Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant calling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources

Production of cytolethal distending toxins by pathogenic Escherichia coli strains isolated from human and animal sources: establishment of the existence of a new cdt variant (Type IV).

Three types of cytolethal distending toxin (CDT), namely, CDT-I, CDT-II, and CDT-III, have been described in Escherichia coli. Using primers designed for the detection of sequences common to the cdtB genes, we analyzed by PCR a set of 21 CDT-producing E. coli strains of intestinal and extraintestinal origins isolated from human and different animal species in several European countries and in the United States. On the basis of the existing differences in the cdtB genes, cdt-I-, cdt-II-, and cdt-III-specific primer pairs were designed and used for cdt typing. These new primers successfully differentiated all of the previously described cdt genes. Six strains proved to be cdt-I; eight strains proved to be cdt-III. However, none of the type I-, II-, and III-specific primers generated amplicons from six CDT(+) strains, suggesting the existence of a new cdt variant. Sequence analysis of the amplicons from two untypeable genes confirmed the existence of a new cdt variant that we called cdt-IV. Using the new specific primers, cdt-IV was detected in human, porcine, and poultry strains of intestinal and extraintestinal origins. To validate all sets of cdt specific primers, a group of 353 human E. coli strains isolated in Hungary was then investigated for the presence of cdt genes. This included 190 strains isolated from patients with urinary tract infections (UTI), 51 strains isolated from other (nonurinary) extraintestinal infections, and 112 intestinal strains isolated from healthy individuals. Of 190 UTI strains, 15 (7.9%) had cdt genes. Of 51 non-UTI extraintestinal strains 3 (5.9%) contained the cdt gene, and 1 (0.9%) of 112 healthy intestinal strains was PCR positive. Five strains proved to be cdt-I, and fourteen strains proved to be cdt-IV. The CDT-producing extraintestinal strains belonged to a wide variety of serogroups, including O2, O6, O75, and O170. In conclusion, we have developed a new PCR typing system for CDT able to detect a new CDT variant present in pathogenic E. coli strains obtained from animals and humans.

Animals↗

Candidate adenoviruses 40 and 41: fastidious adenoviruses from human infant stool.

About 200 antigenically related adenoviruses were isolated from cases of infantile diarrhoea in the Netherlands and North-West Germany. The viruses were fastidious and failed to replicate serially in human diploid fibroblasts and in primary human embryonic kidney cells. A number of strains were established in HeLa, HEp-2, Graham (293), cynomolgus monkey kidney, and Chang conjunctival cells. The viruses were mammalian adenoviruses by the usual criteria. No relationship to the 39 known human adenovirus species was found, either by neutralization tests or by haemagglutination inhibition tests. Neutralization tests showed two distinct variants, represented by strains Tak and Dugan. The variants were identical in haemagglutination inhibition tests. DNA restriction enzyme analysis showed Tak and Dugan to have considerably different genomes, indicating that these variants should be classified as different species (Wadell et al, 1983). It is proposed that the variants should be called Mastadenovirus h 40 (with reference strains Dugan and Hovi X) and Mastadenovirus h 41 (with reference strain Tak). Neutralization and haemagglutination inhibition tests demonstrated that the viruses from Glasgow and Helsinki (Hovi X) described by Johansson et al [1980] and by Kidd and Madeley [1981] belong to these two adenovirus species.

Adenoviridae Infections↗

NABC1 (BCAS1): alternative splicing and downregulation in colorectal tumors.

We have identified a new splicing variant of the gene "novel amplified in breast cancer 1," NABC1 (HGMW-approved symbol BCAS1). This variant, which we call NABC1_5B, uses a previously unidentified 135-bp exon. Also in this report, we confirm that NABC1 is overexpressed in breast tumors and show that both NABC1 and NABC1_5B are downregulated in colorectal tumors.

Alternative Splicing↗

No strategy is evolutionarily stable in the repeated prisoner's dilemma.

