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PubMed1995

Determination of ABO glycosyltransferase genotypes by use of polymerase chain reaction and restriction enzymes.

BACKGROUND: The molecular basis of red cell ABO group antigens has been determined. The genes encoding the group A and B glycosyltransferases and a nonfunctional group O transferase have been cloned and sequenced. All three genes were similar. When compared to the nucleotide sequence of the A gene, the O gene has a one-base deletion that leads to a frame shift and results in a nonfunctional protein. The B gene differs from the A gene at seven nucleotides. STUDY DESIGN AND METHODS: Techniques using polymerase chain reaction and restriction enzymes to determine ABO transferase genotypes from white cell DNA were modified. Nucleotide sequence differences within the genes were analyzed by the application of selected restriction enzymes. Restriction enzymes Asp718 and BstEII were used to analyze the genes at nucleotide 258, and BssHII and Kas I were used to analyze the genes at nucleotide 523. ABO red cell phenotypes were compared in 60 unrelated individuals with ABO transferase genotypes. The ABO phenotypes and genotypes of individuals from two different families were also analyzed to determine if this method could distinguish individuals who were homozygous for A or B transferase genes from those who were heterozygous. RESULTS: The phenotypes and genotypes were consistent for all unrelated individuals, and within the families, heterozygous individuals could be distinguished from homozygous individuals. Nevertheless, two individuals from one family were found to have a group A red cell phenotype, but when the transferase genes were analyzed at nucleotide 523 with enzymes BssHII and Kas I, both A and B transferase genes were detected. Further analysis of the transferase genes at nucleotide 700 by using restriction enzymes Alu I and Hpa II and those at nucleotide 793 by using enzyme BstNI found that both transferase genes in the two individuals were similar to the A transferase gene. CONCLUSION: An A allele of the group A glycosyltransferase was detected that had the same sequence as the B gene at nucleotide 523 but was identical to the A gene at positions 700 and 793. The identification of this variant gene makes genotyping at nucleotide 523 unreliable. However, analysis of the genes at other sites of nucleotide variation may accurately identify phenotypes.

ABO Blood-Group System↗
PubMed2003

Anatomy of the pulmonary veins in patients with atrial fibrillation and effects of segmental ostial ablation analyzed by computed tomography.

INTRODUCTION: The anatomic arrangement of pulmonary veins (PVs) is variable. No prior studies have quantitatively analyzed the effects of segmental ostial ablation on the PVs. The aim of this study was to determine the effect of segmental ostial radiofrequency ablation on PV anatomy in patients with atrial fibrillation (AF). METHODS AND RESULTS: Three-dimensional models of the PVs were constructed from computed tomographic (CT) scans in 58 patients with AF undergoing segmental ostial ablation to isolate the PVs and in 10 control subjects without a history of AF. CT scans were repeated approximately 4 months later. PV and left atrial dimensions were measured with digital calipers. Four separate PV ostia were present in 47 subjects; 3 ostia were present in 2 subjects; and 5 ostia were present in 9 subjects. The superior PVs had a larger ostium than the inferior PVs. Patients with AF had a larger left atrial area between the PV ostia and larger ostial diameters than the controls. Segmental ostial ablation resulted in a 1.5 +/- 3.2 mm narrowing of the ostial diameter. A 28% to 61% focal stenosis was present 7.6 +/- 2.2 mm from the ostium in 3% of 128 isolated PVs. There were no instances of symptomatic PV stenosis during a mean follow-up of 245 +/- 105 days. CONCLUSION: CT of the PVs allows identification of anatomic variants prior to catheter ablation procedures. Segmental ostial ablation results in a significant but small reduction in ostial diameter. Focal stenosis occurs infrequently and is attributable to delivery of radiofrequency energy within the PV.

Atrial Fibrillation↗
PubMed2003

Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units.

