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PubMed2000

Analysis of relative binding affinity of E7-pRB of human papillomavirus 16 clinical variants using the yeast two-hybrid system.

A number of genotypes of the human papillomaviruses (HPV) are associated with malignancies of the uterine cervix. Sequencing work has revealed the existence of intratype HPV variants with minor differences in the nucleotide sequence. More recent data suggest the possibility that some of the variants may have different modes of clinical manifestation. In this study, sequences of the E6 and E7 oncogenes of 17 HPV16 isolates derived from PAP smear samples of Taiwanese patients were analyzed. A number of E6 and E7 novel variants were found. Particularly, a prevalent (64.7%) E6 polymorphic site A442C with an E113D amino acid substitution seems specific to Taiwanese patients. In E7, two novel but silent polymorphic sites G663A (41.2%) and T846C (88.2%) were also prevalent in the samples analyzed. The yeast two-hybrid system was adopted for rapid assessment of relative E7-pRb binding affinity in the variants. The relative binding affinities of the E7 proteins of different HPV types to pRB were in close agreement with previous biochemical data. A T663G/C24W polymorphic change in E7 correlated with a decrease in E7-pRb relative binding affinity the significance of which remains to be clarified. This semi-quantitative biochemical and genetic approach may be useful as a first step in the development of clinical protocols for the screening and identification of important HPV variants for clinical interpretation and for further functional analysis by transfection or other bioassays.

Female↗
PubMedDate not supplied

Analysis of hemoglobin variants by capillary isoelectric focusing.

Clinical laboratory evaluation of congenital hemoglobin disorders requires both the accurate identification of major and minor hemoglobin variants, and precise quantitation of these variants over a wide range of concentrations. Capillary isoelectric focusing is an automated, microanalytical technique that produces diagnostic information comparable to that obtained from multiple conventional assays now used by most hospital laboratories. This report describes the advantages of capillary isoelectric focusing for the routine primary assessment of hemoglobinopathies and thalassemias. The use of capillary isoelectric focusing for the identification of unusual hemoglobinopathies, including an extremely rare doubly heterozygous disorder (hemoglobin C/E disease), is described. Application of the technique for rapid (< 4 minutes) neonatal hemoglobinopathy screening, and for the analysis of Hb A1c to monitor glycemic control in diabetic subjects is also discussed. In an increasingly competitive and cost-conscious clinical diagnostic market, capillary isoelectric focusing is a rapid, specific, precise, and low-cost method for comprehensive primary analysis of hemoglobin variants.

Electrophoresis, Capillary↗
PubMed2001

VpsR, a Member of the Response Regulators of the Two-Component Regulatory Systems, Is Required for Expression of vps Biosynthesis Genes and EPS(ETr)-Associated Phenotypes in Vibrio cholerae O1 El Tor.

The rugose colonial variant of Vibrio cholerae O1 El Tor produces an exopolysaccharide (EPS(ETr)) that enables the organism to form a biofilm and to resist oxidative stress and the bactericidal action of chlorine. Transposon mutagenesis of the rugose variant led to the identification of vpsR, which codes for a homologue of the NtrC subclass of response regulators. Targeted disruption of vpsR in the rugose colony genetic background yielded a nonreverting smooth-colony morphotype that produced no detectable EPS(ETr) and did not form an architecturally mature biofilm. Analysis of two genes, vpsA and vpsL, within the vps cluster of EPS(ETr) biosynthesis genes revealed that their expression is induced above basal levels in the rugose variant, compared to the smooth colonial variant, and requires vpsR. These results show that VpsR functions as a positive regulator of vpsA and vpsL and thus acts to positively regulate EPS(ETr) production and biofilm formation.

Amino Acid Sequence↗
PubMed2002

Two novel CD1 E alleles identified in black African individuals.

CD1 gene (CD1A to CD1E) products are involved in non-peptide antigen presentation, such as lipids and glycolipids, to T cells. With a similar function to MHC, namely antigen presentation, these genes nevertheless displayed a much lower level of polymorphism as compared to MHC. We report here two additional CD1E variants identified in black African individuals, designated herein CD1E*05 and CD1E*06. While the former differs from the common (wild type) allele sequence by two substitutions at nucleotide positions 217 and 229 of exon 2, the latter only by a single base change at position 91 of exon 3. These substitutions lead to amino acid changes at position 73 and 77 of the alpha1 domain in the former and at position 30 of the alpha2 domain in the latter. Identification of these additional variants suggests that the CD1 locus, especially the CD1E gene, is much more polymorphic than previously assumed.

Africa↗
PubMed2005

Genetic variants of Complex I in multiple sclerosis.