Following the influential work of Axelrod, the repeated Prisoner's Dilemma game has become the theoretical gold standard for understanding the evolution of co-operative behavior among unrelated individuals. Using the game, several authors have found that a reciprocal strategy known as Tit for Tat (TFT) has done quite well in a wide range of environments. TFT strategists start out co-operating and then do what the other player did on the previous move. Despite the success of TFT and similar strategies in experimental studies of the game, Boyd & Lorberbaum (1987, Nature, Lond. 327, 58) have shown that no pure strategy, including TFT, is evolutionarily stable in the sense that each can be invaded by the joint effect of two invading strategies when long-term interaction occurs in the repeated game and future moves are discounted. Farrell & Ware (1989, Theor. Popul. Biol. 36, 161) have since extended these results to include finite mixes of pure strategies as well. Here, it is proven that no strategy is evolutionarily stable when long-term relationships are maintained in the repeated Prisoner's Dilemma and future moves are discounted. Namely, it is shown each completely probabilistic strategy (i.e. one that both co-operates and defects with positive probability after every sequence of behavior) may be invaded by a single deviant strategy. This completes the proof started by Boyd and Lorberbaum and extended by Farrell and Ware. This paper goes on to prove that no reactive strategy with a memory restricted to the opponent's preceding move is evolutionarily stable when there is no discounting of future moves. This is true despite the success of a more forgiving variant of TFT called GTFT in a recent tournament among reactive strategies conducted by Nowak & Sigmund (1992, Nature 355, 250) where future moves were not discounted. GTFT, for example, may be invaded by a pair of reactive mutants. Since no strategy is evolutionarily stable when future moves are discounted in the repeated game, the restriction of strategy types to those actually maintained by mutation and phenotypic and environmental variability in natural populations may be the key to understanding the evolution of co-operation. However, the result presented here that the somewhat realistic reactive strategies are also not evolutionarily stable at least in the non-discounted game suggests something else may be going on. For one, the proof that no reactive strategy is evolutionarily stable ironically shows the robustness of TFT-like strategies.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

A novel case of compound heterozygosity with "Normandy"/type I von Willebrand disease (vWD). Direct demonstration of the segregation of one allele with a defective expression at the mRNA level causing type I vWD.

We report the case of a family with type I von Willebrand disease (vWD), characterized by a quantitative defect in von Willebrand factor (vWF), associated with a defective binding of vWF to factor VIII (FVIII) also called the "Normandy" variant of vWD. PCR products from genomic DNA of the family members were analysed in the region coding for the binding domain of vWF to FVIII. It showed that the proposita and one of her sons were heterozygous for the Arg91Gln missense mutation, abolishing an MspI restriction enzyme site located in exon 20. The transcription of the normal and mutated alleles was tested by the amplification of cDNA after reverse transcription of platelet mRNA in this region. A total lack of expression of the normal allele was observed in the proposita, who appeared as a compound heterozygous with one allele mutated at Arg91 and a "silent" expression of the other one. The segregation of the "silent" allele was studied in the family with the exonic BstEII RFLP both at the DNA and mRNA levels. The proposita has transmitted her "silent" allele to her daughter and to another son. As this son was informative for this RFLP, the absence of expression of the allele could be demonstrated at the mRNA level, providing evidence that this defect was responsible for his type I vWD.

Alleles↗

1.3E2, a variant of the B lymphoma 70Z/3, defective in activation of NF-kappa B and OTF-2.

The mouse B-cell cell lymphoma 70Z/3 is a convenient model system in which to study the regulation of immunoglobulin synthesis. Three transcriptional activators of kappa (kappa) light chain synthesis have been identified for these cells: bacterial lipopolysaccharide (LPS), interferon-gamma (IFN), and interleukin-1 (IL-1). The response of the kappa gene in 70Z/3 cells to LPS is mediated by increases in two transcription factors: NF-kappa B and OTF-2. In contrast, IFN has no effect on either of these factors in 70Z/3 cells. We have isolated by immunoselection an LPS- IFN+ variant of 70Z/3 called 1.3E2. We show here that LPS treatment of these cells causes no increase in nuclear localization of either NF-kappa B or OTF-2. Although they have normal levels of cytoplasmic NF-kappa B, it cannot be activated by LPS or by phorbol 12-myristate 13-acetate (PMA) treatment of the cells. These experiments expand the genetic dissection of the molecular pathways of activation of kappa transcription in 70Z/3 cells.