The study of genomic divergence between humans and primates may provide insight into the origins of human beings and the genetic basis of unique human traits and diseases. Chromosome 21 is the smallest chromosome in the human genome, and some of its regions have been implicated in mental retardation and other diseases. In this study, we sequenced the coding and regulatory regions of 127 known genes on human chromosome 21 in DNA samples from human and chimpanzees and a part of the corresponding genes from orangutan, gorilla, and macaque. Overall, 3,003 nucleotide differences between human and chimpanzee were identified over approximately 400 kb. The differences in coding, promoter, and exon-intron junction regions were 0.51 +/- 0.02%, 0.88 +/- 0.03%, and 0.85 +/- 0.02%, respectively, much lower than the previously reported 1.23% in genomic regions, which suggests the presence of purifying selection. Significant variation in substitution rate among genes was observed by comparing the divergence between human and chimpanzee. Furthermore, by implementing a bioinformatics-based approach, we showed that the identification of genetic variants specific to the human lineage might lead to an understanding of the mechanisms that are attributable to the phenotypes that unique to humans, by changing the structure and/or dosage of the proteins expressed. A phylogenetic analysis unambiguously confirms the conclusion that chimpanzees were our closest relatives to the exclusion of other primates and the relative divergence of the Homo-Pan and that of (Homo-Pan)-Gorilla are 4.93 million years and 7.26 million years, respectively.

3' Untranslated Regions↗
PubMed1978

Gonadotropin binding and stimulation of steroidogenesis in Leydig tumor cells.

Testicular tumors are generally characterized by a loss of responsiveness to gonadotropins. The M5480 Leydig cell tumor is unusual, if not unique, in that it responds to human choriogonadotropin and to lutropin via increased steroidogenesis. This report describes the identification of two variants of the original M5480 tumor that have altered steroid output both in the basal state and in response to human choriogonadotropin. One of the tumors produces mainly progesterone, which is stimulated by the choriogonadotropin; the other tumor produces about equal amounts of progesterone and testosterone, and the secretion of both is stimulated by the choriogonadotropin. The dissociation constant describing the interaction between Leydig tumor cells and (125)I-labeled human choriogonadotropin is between 3 and 5x10(-11) M. This agrees with values reported for normal Leydig cells, although the tumor cells appear to have fewer receptors. The differences noted in the two tumors and normal Leydig cells may have arisen from alterations in gene regulation, or in mutations, involving one or more enzymes in the pathway in which progesterone is converted to testosterone. Under the experimental conditions used, all the tumors studied (seven generations) responded to the choriogonadotropin both in binding and in the resultant stimulation of steroidogenesis. This property, together with the characteristic that a homogeneous cell population can be obtained without enzymatic treatment, should qualify the M5480 Leydig cell tumor(s) as a model system for further studies on the mechanism of action of gonadotropin, on hormone receptors, and on hormonally responsive tumors.

Animals↗
PubMed1983

Spontaneous H-2 mutants provide evidence that a copy mechanism analogous to gene conversion generates polymorphism in the major histocompatibility complex.

The analysis of H-2K products from spontaneously generated major histocompatibility complex (MHC) mutants and of the primary structure of other class I antigens suggests the genetic hypothesis that diversity in the MHC results from a copy mechanism analogous to gene conversion. The hypothesis was tested by making precise structural predictions about three partially characterized MHC mutants (bm1, bm3, and bm8). The predictions were based on consensus sequences among class I genes that differ from H-2Kb in the same region of the molecule as do the Kb mutants. In two cases (bm3 and bm8) we successfully predicted the correct amino acid substitution at positions known to be altered but for which the specific nature of the substitution had not been determined. In two additional cases (bm1 and bm8) we predicted and found both new mutation sites and the specific amino acid substitutions. The positions and identifications of the variant amino acids were determined by radiolabeled amino acid sequence analysis and DNA restriction endonuclease analysis. The interaction of MHC genes through a copy mechanism to generate diversity permits the introduction of multiple nucleotide base substitutions into class I sequences by a single genetic event. Such a mechanism may account in part for the large structural divergence among alleles of MHC loci and the high degree of MHC polymorphism among wild mice.