HYPOTHESIS: A mitochondrial mechanism contributes to neurodegeneration in multiple sclerosis (MS). Genetic variants of Complex I genes may influence the nature of tissue response to inflammation in the central nervous system (CNS). BACKGROUND: Complex I is encoded by seven mitochondrial and 38 nuclear genes. Many of the nuclear genes colocalize with regions where full genome scans detected linkage in MS. Previous studies revealed an association between variants of mitochondrial (mt)DNA encoded subunits of Complex I and MS. Biochemical studies suggested a functional involvement of Complex I in the degenerative processes downstream to inflammatory injury in the CNS. METHODS: Patients with all MS phenotypes were included. DNA specimens of affected sib pair, trio and multiplex families were studied. Single nucleotide polymorphisms (SNP) were determined by using the Taqman assay. The association of MS with nuclear DNA encoded alleles and haplotypes of Complex I was tested by the pedigree disequilibrium test (PDT) and by the transmit program in the families. Haplotypes were further investigated by using ldmax (GOLD). The association of mtDNA encoded variants with MS was tested by the Fisher's Exact Test. RESULTS: The previously identified MS-associated mtDNA variants and haplotypes were not increased in mothers as compared to fathers in these families. However, an association of all clinical phenotypes with haplotypes within NDUFS5 (1p34.2-p33), NDUFS7 (19p13) and NDUFA7 (19p13) was detected. The inclusion of families with primary progressive (PP)-MS phenotype did not modify the outcome and, as a subgroup alone, did not have a sufficient size to draw conclusion regarding phenotype specific associations. CONCLUSIONS: SNP haplotypes within Complex I genes are associated with MS. Further studies are needed to refine the identification of disease relevant variants nearby or within these haplotypes. Molecular and functional properties of Complex I subunits may offer novel explanations to better understand the relationship between inflammation and neurodegeneration.

Alleles↗
PubMed2001

Three aberrant splicing variants of the HMGIC gene transcribed in uterine leiomyomas.

Cytogenetic aberrations involving chromosome region 12q13-15 occur frequently among benign mesenchymal tumors in humans, e.g., pleomorphic adenomas of the parotid gland, pulmonary chondroid hamartomas, lipomas, or uterine leiomyomas. HMGIC, a gene encoding a protein of the high-mobility group, has been identified as a target of those events. Using the 3' rapid amplification of cDNA ends (RACE) technique, we identified six different fusion transcripts of the HMGIC gene among 13 uterine leiomyomas; three of these variants had not been described before. Radiation-hybrid mapping located all three of the novel fusion transcripts in the same chromosomal region as the HMGIC gene. Cloning of the entire HMGIC gene in a genomic contig of P1-derived artificial chromosomes and cosmids revealed that the 3' portion of each novel fusion transcript contained cryptic exonic sequences (designated a, b, and c) present in intron 3 of the HMGIC gene. Thus, aberrant alternative splicing was responsible for abnormal HMGIC isoforms in those myomas. Identification of these novel variants suggested that aberrant splicing can join chromosomal translocation and inversion as a mechanism for producing abnormal HMGIC transcripts, and that separation of the DNA binding domains of HMGIC from its acidic carboxyl-terminal regulatory domain can lead to development of benign mesenchymal tumors.

Alternative Splicing↗
PubMed2005

Estrogen receptor-alpha splice variants in the medial mamillary nucleus of Alzheimer's disease patients: identification of a novel MB1 isoform.

Previously we have reported an increased nuclear estrogen receptor-alpha (ERalpha) in the medial mamillary nucleus (MMN) in Alzheimer's disease (AD). In the present study, we addressed the presence of specific ERalpha mRNA splice variants in this brain area of five AD cases compared with five controls using the RT-PCR and quantitative RT-PCR approach. Indeed, the occurrence of isoforms with the deletion of exons 7 (del.7), 4 (del.4), or 2 (del.2) was determined in all patients. However, there were no significant differences in the relative transcription levels of each of the mentioned splice variants between AD and control cases, although the ratio of the del.7 isoform to the canonical ERalpha mRNA was higher in controls. Given that exons 7 and 4 encode the ligand-binding domain of the ERalpha, whereas exon 2 encodes the DNA-binding domain, abundant expression of these splice variants suggests that much of the available ERalpha in the MMN of AD and elderly control patients is nonfunctional because they will be unable to bind either the ligand (del.7 and del.4 variants) or the estrogen-responsive elements on appropriate DNA (del.2 variant). Yet, the wild-type ERalpha mRNA appeared to be 2- to 3-fold up-regulated in AD, confirming the rise in the nuclear immunocytochemical staining and pointing to the potential for a beneficial effect of estrogen replacement therapy on the MMN-associated cognitive functions in AD because it represents the availability of potentially functional ERalpha in the MMN. Noteworthy, the expression of the wild-type, del.7, and del.2 mRNAs declined with advanced age in both AD and control patients. Interestingly, we have identified in two AD and two control patients a novel ERalpha splice variant that we called MB1 (mamillary body, exon 1) with a 168-nucleotide deletion corresponding to a U2-type intron inside exon 1 encoding the major portion of the transactivation function 1 domain of the receptor.

