sequencing to confirm the occurrence of homologous recombination. In this novel strategy gene replacement was achieved in one step and by a single construct.

Animals↗
PubMedDate not supplied

A single-tube PCR test for the diagnosis of Angelman and Prader-Willi syndrome based on allelic methylation differences at the SNRPN locus.

The analysis of allelic methylation differences in 15q11-q13 has been established as a valid test for the Angelman and Prader-Willi syndromes. Current tests use methylation-sensitive restriction enzymes and Southern blot analysis. Here we describe a single-tube PCR test. It is based on sodium bisulfite treatment of DNA, which converts unmethylated, but not methylated cytosine residues to uracil, and PCR primers specific for the maternal and the paternal allele. The method was validated in a blinded retrospective study on 87 DNA samples from normal controls and patients. Prospective studies by independent laboratories will be needed before this assay can replace Southern blot analysis in routine diagnostic procedures.

Alleles↗
PubMed1995

Relationship between the reactivity to hepatitis B virus vaccination and the frequency of MHC class I, II and III alleles in haemodialysis patients.

To study the immunoreactivity genes in a heterogeneous human population needs a large number of individuals. Associations between HLA antigens and immunoresponse to viral or bacterial antigens have been studied with controversial results. As a homogeneous population, the MHC class I, II and III allele distribution was studied in 153 end-stage renal disease patients (ESRD, average duration of renal replacement: 8.2 + 5.1 years) immunized with a recombinant hepatitis B vaccine in accordance to the standard vaccination schedule. Thirty-four patients with an antibody titre of less than 10 U/l following the last booster injection were considered as non-responders while 119 patients with antibody titre equal to or more than 10 U/l were considered as responders. The responder group was divided into two subgroups: low responders (antibody titre: < or = 1000 U/l) and high responders (antibody titre: > 1000 U/1). Marked differences were observed between responders and non-responders in the occurrence of carriers of different MHC class I, II and III alleles. Homozygotes for HLA-A1, HLA-B8, HLA-DR3 and HLA-DQ2 were found almost exclusively in the non-responder group and significantly more heterozygotes for these alleles were found in the non-responder group compared to the responders. Similar albeit less marked differences were found in the frequency of some MHC class III alleles (C4A*6, C4A*QO, Bf*F, Bf*S0.7). Within the responder group, carriers of HLA-A2, HLA-B7 and HLA-DR4 were found to be clustered in the low responder sub-group whereas carriers of HLA-A1, HLA-B27, HLA-Cw2, C4A*6 and Bf*F were observed more frequently in the group of high responders. Similar differences were found with extended haplotypes as well. For example, the extended haplotypes HLA-A1, B8, BfS, C4AQO, C4B1, DR3, DQ2 and HLA-A1, B8, BfF, C4A6, C4B2, DR3, DQ2 were present in nine of 34 cases of non-responders but only in one of 119 case of responders (P < 0.000001). These observations indicate that the presence or absence of certain MHC alleles even in heterozygous form determine the responsiveness to hepatitis B vaccination in end-stage renal disease patients, and among responders, the intensity of antibody response is also markedly influence by immunogenetic factors.

Adult↗
PubMed1984

Replacement of serine 373 by phenylalanine in the alpha subunit of Escherichia coli F1-ATPase results in loss of steady-state catalysis by the enzyme.

The mutant allele (uncA401) of the gene for the alpha subunit of Escherichia coli F1-ATPase was cloned from the total DNA of the mutant AN120 on a hybrid plasmid pAN120. Determination of the DNA sequence of the alpha subunit gene from pAN120 revealed a single base change of cytosine at nucleotide residue 1118 to thymine and indicated that serine 373 was replaced by phenylalanine. It has been reported that the mutant F1 is defective in a step of steady-state catalysis, whereas its single turnover process is normal (Kanazawa, H., Noumi, T., Matsuoka, I., Hirata T., and Futai, M. (1984) Arch. Biochem. Biophys. 228, 258-269). Thus, we concluded that serine 373 in the alpha subunit is essential for steady-state catalysis by F1-ATPase.