Amino Acid Sequence↗
PubMed2004

High level expression of human immunodeficiency virus type-1 Vif inhibits viral infectivity by modulating proteolytic processing of the Gag precursor at the p2/nucleocapsid processing site.

The human immunodeficiency virus type-1 Vif protein has a crucial role in regulating viral infectivity. However, we found that newly synthesized Vif is rapidly degraded by cellular proteases. We tested the dose dependence of Vif in non-permissive H9 cells and found that Vif, when expressed at low levels, increased virus infectivity in a dose-dependent manner. Surprisingly, however, the range of Vif required for optimal virus infectivity was narrow, and further increases in Vif severely reduced viral infectivity. Inhibition of viral infectivity at higher levels of Vif was cell type-independent and was associated with an accumulation of Gag-processing intermediates. Vif did not act as a general protease inhibitor but selectively inhibited Gag processing at the capsid and nucleocapsid (NC) boundary. Identification of Vif variants that were efficiently packaged but were unable to modulate Gag processing suggests that Vif packaging was necessary but insufficient for the production of 33- and 34-kDa processing intermediates. Interestingly, these processing intermediates, like Vif, associated with viral nucleoprotein complexes more rigidly than mature capsid and NC. We conclude that virus-associated Vif inhibits processing of a subset of Gag precursor molecules at the p2/NC primary cleavage site. Modulation of processing of a small subset of Gag molecules by physiological levels of Vif may be important for virus maturation. However, the accumulation of such processing intermediates at high levels of Vif is inhibitory. Thus, rapid intracellular degradation of Vif may have evolved as a mechanism to prevent such inhibitory effects of Vif.

CD4-Positive T-Lymphocytes↗
PubMed2005

Selective uncoupling of G alpha 12 from Rho-mediated signaling.

The heterotrimeric G protein G(12) has been implicated in such cellular regulatory processes as cytoskeletal rearrangement, cell-cell adhesion, and oncogenic transformation. Although the activated alpha-subunit of G(12) has been shown to interact directly with a number of protein effectors, the roles of many of these protein-protein interactions in G(12)-mediated cell physiology are poorly understood. To begin dissecting the specific cellular pathways engaged upon G(12) activation, we produced a series of substitution mutants in the regions of Galpha(12) predicted to play a role in effector binding. Here we report the identification and characterization of an altered form of Galpha(12) that is functionally uncoupled from signaling through the monomeric G protein Rho, a protein known to propagate several Galpha(12)-mediated signals. This mutant of Galpha(12) fails to bind the Rho-specific guanine nucleotide exchange factors p115RhoGEF and LARG (leukemia-associated RhoGEF), fails to stimulate Rho-dependent transcriptional activation, and fails to trigger activation of RhoA and the Rho-mediated cellular responses of cell rounding and c-jun N-terminal kinase activation. Importantly, this mutant of Galpha(12) retains coupling to the effector protein E-cadherin, as evidenced by its ability both to bind E-cadherin in vitro and to disrupt E-cadherin-mediated cell-cell adhesion. Furthermore, this mutant retains the ability to trigger beta-catenin release from the cytoplasmic domain of cadherin. This identification of a variant of Galpha(12) that is selectively uncoupled from one signaling pathway while retaining signaling capacity through a separate pathway will facilitate investigations into the mechanisms through which G(12) proteins mediate diverse biological responses.

Cadherins↗
PubMed2005

Primary lateral sclerosis, hereditary spastic paraplegia and amyotrophic lateral sclerosis: discrete entities or spectrum?