Animals↗

Hemoglobin types in Saanen goats and Barbary sheep: genetic and comparative aspects.

By the use of the Immobiline technique at pH ranges 7.0-7.6 and 6.9-7.9, 16 different hemoglobin (Hb) phenotypes were observed in 61 English Saanen goats. They are explained in this breed by a genetic theory of five beta-globin genes (A4, A6, A8, E, and D) and two closely linked alpha-globin loci ('alpha and "alpha) of which the "alpha has a variant allele, provisionally called "alpha X. Family data together with observed and expected Hb frequencies were in agreement with the genetic theory. Among six Barbary sheep there were three Hb phenotypes explained by the occurrence of the beta-chain alleles B and Cna.

Alleles↗

Growth advantage ("clonal dominance") of metastatically competent tumor cell variants expressed under selective two- or three-dimensional tissue culture conditions.

In previous experiments it was shown that injection into syngeneic CBA/J mice of cell mixtures containing an excess of non-metastatic SP1 mouse mammary carcinoma cells with a ras transfected metastatic variant of SP1 called C1, always resulted in the eventual dominance of the C1 subpopulation at the site of inoculation. This occurred despite the growth rates of the two cell populations being identical in vivo when grown separately. The means by which the C1 subpopulation achieved "clonal dominance" is thought to involve its responsiveness to stimulatory paracrine growth factors liberated by the non-metastatic SP1 population. The clonal dominance process, however, could not be recapitulated in conventional monolayer tissue culture conditions in which SP1 and C1 cells were grown together in high concentrations of serum, i.e. under non-limiting culture conditions. We now show that clonal dominance of C1 cells can be observed when the cell mixture is maintained in tissue culture for extended periods, or when the cells are grown under selective, limiting conditions, some of which may mimic growth conditions in vivo more accurately. These conditions were a) growth in low (limiting) serum concentrations; and b) growth as three-dimensional multicellular aggregates, i.e. as "tumor spheroids". Under all of these conditions dominance of the C1 subpopulation always took place, but with an efficiency 6- to 40-fold less than generally observed in vivo. C1 cells were also able to form more stable (compact) spheroids compared to SP1 cells. Entrapment of the latter in mixed C1/SP1 spheroids increased the recovery of the SP1 cells suggesting some kind of "rescue" mechanism in which cells are protected from physical forces by three-dimensional structure. The relevance of these in vitro interactions for clonal dominance in primary tumors and metastasis in vivo are discussed.

Adenocarcinoma↗

Ulnar variance in Kienböck's disease.

Forty four patients with forty seven wrists suffering from Kienböck's disease were re-examined. The mean observation time was 20.5 years. In all forty seven wrists the treatment had been immobilization. Using a standard X-ray projection, and a reliable method of ulnar variance measuring, the ulnar variance was determined by three observers independently. Comparing the result with the ulnar variance in normal wrists we found the so-called "ulnar minus variant" overrepresented in patients with Kienböck's disease. However, comparing X-rays taken at the time of diagnosis with X-rays at re-examination, we found in eight out of forty seven wrists that a subchondral bone formation in the distal radium opposite the lunate bone had taken place. This bone formation will tend to enhance the negative value of ulnar variance measurements, and suggests an explanation of the overrepresentation of "ulnar minus variants" in Kienböck's disease. Excluding these eight wrists from the material and comparing the mean ulnar variance value in the remaining thirty nine wrists with the mean value in normal wrists no statistical difference was shown. Based on these observations it seems unlikely that the "ulnar minus variant" has any bearing on the cause of Kienböck's disease.

Adolescent↗

Kienböck's disease--the influence of arthrosis on ulnar variance measurements.

The individual difference in ulnar variance measurements between diseased and unaffected wrists in 38 patients with unilateral Kienböck's disease was determined and related to the degree of arthrosis in the affected wrists. In patients without arthrosis there was no difference in measurements. With increasing arthrosis there was a progressive increase of patients with individual difference in ulnar variance measurements: up to 50% in those with severe arthrosis. Where a difference in ulnar variance was encountered, the wrist with Kienböck's disease represented the more negative value in 90%. It is concluded that over-representation of the so-called "ulnar minus variant" in Kienböck's disease is based on osteo-arthritic changes in the wrist, resulting in a pseudo-lengthening of the distal radius, and that this is therefore a consequence of the disease. The "ulnar minus variant" seems to have no bearing on the cause of Kienböck's disease.