Alleles↗
PubMed1992

Molecular analysis of human glycophorin MiIX gene shows a silent segment transfer and untemplated mutation resulting from gene conversion via sequence repeats.

The human glycophorin (HGp) loci that define the red blood cell surface antigens of the MNSs blood group system exhibit considerable allelic variation. Previous studies have identified gene conversion events involving HGpA(alpha) and HGpB(delta) that produced delta-alpha-delta hybrid genes which differ in the location of breakpoints. This report presents the molecular analysis of HGpMilX, the first example of a reverse alpha-delta-alpha hybrid gene that specifies a newly described phenotype of the Miltenberger complex. A novel restriction fragment unique to the HGpMilX gene was detected by Southern blot hybridization. The structure of the genomic region encoding the entire extracellular domain of the MilX protein was determined. Nucleotide sequencing of amplified genomic DNA showed that a silent segment of the HGpB(delta) gene had been transposed to replace the internal part of exon III in the HGpA(alpha) gene, thereby resulting in the formation of the MilX allele with an alpha-delta-alpha configuration. The proximal alpha-delta breakpoint was found to be flanked by a direct repeat of the acceptor splice site, whereas the distal delta-alpha breakpoint was localized to a palindromic region. This DNA rearrangement, with a minimal transfer of 16 templated nucleotides and a single mutation of untemplated adenyl nucleotide, not only created two intraexon hybrid junctions but transactivated the expression of a new stretch of amino acid residues in the MilX protein. Such a segment replacement may have occurred through the directional transfer from one duplex to the other via the mechanism of gene conversion. The occurrence of HGpMilX as another hybrid derived from parts of parent genes underlines the role of the recombinational "hotspot" in the generation of allelic diversity in the glycophorin family.

Amino Acid Sequence↗
PubMed1997

Detection of polymorphisms in the human urokinase-type plasminogen activator gene.

Expressed polymorphisms in the genes encoding components of the fibrinolytic cascade could have implications for the predisposition to thrombolytic disorders and/or for tumor metastasis. The occurrence of published two amino acid sequences at position 194 of the human urokinase-type plasminogen activator prompted us to search by SSCP for frequent polymorphisms in several exons of the gene. Surprisingly, only one sequence was detected in codon 194 (> 200 alleles). Two polymorphisms were observed in this study: the most frequent one, a C to T change near the beginning of exon 8, is probably silent; a less frequent polymorphism results in the replacement of a Leu residue by a Pro, in the kringle domain.

Alleles↗
PubMed2000

Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data.

Multilocus sequence typing (MLST) is a highly discriminatory molecular typing method that defines isolates of bacterial pathogens using the sequences of approximately 450-bp internal fragments of seven housekeeping genes. This technique has been applied to 575 isolates of Streptococcus pneumoniae and identifies a number of discrete clonal complexes. These clonal complexes are typically represented by a single group of isolates sharing identical alleles at all seven loci, plus single-locus variants that differ from this group at only one out of the seven loci. As MLST is highly discriminatory, the members of each clonal complex can be assumed to have a recent common ancestor, and the molecular events that give rise to the single-locus variants can be used to estimate the relative contributions of recombination and mutation to clonal divergence. By comparing the sequences of the variant alleles within each clonal complex with the allele typically found within that clonal complex, we estimate that recombination has generated new alleles at a frequency approximately 10-fold higher than mutation, and that a single nucleotide site is approximately 50 times more likely to change through recombination than mutation. We also demonstrate how to estimate the average length of recombinational replacements from MLST data.

Alleles↗
PubMed2002

Interleukin-6 from intrahepatic cells of bone marrow origin is required for normal murine liver regeneration.