Among the motor neuron diseases, three share the clinical features of prominent upper motor neuron signs--amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS) and the hereditary spastic paraplegias (HSP). While genetic testing can assist in the identification of several variants of the latter, in the remaining cases, including those in which spasticity may be associated with amyotrophy, clinical differentiation of the three disorders may prove difficult. In this paper we review the evidence that these are distinct disorders and conclude that, for ALS and PLS particularly, there may be justification in considering them as single points along a continuum of multisystem disorders with conspicuous motor neuron involvement. Only through the development and application of exacting clinical diagnostic criteria to epidemiological studies, along with greater numbers of post-mortem examinations, however, will these questions be answered fully.

Amyotrophic Lateral Sclerosis↗
PubMed2004

Zinc absorption from low-phytate hybrids of maize and their wild-type isohybrids.

BACKGROUND: Identification of allelic variants in a single gene that determine the phytate content of maize kernels and the subsequent breeding of low-phytate maize have facilitated studies designed to determine quantitatively the effects of maize phytate on the bioavailability of minerals in maize. OBJECTIVE: The objective was to determine the relation between the fractional absorption of zinc (FAZ) and the phytate content and phytate:zinc molar ratios of maize tortillas prepared from hybrids with different phytate contents. DESIGN: Six healthy adults were fed, as the only food for 2 d, maize tortillas prepared from 1 of 2 low-phytate mutants: lpa1-1 (lpa1-1-LP) or Nutridense Low Phytate (ND-LP), which have phytate reductions of approximately 60% and approximately 80%, respectively, compared with their respective wild-type isohybrids. Four additional subjects were fed tortillas prepared from the corresponding wild-type isohybrids (lpa1-1-WT and ND-WT) according to the same study design. Meals were extrinsically labeled with zinc stable isotopes, and FAZ was determined with a dual-isotope-tracer ratio technique. Overall FAZ values were examined in relation to dietary phytate and phytate:zinc molar ratios by using a mixed nonlinear regression model. RESULTS: The mean (+/-SD) FAZ values from tortillas prepared from ND-LP, lpa1-1-LP, lpa1-1-WT, and ND-WT were 0.38 +/- 0.07, 0.28 +/- 0.04, 0.15 +/- 0.07, and 0.13 +/- 0.05, respectively. A negative relation (P < 0.001) was found between FAZ and both dietary phytate and the phytate:zinc molar ratio. The effect of dietary zinc (8-14 mg Zn/d) under these experimental conditions was not significant. CONCLUSIONS: FAZ from maize tortillas is positively related to the extent of phytate reduction achieved with low-phytate hybrids.

Adult↗
PubMed2026

map3C: a computational tool for processing multiomic single-cell Hi-C data.

SUMMARY: The emergence of multiomic single-cell Hi-C (scHi-C) methods, which simultaneously profile chromatin conformation and other modalities such as gene expression or DNA methylation, creates tremendous opportunities for studying the genome's structure-function relationships. Existing tools for processing multiomic scHi-C datasets lack certain key functions for downstream bioinformatics analysis. We present map3C, a software tool that incorporates additional key functions. Specifically, we demonstrate that map3C facilitates multiomic scHi-C processing, quality control, and identification of structural variant locations in the genome. AVAILABILITY AND IMPLEMENTATION: map3C is available at https://github.com/luogenomics/map3C and is archived at https://doi.org/10.5281/zenodo.20724719.

Software↗
PubMed1999

Forward genetics in mammalian cells: functional approaches to gene discovery.

Definitive proof of function in biological systems requires genetic analysis. Only when the loss of a particular protein corresponds to the loss of a specific function can one be sure that the protein truly affects the function. Changing the pattern of gene expression through random mutagenesis or by introducing expression libraries, followed by selection of mutant or variant cells and identification of a missing or overexpressed protein, has the power to reveal or confirm the roles of specific components of signaling pathways and to provide mutant cell lines and cDNA reagents to be used in defining detailed mechanisms through structure-function analyses. These examples of forward genetics contrast with reverse genetic approaches, where the function of a known gene product is explored by knockout or replacement. Here we review a broad range of techniques that have been used to alter gene expression randomly in mammalian cells, with examples of specific discoveries that have resulted from these applications of forward genetics.