Adult↗

Distribution of [Leu31,Pro34]NPY-sensitive, BIBP3226-insensitive [125I]PYY(3-36) binding sites in rat brain: possible relationship to Y5 NPY receptors.

Recently, using molecular cloning approaches, three new neuropeptide Y (NPY)/peptide YY (PYY) receptors have been described in rodent brain, with pharmacological profiles that differ from the three previously described Y1, Y2 and Y3 NPY receptors and the Y4 pancreatic polypeptide- (PP-) preferring receptor. Two of these new receptors are spice variants and are called Y5 receptors, whilst a third receptor has been called Y6 and has been suggested to be expressed only in the mouse. In the absence of a totally selective Y5 and/or Y6 radioligands, we have examined [125I]PYY(3-36) binding, which binds Y2 and Y5/Y6 receptors, using homogenate assays and quantitative receptor autoradiography to study the distribution of the three newly discovered Y5/Y6 receptors by masking binding to Y1 receptors with high concentrations of the non-peptidergic selective Y1 antagonist, BIBP3226, and using either [Leu31,Pro34]NPY or human PP to mask binding to Y5 and Y6 receptors, leaving binding to Y2 receptors. Using this approach, [125I]PYY(3-36) labels a small population of Y1 receptors and a larger population of binding sites that are insensitive to BIBP3226, human PP and [Leu31,Pro34]NPY, presumed to be Y2 receptors. There was also [125I]PYY(3-36) binding to sites sensitive to NPY, human PP and [Leu31,Pro34]NPY, but insensitive to BIBP3226, located in the hypothalamus, amygdala, hippocampus and thalamus. As one of the recently cloned Y5 receptors is synthesized in these regions, as shown by in-situ hybridization techniques, we suggest that the small population of [125I]PYY(3-36) binding sites which are sensitive to human PP and [Leu31,Pro34]NPY, but insensitive to BIBP3226, may represent binding to Y5 receptors. We have been unable, however, to visualize a smaller population of Y6 receptors which are labelled by [125I]PYY3-36 and sensitive to [Leu31,Pro34]NPY, but not to BIBP3226 and human PP, confirming that the murine Y6 receptor does not appear to be expressed in rat brain.

Animals↗

Role of electron microscopy in the evaluation of soft tissue neoplasms, with emphasis on spindle cell and pleomorphic tumors.

The current significant role of transmission electron microscopy in the evaluation of soft tissue tumors when correlated with conventional histological and immunohistochemical studies is discussed for the following entities: myxofibrosarcoma, storiform-pleomorphic fibrosarcoma (malignant fibrous histiocytoma), and myofibrosarcoma; dermatofibrosarcoma protuberans; hemangiopericytoma; monophasic synovial sarcoma; extrarenal rhabdoid tumor; soft tissue perineurioma; and gastrointestinal stromal tumors, notably the so-called autonomic nerve variant.

Adult↗

Assessing the (a)symmetry of concentration-effect curves: empirical versus mechanistic models.

Modeling the shape of concentration-effect curves is of prime importance in pharmacology. Geometric descriptors characterizing these curves (the upper and lower asymptotes, the mid-point, the mid-point slope, and the point of inflection) are used for drug comparison or for assessing the change in agonist function after a system modification. The symmetry or asymmetry around the mid-point of a concentration-effect curve is a fundamental property that, regretfully, is often overlooked because, generally, models yielding exclusively symmetric curves are used. In the present review, empirical and mechanistic models are examined in their ability to fit experimental data. The geometric parameters of a survey of empirical models, the Hill equation, a logistic variant that we call the modified Hill equation, the Richards function, and the Gompertz model are determined. To analyze the relationship between asymmetry and mechanism, some examples from the ionic channel field, in an increasing degree of complexity, are used. It is shown that asymmetry arises from ionic channels with multiple binding sites that are partly occupied. The operational model of agonism is discussed both in its empirical general formulation and including the signal transduction mechanisms through G-protein-coupled receptors. It is shown that asymmetry results from systems where receptor distribution is allowed. Developed mathematical models are compared for describing experimental data on alpha-adrenoceptors. The existence or not of a relationship between the shape of the curves and receptor reserve is discussed.

