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PubMed2000

Trans complementation of variant Cre proteins for defects in cleavage and synapsis.

The Cre recombinase is a member of the integrase family of conservative site-specific recombinases. These proteins share five conserved catalytic residues, one of which is a tyrosine that acts as the nucleophile to attack the scissile phosphodiester bond in the DNA target. Recombination by the Cre recombinase takes place in a supramolecular structure called a synapse that consists of four molecules of Cre bound to two DNA target sequences called lox sites. The synapse is held together by an intricate network of protein-protein interactions. They bend the two sites into square planar structure that resembles a Holliday intermediate. We have studied three mutant Cre proteins that appear to have defects in synapsis (Cre A36V, Cre T41F, and Cre G314R). We found that they were unable to carry out strand cleavage but that cleavage occurred if they were mixed with a cleavage-defective Cre protein that lacks the catalytic nucleophilic tyrosine residue. The three variant proteins could also be complemented for the formation of a novel structure ("complexV"), which may be a cleaved synaptic intermediate. We suggest that these three mutant proteins have a defect in DNA bending and discuss the relationship between bending, synapsis, and cleavage.

DNA↗
PubMed1986

A deletion mutant defines DQ beta variants with DR4 positive DQw3 positive haplotypes.

We describe the production of an HLA deletion mutation by radiation mutagenesis of a DR4- and DQw3-homozygous, Dw4- and Dw14-heterozygous cell line designed to analyze polymorphisms associated with DR4 and DQw3. Southern blot analysis confirms a deletion of class I and class II genes on one haplotype. Variation in DQ beta alleles associated with DQw3 was previously described by characteristic RFLP patterns for a DQ beta bene. One pattern, which correlated precisely with A-10-83 monoclonal antibody reactivity (TA10), defined an allele which we call DQ"3.1". The mutant cell line has lost the polymorphic bands on Southern blots corresponding to the DQ"3.1" allele, while the intact Dw14 haplotype retains the alternate allele at DQ beta which is DQw-3 positive. TA10-negative. These data demonstrate the segregation of two DQw3 positive DQ beta allelic variants, both associated with DR4, which can be distinguished on the basis of both RFLP and monoclonal antibody reactivity.

Antibodies↗
PubMed1999

Rank-order of potencies for inhibition of the secretion of abeta40 and abeta42 suggests that both are generated by a single gamma-secretase.

The Alzheimer's disease amyloid peptide Abeta has a heterogeneous COOH terminus, as variants 40 and 42 residues long are found in neuritic plaques and are secreted constitutively by cultured cells. The proteolytic activity that liberates the Abeta COOH terminus from the beta-amyloid precursor protein is called gamma-secretase. It could be one protease with dual specificity or two distinct enzymes. By using enzyme-linked immunosorbent assays selective for Abeta40 or Abeta42, we have measured Abeta secretion by a HeLa cell line, and we have examined the dose responses for a panel of five structurally diverse gamma-secretase inhibitors. The inhibitors lowered Abeta and p3 secretion and increased levels of the COOH-terminal 99-residue beta-amyloid precursor protein derivative that is the precursor for Abeta but did not alter secretion of beta-amyloid precursor protein derivatives generated by other secretases, indicating that the inhibitors blocked the gamma-secretase processing step. The dose-dependent inhibition of Abeta42 was unusual, as the compounds elevated Abeta42 secretion at sub-inhibitory doses and then inhibited secretion at higher doses. A compound was identified that elevated Abeta42 secretion at a low concentration without inhibiting Abeta42 or Abeta40 at high concentrations, demonstrating that these phenomena are separable pharmacologically. Using either of two methods, IC50 values for inhibition of Abeta42 and Abeta40 were found to have the same rank-order and fall on a trend line with near-unit slope. These results favor the hypothesis that Abeta variants ending at residue 40 or 42 are generated by a single gamma-secretase.

Amyloid Precursor Protein Secretases↗
PubMed2007

Fine-needle aspiration biopsy of monophasic variant of spindle epithelial tumor with thymus-like differentiation of the thyroid: report of one case and review of the literature.