Animals↗
PubMed2001

Translocation t(1;3)(p36.3;q25) is a nonrandom aberration in epithelioid hemangioendothelioma.

The cytogenetic findings for two epithelioid hemangioendotheliomas are reported. An identical chromosomal translocation involving chromosomes 1 and 3 [t(1;3)(p36.3;q25)] was detected in both cases of epithelioid hemangioendothelioma, possibly representing a characteristic rearrangement for this histopathologic entity. The presence of clonal karyotypic abnormalities supports a neoplastic origin for the epithelioid variant of hemangioendothelioma. Identification of the 1;3 translocation may be useful diagnostically. Should additional studies confirm these data, this could lead to the identification of the gene(s) central to this neoplastic process.

Adult↗
PubMed1989

Biological attributes of colony-type variants of Candida albicans.

Twenty 'commensal' oral or 'pathogenic' vaginal isolates of Candida albicans were examined for colony morphology on malt/yeast-extract and serum-based agar media. Diverse and variable colony morphology was seen on serum agar. In 17 strains, selective subculture of morphologically atypical colonies produced progeny which had reverted to the morphology of the majority of parental colonies. However, in one strain, a highly stable colony variant was isolated which did not revert on subculture. In two further strains, variants were isolated which could be maintained with at least 99% homogeneous colony type by selective colony subculture, but reversion to the parental type or switching to other morphologies occurred at rates of 10(-2) to 10(-4): a rapid switching phenomenon. The relative proportions of mycelial or yeast forms were the main determinants of colony morphology. The variants were biotyped using a selection of biochemical tests. The stable variant differed from its parent in several characters, including rate of production of a proteinase enzyme. The pathogenicity of variants was compared in mice, and both stable and switching variants differed in virulence from their parental strains. Colony-type variation on suitable media is thus a powerful tool in the isolation of mutants or variants of C. albicans which differ from 'isogenic' parents in significant biological properties. Such variants may aid identification and characterization at the molecular level of determinants of, for example, pathogenicity and morphogenesis.

Animals↗
PubMed1996

Monoclonal antibody recognition of members of the meningococcal P1.10 variable region family: implications for serological typing and vaccine design.

Identification of antigenic variants of the PorA protein of Neisseria meningitidis with specific mAbs (serosubtyping) is used in meningococcal strain characterization and the resultant data has been exploited in the design of novel multivalent vaccines against this important pathogen. The reactivity of the P1.10 serosubtyping mAb MN20F4.17 with eight members of the meningococcal P1.10 variable region (VR) family (prototype P1.10 and variants P1.10a-P1.10g), identified by nucleotide sequence analysis of porA genes, was investigated. Analysis of overlapping synthetic octapeptides by ELISA demonstrated that the peptide sequence, QNQRPTL, present only in the prototype P1.10, was sufficient for binding of the mAb. A linear peptide of 14 amino acids, containing the minimum epitope, inhibited binding of mAb MN20F4.17 to whole cells in a competitive ELISA. This binding was weak compared with a tethered peptide or the native protein. In whole-cell ELISA or dot-blot assays using low concentrations of mAb MN20F4.17 only the prototype P1.10 was detected. However, when higher concentrations of antibody were used the prototype P1.10 was detected, together with variants P1.10a, P1.10c and P1.10e by whole-cell ELISA and P1.10a and P1.10c by the immunoblot technique. The variants P1.10b, P1.10d, P1.10f and P1.10g showed no reactivity with mAb under any of the conditions tested. A survey of the porA genes in serogroup B and C strains revealed that the P1.10a variant, rather than the prototype P1.10, was the most common member of the P1.10 VR family in England and Wales. These data illustrate: (i) the problems associated with epidemiological analyses that rely solely on monoclonal antibodies; (ii) the importance of using defined assay conditions for serosubtyping; and (iii) that genetical analyses provide more reliable information than serological data based on murine reagents for the design of candidate vaccines that include PorA.