Interleukin-6 (IL-6) is required for normal liver regeneration, but the specific cellular source of this growth factor is unknown. We investigated whether this signal originates from the resident macrophage, the Kupffer cell. Using a murine model of bone marrow transplantation, we replaced recipient bone marrow-derived cells, including Kupffer cells, with cells of donor genetic phenotype. Recipients deficient in IL-6 (IL-6(-/-)) were lethally irradiated, then rescued with 10(7) donor bone marrow cells capable of expressing IL-6 (IL-6(+/+)). Conversely, IL-6(+/+) recipients received IL-6(-/-) marrow. Successful engraftment was measured by the presence of the Y chromosome SRY locus in the livers of female recipients receiving male marrow, in situ IL-6 expression by Kupffer cells, and up-regulation of IL-6 in splenocytes after activation with lipopolysaccharide (LPS). Kupffer cell isolation in IL-6(-/-) females receiving IL-6(+/+) male marrow clearly showed the presence of the SRY locus and IL-6 disrupted allele, whereas males receiving female marrow demonstrated no SRY or IL-6 signals, confirming the extent of replacement. Replacement of these cells in IL-6(-/-) mice with IL-6(+/+) bone marrow successfully restored the regenerative response after partial hepatectomy (PHx) as indicated by signal transduction and activator of transcription 3 (STAT3) activation and hepatocyte DNA replication. Alternatively, complete replacement of Kupffer cells in IL-6(+/+) mice by transplantation with IL-6(-/-) cells significantly inhibited liver regeneration and was partially restored by administration of IL-6. This investigation demonstrates a paracrine mechanism by which cells of bone marrow origin, most likely Kupffer cells, regulate the regenerative capacity of the hepatocyte through IL-6 expression.

Animals↗
PubMed1999

Major histocompatibility complex differentiation in Sacramento River chinook salmon.

The chinook salmon of the Sacramento River, California, have been reduced to a fraction of their former abundance because of human impact and use of the river system. Here we examine the genetic variation at a major histocompatibility complex class II exon in the four Sacramento chinook salmon runs. Examination of the alleles found in these and other chinook salmon revealed nucleotide patterns consistent with selection for amino acid replacement at the putative antigen-binding sites. We found a significant amount of variation in each of the runs, including the federally endangered winter run. All of the samples were in Hardy-Weinberg proportions. A significant amount of genetic differentiation between runs was revealed by several measures of differentiation. Winter run was the most genetically divergent, while the spring, late-fall, and fall runs were less differentiated.

Alleles↗
PubMed1993

Isolation and characterization of two new functional subtypes of HLA-B35.

Human minor histocompatibility antigen-specific, HLA-B*3501-restricted cytotoxic T-cell clones were assayed on a panel of 25 different target cells previously typed by serology as HLA-B35. Cells from 6 donors were not killed and cells from 2 of these were further studied by molecular cloning to characterize their HLA class I alleles. Two new HLA-B35 subtypes were identified. The sequence of one of them differs from B*3501 by one nucleotide change at codon 156, replacing a Leu for an Arg. The sequence of the other new subtype also shows a single nucleotide change compared to B*3501, with Gly-->Val substitution at residue 16. With these new variants, the allelic complexity of HLA-B35 extends now to eight subtypes.

Alleles↗
PubMed1996

Requirement for the Candida albicans FAS2 gene for infection in a rat model of oropharyngeal candidiasis.

The virulence of Candida albicans strains deficient in fatty acid synthase activity by virtue of disruption/deletion of the FAS2 gene was examined in a rat model of oropharyngeal candidiasis. The FAS2 alleles of C. albicans CAI4 (delta ura3::imm434/delta ura3::imm434) were sequentially disrupted with a cassette that included a portion of FAS2 from which a 984 bp fragment containing the FAS condensing reaction domain was deleted and replaced with hisG-URA3-hisG sequences. Verification of fatty acid synthase inactivation was obtained from assays of enzyme activity. Strains in which a single allele was disrupted (CFD1 and CFD3) exhibited an approximately 20% reduction in activity, when compared to wild-type. In addition, fatty acid synthase activity was abolished in a FAS2 null mutant strain (CFD2), and growth of CFD2 occurred only when the growth medium was supplemented with Tween 40 and certain fatty acids. Strain CFD2 was avirulent in the rat model, indicating that fatty acid synthase activity is required for C. albicans oropharyngeal infection. Strains with a single FAS2 allele disruption colonized the oral cavity, but the number of cells recovered from infected animals was approximately fivefold less than for the parental strain. The results suggest that FAS may be exploited as a possible target for the development of new antifungal agents.