Aged↗
PubMed2001

Secreted variant of nucleoside diphosphate kinase from the intracellular parasitic nematode Trichinella spiralis.

The molecular components involved in the survival of the parasitic nematode Trichinella spiralis in an intracellular environment are poorly characterized. Here we demonstrate that infective larvae secrete a nucleoside diphosphate kinase when maintained in vitro. The secreted enzyme forms a phosphohistidine intermediate and shows broad specificity in that it readily accepts gamma-phosphate from both ATP and GTP and donates it to all nucleoside and deoxynucleoside diphosphate acceptors tested. The enzyme was partially purified from culture medium by ATP affinity chromatography and identified as a 17-kDa protein by autophosphorylation and reactivity with an antibody to a plant-derived homologue. Secreted nucleoside diphosphate kinases have previously been identified only in prokaryotic organisms, all of them bacterial pathogens. The identification of a secreted variant of this enzyme from a multicellular eukaryote is very unusual and is suggestive of a role in modulating host cell function.

Animals↗
PubMedDate not supplied

[Neuropathology of the new variant of Creutzfeldt-Jakob disease].

Identification in the United Kingdom of cases of Creutzfeldt-Jakob disease with clinical, genetic, neuropathological and phenotype characteristics different from those previously reported, together with its relation to bovine spongiform encephalopathy led to the establishment of a new condition known as a new variant of Creutzfeldt-Jakob disease. In this article we describe the neuropathology and immunohistochemistry of the prion protein involved.

Animals↗
PubMed2006

Identification in triatomine vectors of feeding sources and Trypanosoma cruzi variants by heteroduplex assay and a multiplex miniexon polymerase chain reaction.

Feeding sources of triatomine vectors (Triatoma longipennis) collected in peridomiciles in Mexico were identified by a heteroduplex assay developed with triatomine blood meals. Trypanosoma cruzi parasites were also characterized in the same blood meal samples by multiplex-polymerase chain reaction assay of mini-exon gene inter-genic regions. The main blood meal source was from rats, but the bugs were able to feed on a wide variety of hosts, and human blood meals were identified. Trypanosoma cruzi was the only flagellate species identified in the blood meals. All populations belong to the T. cruzi I lineage, a result that is consistent with the previously assumed predominance of this lineage in Mexico. This combination of blood meal and T. cruzi lineage identification provides a powerful tool for understanding T. cruzi transmission cycles.

Animals↗
PubMed1977

[Generalized saturnine paralysis. Discovery of a double congenital disease: glucose-6-phosphate dehydrogenase deficiency (new variant) and distal tubular acidosis].

A case of severe lead poisoning with haemolytic anemia, extensive polyneuropathy and arterial hypertension is reported in a patient for whom G-6-P-D deficiency and renal tubular acidosis were discovered. Both traits were present in his family. Incomplete regression of paralysis and persistant biological abnormalities after chelating treatment were demonstrative of heavy saturnine load even though the toxic exposure was brief. The role of the two deficiencies in the mechanism of intoxication is discussed: facilitation of haemolysis by enzymopathy and bone lead redistribution resulting from osteolysis probably due to the tubulopathy. The authors emphasize the fact that thorough and serial biological investigation is essential in the discovery of factors which may precipitate lead poisoning, as well as in the determination of follow-up criteria of efficient toxic epuration with sufficient delay. Typing of the enzyme has led to the identification of a new variant of glucose-6-phosphate dehydrogenase deficiency.

Acidosis, Renal Tubular↗
PubMed1977

Isolation of UV-sensitive variants of CHO-K1 by nylon cloth replica plating.