Amino Acid Sequence↗
PubMed1981

Factor VII deficiency: immunological characterization of genetic variants and detection of carriers.

Twenty-one patients with congenital factor VII deficiency belonging to 16 different kindreds were investigated. The existence of three immunochemical variants on the ground of factor VII activity (VII:C) and factor VII-related antigen (VII:Ag) levels (VII-, VII+ and VIIR) was established. There was no correlation between the presence of factor VII:Ag and either the clinical picture or the specific function as studied with the Km calculations. Genetically the model of inheritance is the same whatever the immunological variant, but the identification of carriers is simplified when the presence of factor VII-related antigen is assayed throughout a kindred.

Antigens↗
PubMed1990

Geographically distinct isolates of Mycobacterium leprae exhibit no genotypic diversity by restriction fragment-length polymorphism analysis.

Differentiation of microorganisms for taxonomic purposes is based primarily on phenotypic characteristics, which are the direct or cumulative result of gene expression. Since expression of phenotypic characteristics usually relies on in vitro growth of a microorganism, non-cultivable organisms, such as Mycobacterium leprae, present major problems for the identification of potential variants based on phenotypic similarities or differences between individual isolates. We have employed the use of restriction fragment-length polymorphism (RFLP) analysis of chromosomal DNA of M. leprae isolates, including human isolates from geographically distinct regions of the world and isolates from a Sooty Mangabey monkey and an armadillo, to assess the relatedness among these isolates. Restriction endonuclease (EcoRI, BstEII, PstI, and PvuI) digests of chromosomal DNA were analysed using DNA probes encoding all or part of the 12 kD, 18 kD, 28 kD, 65 kD and 70 kD proteins of M. leprae as well as a probe containing an M. leprae-specific sequence repeated up to 20 times in the M. leprae chromosome. Comparison of the resulting autoradiographs showed that the RFLP patterns were all identical, indicating that these isolates contained no polymorphism with respect to the restriction endonuclease sites analysed. In addition, RFLP patterns of two separate human M. leprae isolates remained unchanged after three cycles of experimental infection in the armadillo model. These results indicated that the M. leprae isolates tested in this study were indistinguishable at the genotypic level, strongly suggesting homogeneity among members of this species.

Animals↗
PubMed2006

Pyrosequencing for rapid identification of carbapenem-hydrolysing OXA-type beta-lactamases in Acinetobacter baumannii.

Carbapenem-resistant Acinetobacter baumannii isolates producing carbapenem-hydrolysing oxacillinases are emerging worldwide. These enzymes are divided into four phylogenetic subgroups: OXA-23-like, OXA-51-like, OXA-24-like and OXA-58-like. A PCR-based approach linked to pyrosequencing analysis was developed to identify the genes for these beta-lactamases. Carbapenem-hydrolysing oxacillinases were rapidly and unambiguously identified in a collection of carbapenem-resistant clinical isolates of A. baumannii and Acinetobacter junii. Pyrosequencing may provide a rapid tool for identification of OXA variants, thus avoiding delays inherent in classical sequencing methods.

Acinetobacter↗
PubMed1975

Genetic regulation: the Lac control region.

The nucleotide sequence of the lac promoter-operator region has been determined. The 122 base pairs comprising this region include the recognition sites for RNA polymerase, the positive regulatory protein, CAP, and the negative regulatory protein, the repressor. Identification of mutant variants of the sequence combined with the in vitro biochemical studies of others has allowed us to tentatively identify the recognition site for each of these proteins, and to suggest how CAP might act at a distance to affect the interaction of RNA polymerase with the promoter.

Base Sequence↗