Spindle epithelial tumor with thymus-like differentiation (SETTLE) is a rare biphasic tumor of the thyroid with approximately 20 well-documented cases reported in the English literature. Although a monophasic variant of SETTLE is conceivable, the majority of the reported cases were truly biphasic tumors. A minimal amount of epithelial component was present in the reported cases of so-called spindle-cell predominant SETTLE. Here, we report an apparently monophasic case of SETTLE in a 16-yr-old girl, in which no epithelial cells were identified in either fine-needle aspiration biopsy (FNAB) or the subsequent hemithyroidectomy specimen. The FNAB smears were moderately cellular and composed of single and loosely grouped spindle cells with homogenous metachromatic material, which could be mistaken as amyloid, erroneously suggesting medullary thyroid carcinoma. The compact nodules of uniform spindle cells in histology sections raised the possibility of monophasic synovial sarcoma. The spindle cells stained positive for both cytokeratin and vimentin, but were negative for thyroglobulin and calcitonin as well as neuroendocrine markers, confirming the diagnosis of SETTLE.

Adolescent↗
PubMed1982

Cloning and characterization of a genomic DNA fragment carrying the basic copy of the gene coding for variant surface antigen 118 of Trypanosoma brucei.

It has been proposed (Hoeijmakers et al., 1980b) that variant surface antigen (VSA) gene expression in Trypanosoma brucei is accomplished by a gene re-arrangement involving the basic copy of the VSA gene to give the so-called expression-linked copy (which is present only in the strain expressing that particular antigen). In this publication, the basic and expression-linked copies of the gene have been visualized by Southern blot analysis of nuclear DNA and shown to be located on HindIII fragments of 4.5 and 10-12 kb, respectively. In addition, several other bands of weaker hybridization are seen, probably representing evolutionary relatives. Using a shotgun approach, HindIII gene banks have been constructed and recombinants isolated which carry the 4.5-kb HindIII fragment containing the VSA118 gene basic copy. Several clones containing evolutionary relatives were also found. The 4.5-kb HindIII fragment is able to hybridize to probes derived from both the 5' and 3' ends of the cDNA, while the relatives have homology only to the 3' end. A detailed comparison of the restriction map of VSA118 cDNA with that of the VSA118 basic copy showed no differences, demonstrating that the gene contains no introns. This result also indicates that the gene from which VSA118 mRNA is transcribed (whether this be the basic copy or the expression-linked copy) is identical to the basic copy over the region analysed.

Animals↗
PubMed2005

Haplotype assembly from aligned weighted SNP fragments.

Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211-213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.

Algorithms↗
PubMed2026

Persistent tic disorders are associated with 17q12 duplications.

Tourette Syndrome (TS) and Persistent Tic Disorder (PTD) are childhood-onset neuropsychiatric conditions with high heritability. Due to current sample size limitations, identifying TS/PTD risk genes has been challenging. This study addressed this issue by conducting a meta-analysis of microarray copy number variant (CNV) studies from three TS/PTD genomics consortia, supplemented with new data from 3291 cases. This approach more than doubled the sample size of previous TS/PTD CNV studies, with CNV calls generated from 5725 TS/PTD cases and 10,982 matched controls. The results confirmed that TS/PTD cases 1) have a higher burden of ultra-rare deletions overlapping loss-of-function intolerant genes (OR = 1.68, P = 9.3×10-5) and 2) are more likely to carry established neurodevelopmental CNVs (OR = 1.42, P = 3.9×10-2) compared to controls. Additionally, a novel, genome-wide significant CNV locus for TS/PTD was discovered, involving duplications at 17q12 (hg19 chr17:34.8 - 36.2 Mb). This locus is associated with a known duplication syndrome associated with variable neuropsychiatric traits, but has not been previously linked to tic disorders. Eight cases and one control carried the canonical ~1.4 Mb duplication at chr17:34.8-36.2 Mb, while one additional case had a smaller 110 kb duplication within this known CNV that included only one gene, ACACA (acetyl-CoA carboxylase, OR = 26.7, P = 5.69×10-7). Overall, this study provides further evidence that rare, genic CNVs play a substantial role in the genetic architecture of TS/PTD and identifies a new genome-wide significant association with this neurodevelopmental disorder.

Journal Article↗
PubMed2005

Bordetella filamentous hemagglutinin plays a critical role in immunomodulation, suggesting a mechanism for host specificity.