Techinques are described which permit the identification and isolation of UV-sensitive variants from mutagenized populations of Chinese hamster ovary (CHO) cells. Identification is based on the observation that within two days after receiving a dose of approximately 240 ergs/mm2 of UV irradiation most of the cells in a colony of CHO detach from the surface of a plastic tissue culture dish. At a lower dose of UV, which does not kill or detach a significant number of parental cells, UV-sensitive colonies are killed and become detached. Thus a clear plaque is produced in a lawn of unirradiated parental cells, marking the site occupied by a sensitive colony. Live cells from such sensitive colonies have been recovered from a nylon cloth replica prepared prior to irradiation and characterized. One UV-sensitive variant (CHO-UV-1) is indistinguishable from parental cells in X-ray resistance, chromosome number, generation time, and duration of the phases of the cell cycle. For UV irradiation the hit number (-n), shoulder width (Dq), and mean lethal dose (Do) for the variant are 2.8, 21 ergs/mm2, and 21 ergs/mm2, respectively, as compared to 2.6, 36 ergs/mm2, and 45 ergs/mm2 for CHO-K1 cells. These values have not changed for a period of eight months in culture.

Cell Line↗
PubMed2006

Polymorphisms within the lactoferrin gene promoter in various cattle breeds.

Lactoferrin (Lf) is an iron-binding protein and belongs to the serum transferrin family. It has broad spectrum antimicrobial action, and it is found in exocrine secretions including milk. The sequence of the bovine lactoferrin gene promoter was analyzed in five different cattle breeds (Holstein Friesian, New Zealand Holstein, Montebéliard, Normande, and Norwegian Red) to determine the extent of polymorphic variation, which exists in this region both within and across cattle breeds. Fifteen different single nucleotide polymorphisms (SNPs) were identified throughout this region. Numerous polymorphisms were found throughout the Holstein Friesian, New Zealand Holstein, Montebéliard, and Normande populations. The most frequently encountered polymorphism found in all breeds was at position -28, which is immediately proximal to the TATA box of the promoter. The most variable base position was -131, which included three types of heterozygotes including a single base deletion in one allele, and three homozygote variants. This polymorphism occurs in a putative transcription factor binding site, for the nuclear factor of activated T cells (NF-ATc). A unique polymorphism was identified in one Normande animal, and three polymorphisms were found in one Montebéliard animal. In general, Norwegian Red cattle displayed fewer SNPs than other breeds. Most nucleotide changes in these animals were within the 190 base pairs of the transcription start point, with the exception of an insertion seen in three animals at position -478. In conclusion, SNPs were found in abundance throughout this regulatory region. Whether or not these polymorphisms have an effect on the regulation of the bovine lactoferrin gene is yet to be elucidated. However, the identification of lactoferrin promoter variants may serve as a marker for healthier animals, thereby accelerating the improvement of animals through breeding.

Animals↗
PubMed1998

Hb Peterborough [beta 111(G13)Val-->Phe] in Japan; rapid identification by ESI/MS using proteolytic digests of oxidized globin.

A variant hemoglobin was found in a Japanese female whose hemoglobin was studied to clarify the cause of a low Hb A1c value, found during a routine medical examination. The detection and identification of the variant was performed by electrospray ionization mass spectrometry. Its structure was revealed to be the same as Hb Peterborough [beta 111(G13)Val-->Phe]. For sequence determination, oxidized globin as well as non-derivatized globin were cleaved by trypsin and lysyl endopeptidase. An abnormal peptide was found in digests of oxidized globin, as shown by electrospray ionization mass spectrometry. Cysteic acid in oxidized peptides enhanced the abundance of fragment ions in tandem mass spectrometry, which helped to quickly and accurately determine the substitution in beta T-12, a peptide in the core region. Electrospray ionization mass spectrometry analysis of the hemolysate also showed a low level of glycated hemoglobin. The patient's hemolysate showed decreased stability in the isopropanol test. An abnormal band was detected on isoelectrofocusing on the cathodic side of normal Hb A. This is the second report of Hb Peterborough and the first of its occurrence in Japan.

Adult↗
PubMed2002

[RadGenomics project].

Human health conditions are largely determined by a complex interplay among genetic susceptibility, environmental factors, and aging. The RadGenomics project, which began in April 2001, promotes analysis of genes in response to irradiation, identification of their allelic variants in the human population, development of an effective procedure for quantitating individual radio-sensitivity, and analysis of the interrelationship between genetic heterogeneity and susceptibility to irradiation. Major groups of genes with which the project will concern itself include DNA repair genes, cell cycle genes, oncogenes, tumor suppressor genes, genes for programmed cell death, genes for signal transduction, and genes for oxidative processes. The outcome of the RadGenomics project should lead to improved protocols for personalized radiotherapy and reduce the possible side effects of treatment. The project will contribute to future research on the molecular mechanisms of radiation sensitivity in humans and stimulate the development of new high-throughput technology for a broader application of the biological and medical sciences. Identification of functionally important polymorphisms in the radiation response genes may determine individual differences in sensitivity to radiation exposure. The staff members, who are specialists in a variety of fields including genome science, radiation biology, medical science, molecular biology, and bioinformatics, have come to the RadGenomics project from various universities, companies, and research institutes.