Animals↗

Structure/function analysis of the domains required for the multimerisation of phenylalanine hydroxylase.

Phenylalanine hydroxylase (PAH) exists as an equilibrium of dimers and tetramers. However, there is little information concerning the inter- or intra-molecular interactions required for enzyme quaternary structure. It is predicted that the formation of a PAH tetramer will require at least two points of contact per enzyme subunit. Sequence analysis has suggested the existence of a C-terminal domain with characteristics of a leucine zipper or a variant of this called a coiled-coil. By deletion of 24 amino acids from the C-terminus or conversion of leucine 448 to an alanine residue, we have shown that this putative leucine zipper/coiled-coil domain is involved in the assembly of an active enzyme tetramer from dimers. The removal of this C-terminal domain of PAH reduces enzyme activity but does not abolish it. Furthermore, we report that an alanine 447 to aspartate mutation associated with phenylketonuria may affect subunit assembly which suggests the formation of enzyme tetramers is physiologically relevant. Our analysis of subunit interactions in vivo, show that in the absence of the C-terminal coiled-coil domain, dimers can form and this is only possible when the N-terminal domain is present. This provides the first evidence that N-terminal domain is required for multimerisation. We propose that the N-terminal regulatory domain in conjunction with the C-terminal coiled-coil domain, mediates the formation of fully active enzyme tetramers.

Amino Acid Sequence↗

Two distinct mechanisms of fibroblast adhesion.

The adhesion of cells to the connective tissue matrix is commonly thought to be governed by fibronectin, a pericellular glycoprotein with binding sites for cell surfaces, collagen and glycosaminoglycans. Here we report evidence that Chinese hamster ovary (CHO) cells possess an alternative mechanism for adhesion which is independent of fibronectin. Cells of a variant CHO clone called ADvF11 are defective in their ability to adhere to fibronectin-coated substrata, but can adhere to a substratum coated with SAM (substrate-attached material), a pericellular material produced by fibroblasts. The adhesion of wild-type CHO cells to fibronectin-coated substrate and adhesion of ADvF11 cells to SAM-coated substrata are differentially sensitive to proteolytic treatment. This suggests that there are two distinct adhesion mechanisms for CHO cells, only one of which is dependent on fibronectin.

Animals↗

Mutation of BSND causes Bartter syndrome with sensorineural deafness and kidney failure.

Antenatal Bartter syndrome (aBS) comprises a heterogeneous group of autosomal recessive salt-losing nephropathies. Identification of three genes that code for renal transporters and channels as responsible for aBS has resulted in new insights into renal salt handling, diuretic action and blood-pressure regulation. A gene locus of a fourth variant of aBS called BSND, which in contrast to the other forms is associated with sensorineural deafness (SND) and renal failure, has been mapped to chromosome 1p. We report here the identification by positional cloning, in a region not covered by the human genome sequencing projects, of a new gene, BSND, as the cause of BSND. We examined ten families with BSND and detected seven different mutations in BSND that probably result in loss of function. In accordance with the phenotype, BSND is expressed in the thin limb and the thick ascending limb of the loop of Henle in the kidney and in the dark cells of the inner ear. The gene encodes a hitherto unknown protein with two putative transmembrane alpha-helices and thus might function as a regulator for ion-transport proteins involved in aBS, or else as a new transporter or channel itself.

Animals↗

Urinary free cortisone and the assessment of 11 beta-hydroxysteroid dehydrogenase activity in man.