Alleles↗
PubMed1995

Allosteric regulation of carbamoylphosphate synthetase-aspartate transcarbamylase multifunctional protein of Saccharomyces cerevisiae: selection, mapping and identification of missense mutations define three regions involved in feedback inhibition by UTP.

The positive screening procedure previously described was used in order to select, clone and characterize mutants defective in negative feedback control by UTP of the yeast carbamoylphosphate synthetase-aspartate transcarbamylase protein (CPSase-ATCase). The selection procedure was improved by adding a general mapping method for dominant mutations in order to avoid sequencing the whole URA2 allele (7 kb). All 16 mutants obtained carry missense mutations leading to single amino acid replacements: five of them are located in the CPSase domain while the other 11 are in the ATCase domain. In these 16 mutants, ATCase is no longer inhibited by UTP although CPSase retains full sensitivity to the effector, suggesting that the regulation of the two activities involve distinct mechanisms. Amino acid replacements in the ATCase domain were located on a three-dimensional model structure of the yeast ATCase domain. They are clustered in two regions of this domain which must be directly involved in the feedback process.

Allosteric Regulation↗
PubMed1985

The F1F0-ATPase of Escherichia coli. The substitution of alanine by threonine at position 25 in the c-subunit affects function but not assembly.

A mutant strain of Escherichia coli carrying a mutation in the uncE gene which codes for the c-subunit of the F1F0-ATPase has been isolated and examined. The mutant allele, designated uncE513, results in alanine at position 25 of the c-subunit being replaced by threonine. The mutant F1F0-ATPase appears to be fully assembled and is partially functional with respect to oxidative phosphorylation. The ATPase activity of membranes from the mutant strain is resistant to the inhibitor dicyclohexylcarbodiimide, but this is due to the F1-ATPase being lost from the membranes in the presence of the inhibitor. Mutant membranes from which the F1-ATPase has been removed have a greatly reduced proton permeability compared with similarly treated normal membranes. The results are discussed in relation to a previously proposed mechanism of oxidative phosphorylation.

Amino Acid Sequence↗
PubMed1994

Rapid GDP release from Gs alpha in patients with gain and loss of endocrine function.

Luteinizing hormone stimulates testicular Leydig cells to produce testosterone by binding to a receptor that activates the G protein Gs and adenylyl cyclase. Testotoxicosis is a form of precocious puberty in which the Leydig cells secrete testosterone in the absence of luteinizing hormone, often due to constitutive activation of the luteinizing hormone receptor and (indirectly) Gs (refs 1-4). Here we study two unrelated boys suffering from a paradoxical combination of testotoxicosis and pseudohypoparathyroidism type Ia (PHP-Ia), a condition marked by resistance to hormones acting through cyclic AMP (parathyroid hormone and thyroid-stimulating hormone) as well as a 50% decrease in erythrocyte Gs activity (the remaining 50% is due to the normal Gs allele). In both patients, a mutation in the gene encoding the Gs alpha-subunit replace alanine at position 366 with serine. We show that this alpha s-A366S mutation constitutively activates adenylyl cyclase in vitro, causing hormone-independent cAMP accumulation when expressed in cultured cells, and accounting for the testotoxicosis phenotype (as cAMP stimulates testosterone secretion). Although alpha s-A366S is quite stable at testis temperature, it is rapidly degraded at 37 degrees C explaining the PHP-Ia phenotype caused by loss of Gs activity. In vitro experiments indicate that accelerated release of GDP causes both the constitutive activity and the thermolability of alpha s-A366S.

Adenylyl Cyclases↗
PubMed1996

Creation of homozygous mutants of Leishmania donovani with single targeting constructs.