Animals↗
PubMed1999

Two-dimensional gene scanning: exploring human genetic variability.

Current methods for mutation detection are not optimized for the generation of highly accurate data on multiple genes of hundreds of individuals in population-based studies. Two-dimensional gene scanning (TDGS) is a high-resolution system for detecting mutational variants in multiple genes in parallel. TDGS is based on a combination of extensive multiplex polymerase chain reaction (PCR) and two-dimensional (2-D) DNA electrophoresis. The latter involves a size separation step followed by denaturing gradient gel electrophoresis (DGGE). TDGS tests for a number of large human disease genes have been designed, using a computer program to optimally position PCR primers around the relevant target sequences (e.g., exons) and evaluated using panels of samples with previously detected mutations. The results indicate a high sensitivity and specificity, equal to nucleotide sequencing, which is generally considered as the gold standard. Here, we describe the different components of the TDGS process and its potential application as a high-throughput system for the systematic identification of human gene variants.

Automation↗
PubMed1998

Human herpesvirus type 6 variants identified by single-strand conformation polymorphism analysis.

Six human herpesvirus 6 (HHV-6) variants were analyzed for heterogeneity using the polymerase chain reaction (PCR) and single-strand conformation polymorphism (SSCP). Two independent DNA regions were selected: a fragment of the gene U11 (position 18966-21578) coding for a basic phosphoprotein, the major antigenic structural protein pp100; and a fragment from an open reading frame (ORF) area of the gene U67, previously referred to as 13R (position 102458-103519), coding for a product of unknown function. The two PCR systems based on the above DNA sequences yielded products of 187 bp and 223 bp, respectively. DNA obtained from three laboratory reference strains (U1102, R104 and St.W.) and from HHV-6 infected peripheral white blood cells of bone marrow transplant patients and blood donors was used to test the applicability of two different SSCP analysis systems for the identification of HHV-6 variants using amplicons derived by PCR from the two genomic regions described above (U11 [pp100], U67 [13R-ORF]). The generation of characteristic SSCP patterns enables the rapid differentiation of HHV-6 A and B strains for the classification of variants derived from clinical samples, reducing the need for expensive and time-consuming direct sequencing analyses.

Base Sequence↗
PubMed2026

First nationwide full-genome characterisation of human-derived Andes virus in Chile: a retrospective genomic epidemiology study.

BACKGROUND: Andes virus (ANDV) is the only hantavirus known to transmit between humans and causes hantavirus cardiopulmonary syndrome in Chile and Argentina. In Chile, ANDV genomic diversity remains incompletely characterised. This study aimed to characterise the genetic diversity, geographical structure, and molecular signatures of ANDV using human clinical samples collected over a 13-year period (2011-24). METHODS: We conducted a retrospective genomic epidemiology study of ANDV infections in Chile. Clinical samples from patients with confirmed ANDV, collected between March 9, 2011, and June 27, 2024, were analysed and sequenced. Clinical and epidemiological data were obtained from diagnostic laboratories and surveillance programmes. Consensus sequences for the S, M, and L segments were generated, and genetic clustering and divergence were assessed using phylogenetic inference and variant calling. FINDINGS: We analysed clinical samples from 58 infected individuals and identified two major genomic variants of ANDV with distinct geographical distributions, defined by regionally structured patterns of nucleotide and amino acid substitutions across the S, M, and L segments: ANDV Chi-North (central Chile) and ANDV-South (southern Chile). No consistent clustering by clinical severity was observed, and no recurrent non-synonymous substitutions were uniquely associated with severe disease. Substitutions previously associated with person-to-person transmission in outbreaks in Argentina were not consistently observed in Chilean sequences, including in four person-to-person transmission cases. Although some substitutions described in ANDV-like viruses were present in the Chi-North lineage, this lineage remained phylogenetically distinct and geographically restricted to central Chile. INTERPRETATION: To our knowledge, this study provides the first nationwide genomic characterisation of human-derived ANDV in Chile. The identification of geographically structured variants indicates that ANDV diversity in Chile is driven by regional diversification rather than clinical outcome. The absence of consistent amino acid signatures associated with disease severity or person-to-person transmission suggests that these phenotypes are unlikely to be explained by viral genetic variation alone. These findings refine current understanding of ANDV evolution and highlight the need for continued integrated genomic surveillance in endemic regions. FUNDING: Agencia Nacional de Investigaci&#xf3;n y Desarrollo de Chile and National Institutes of Health.

Humans↗