OBJECTIVE: Two isoforms of 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD) catalyse the interconversion of cortisol to hormonally inactive cortisone; defects in the 11 beta-HSD2 isoform result in hypertension. The kidney, expressing high levels of 11 beta-HSD2, is the principal source of cortisone in man. We have validated the measurement of urinary free cortisone (UFE) excretion in normals and in patients with disorders of the pitultary-adrenal axis in an attempt to more accurately measure the activity of 11 beta-HSD2 in vivo. SUBJECTS: Forty-one normal adults, 12 normal children < 12 years of age, 15 patients with Cushing's syndrome, 12 with hypopitultarism on replacement hydrocortisone, 12 with the syndrome of apparent mineralocorticoid excess (AME) and 7 volunteers consuming liquorice. MEASUREMENTS: A complete 24-hour urine collection was analysed by gas chromatography/mass spectrometry for "A-ring' reduced cortisol and cortisone metabolites, i.e. tetrahydrocortisols (THF and allo-THF) and tetrahydrocortisone (THE). In addition, urinary free cortisol (UFF) and urinary free cortisone were quantified using deuterium-labelled internal standards. RESULTS: In normal adults and children, UFE excretion exceeded that of UFF (UFF 30.4 +/- 2.4 micrograms/24h (mean +/- SE), UFE 54.6 +/- 4.1 micrograms/24h, adults) (for conversion to nmol/24h multiply E by 2.78 and F by 2.76 respectively). Thus the normal UFF/UFE ratio was 0.54 +/- 0.05 in contrast to the (THF + allo-THF)/THE ratio of 1.21 +/- 0.06. UFE excretion was normal in hypopituitary patients on replacement hydrocortisone. Although UFE was elevated in all forms of Cushing's syndrome, the UFF/UFE ratio was grossly elevated in patients with the ectopic ACTH syndrome (14.0 +/- 6.7, n = 6). UFE was below the lower limit of the assay (< 1 microgram/24h) in most patients with the so-called type 1 variant of AME and significantly reduced in 4 patients described as having the type 2 variant of AME (10.5 +/- 3.5 micrograms/h, P < 0.05) and in 7 volunteers consuming liquorice (26.8 +/- 10.0 micrograms/24h, P < 0.01). In ectopic ACTH syndrome, AME, and liquorice ingestion the UFF/UFE ratio was more deranged than the (THF + allo-THF)/THE ratio. CONCLUSION: In normals the discrepant THF + allo-THF/ THE and UFF/UFE ratio suggests that much more of the UFE is derived from the kidney. Reduction in UFE excretion is seen following liquorice ingestion and in both variants of AME, though it is more profound in AME1. The high UFF/UFE ratio in the mineralocorticoid excess state seen in the ectopic ACTH syndrome is compatible with substrate-saturation of renal 11 beta-HSD2. The measurement of UFE and the UFF/UFE ratio is a significant advance in the analysis of human 11 beta-HSD activity in vivo; in particular, the UFF/UFE ratio appears to be a more sensitive index than the (THF + allo-THF)/THE ratio of renal 11 beta-HSD2 activity.

11-beta-Hydroxysteroid Dehydrogenases↗

Leiomyosarcoma of the heart and its pulmonary metastasis, both with prominent osteoclast-like multinucleated giant cells expressing tartrate-resistant acid phosphatase activity.

An autopsy case of cardiac leiomyosarcoma and its pulmonary metastasis, both with osteoclast-like multinucleated giant cells (OMGC) mimicking the so-called giant cell variant of malignant fibrous histiocytoma (MFH), is reported. The patient, a 70-year-old male, was admitted for sudden dyspnea. Extensive work-up established only a left atrial tumor mass. Three months after admission, the patient developed multiple intracranial and pulmonary metastases, followed by a worsening clinical course characterized by semicoma and dyspnea, and subsequently died 6 months after the onset of his symptoms. At subsequent autopsy, the left atrial polypoid tumor was found to have invaded destructively to the left half of the cardiac wall. Histology of the cardiac tumor revealed a bimorphic sarcoma in which a poorly differentiated leiomyosarcoma comfirmed by histologic and immunohistochemical findings was juxtaposed to a small nodule with features closely mimicking giant cell MFH. The pulmonary metastatic nodules exhibited features that were entirely indistinguishable from giant cell MFH except for the fact that a minority of polymorphic cells manifested myogenic differentiation. We believe that such a MFH-like pattern represents a pleomorphic form of leiomyosarcoma rather than a dedifferentiated one. The OMGC within the MFH-like component coexpressed CD68 and tartrate-resistant acid phosphatase activity.

Acid Phosphatase↗