Homozygous null mutants of the hypoxanthine-guanine phosphoribosyltransferase (hgprt) and adenine phosphoribosyltransferase (aprt) loci were created in Leishmania donovani in which both alleles were eliminated using only a single targeting construct. Functional heterozygotes were first generated by homologous recombination after transfection with vectors containing 5'- and 3'-flanking regions of either the hgprt or the aprt gene circumscribing drug resistance markers. Homozygous null mutants were then isolated from the heterozygotes by negative selection in media containing subversive substrates of the encoded proteins, i.e. allopurinol for HGPRT and 4-aminopyrazolopyrimidine for APRT. The novel alleles created by homologous recombination were verified by Southern blotting, and the effects of gene replacement upon gene expression in intact parasites were evaluated by direct enzymatic assay and by immunoblotting. All mutant strains were viable under the selection conditions and exhibited appropriate drug resistance phenotypes. The ability to generate homozygous knockouts with single targeting constructs greatly facilitates the genetic dissection and subsequent biochemical investigations of the purine pathway in Leishmania and has important general implications for the genetic manipulation and analysis of the leishmanial genome.

Adenine Phosphoribosyltransferase↗
PubMed1993

Pl-Bh, an anthocyanin regulatory gene of maize that leads to variegated pigmentation.

Anthocyanins are purple pigments that can be produced in virtually all parts of the maize plant. The spatial distribution of anthocyanin synthesis is dictated by the organ-specific expression of a few regulatory genes that control the transcription of the structural genes. The regulatory genes are grouped into families based on functional identity and DNA sequence similarity. The C1/Pl gene family consists of C1, which controls pigmentation of the kernel, and Pl, which controls pigmentation of the vegetative and floral organs. We have determined the relationship of another gene, Blotched (Bh), to the C1 gene family. Bh was originally described as a gene that conditions blotches of pigmentation in kernels homozygous for recessive c1, suggesting that Bh could functionally replace C1 in the kernel. Our genetic and molecular analyses indicate that Bh is an allele of Pl, that we designate Pl-Bh. Pl-Bh differs from wild-type Pl alleles in two respects. In contrast to the uniform pigmentation observed in plants carrying Pl, the pattern of pigmentation in plants carrying Pl-Bh is variegated. Pl-Bh leads to variegated pigmentation in virtually all tissues of the plant, including the kernel, an organ not pigmented by other Pl alleles. To address the molecular basis for the unusual pattern of expression of Pl-Bh, we cloned and sequenced the gene. The nucleotide sequence of Pl-Bh showed only a single base-pair difference from that of Pl. However, genomic DNA sequences associated with Pl-Bh were found to be hypermethylated relative to the same sequences around the wild-type Pl allele. The methylation was inversely correlated with Pl mRNA levels in variegated plant tissues. Thus, we conclude that DNA methylation may play a role in regulating Pl-Bh expression.

Alleles↗
PubMed2005

Functional conservation of Notch1 and Notch2 intracellular domains.

The Notch receptor is a key component of a highly conserved signaling pathway that regulates cell fate determination during development. In Drosophila, where Notch signaling was first identified and studied, there is only one Notch receptor. In contrast, mammals have four Notch receptor genes, Notch1-4. Notch1 and Notch2 are both required for embryo viability, are widely expressed in mammals, and are structurally conserved. It is presently unknown if these two receptors are functionally redundant or if they have unique capabilities related to differences in their amino acid sequences. In contrast to the rest of the molecule, the amino acid sequences of a large region of the Notch intracellular domain are not highly conserved and thus may be able to interact with distinct transcription factors and mediate the expression of different sets of genes. To determine if the function of this region is conserved, the last 426 amino acids of the Notch2 receptor have been replaced with the corresponding region of Notch1 in mice by using gene targeting. We have determined that even though the amino acid sequences of this region are only 37% identical (137/426), the C-terminal region of the Notch1 intracellular domain can functionally replace that of Notch2 in vivo.

Alleles↗