Bordetella pertussis, the causative agent of the acute childhood respiratory disease whooping cough, is a human-adapted variant of Bordetella bronchiseptica, which displays a broad host range and typically causes chronic, asymptomatic infections. These pathogens express a similar but not identical surface-exposed and secreted protein called filamentous hemagglutinin (FHA) that has been proposed to function as both a primary adhesin and an immunomodulator. To test the hypothesis that FHA plays an important role in determining host specificity and/or the propensity to cause acute versus chronic disease, we constructed a B. bronchiseptica strain expressing FHA from B. pertussis (FHA(Bp)) and compared it with wild-type B. bronchiseptica in several natural-host infection models. FHA(Bp) was able to substitute for FHA from B. bronchiseptica (FHA(Bb)) with regard to its ability to mediate adherence to several epithelial and macrophage-like cell lines in vitro, but it was unable to substitute for FHA(Bb) in vivo. Specifically, FHA(Bb), but not FHA(Bp), allowed B. bronchiseptica to colonize the lower respiratory tracts of rats, to modulate the inflammatory response in the lungs of immunocompetent mice, resulting in decreased lung damage and increased bacterial persistence, to induce a robust anti-Bordetella antibody response in these immunocompetent mice, and to overcome innate immunity and cause a lethal infection in immunodeficient mice. These results indicate a critical role for FHA in B. bronchiseptica-mediated immunomodulation, and they suggest a role for FHA in host specificity.

Adhesins, Bacterial↗
PubMed1993

Population structure in Daphnia obtusa: quantitative genetic and allozymic variation.

Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: GST = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, GST can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call QST. The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.

Analysis of Variance↗
PubMed1994

A conserved DNA sequence is required for efficient gonococcal pilin antigenic variation.

Antigenic variation of the Neisseria gonorrhoeae pilus occurs when a variant pilin sequence from a silent locus recombines into the expression locus by predominantly unidirectional, homologous recombination. At the 3' end of all pilin loci lies a conserved DNA sequence, called the Sma/Cla repeat, which has sequence similarity to several recombinase-binding sites, and therefore may be involved in pilin recombination. We have developed a novel reverse transcriptase/polymerase chain reaction (RT-PCR) assay for direct monitoring of pilin recombination, and both RT-PCR and phase variation were used to examine pilin recombination in a gonococcal strain that had had the pilE Sma/Cla repeat removed. Results from these experiments showed a decrease in pilin recombination when the Sma/Cla sequence was deleted from the expression locus, showing that a specialized site (Sma/Cla) is involved in efficient pilin recombination.

Antigenic Variation↗
PubMed2002

Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells.

Many proteins associated with the plasma membrane are known to partition into submicroscopic sphingolipid- and cholesterol-rich domains called lipid rafts, but the determinants dictating this segregation of proteins in the membrane are poorly understood. We suppressed the tendency of Aequorea fluorescent proteins to dimerize and targeted these variants to the plasma membrane using several different types of lipid anchors. Fluorescence resonance energy transfer measurements in living cells revealed that acyl but not prenyl modifications promote clustering in lipid rafts. Thus the nature of the lipid anchor on a protein is sufficient to determine submicroscopic localization within the plasma membrane.

Acylation↗
PubMed1997

Molecular cloning of ovine and bovine type I interferon receptor subunits from uteri, and endometrial expression of messenger ribonucleic acid for ovine receptors during the estrous cycle and pregnancy.

Interferon-tau (IFN-tau), a type I IFN structurally related to IFN-alpha, is regarded as the major antiluteolytic factor secreted by the conceptus of ruminant ungulate species before definitive trophoblast attachment and implantation. It mediates its effects by acting on the uterine endometrium, where it blunts the normal pulsatile production of PGF2alpha, presumably as a result of its binding to type I IFN receptors. In this study, we describe the complementary DNAs for the two known subunits, IFNAR1 and IFNAR2, of this receptor isolated from bovine and ovine endometrial complementary DNA libraries by homology cloning. Although there is extensive inferred amino acid sequence similarity between bovine and ovine IFNAR1 (92% identity) and between bovine and ovine IFNAR2 (88% identity), they have diverged extensively from the human receptor subunits (approximately 67% and approximately 58% identity, respectively). Despite these differences in primary structure, the respective subunits from all three species are organized similarly in their extracellular and cytoplasmic regions, and the bovine and ovine subunits have each retained a number of polypeptide motifs implicated in signal transduction. These uterine receptors also appear not to be splice variants. The cloned ovine IFNAR1 subunit, for example, possesses the expected four extracellular SD100 domains of full-length bovine and huIFNAR1, and only the homologs of the so-called long form (huIFNAR2c) of human IFNAR2 have so far been identified. RT-PCR procedures indicate that the messenger RNA for both subunits are found, not only in endometrium, but in all other tissues examined except those ofpreimplantation conceptuses, which presumably cannot respond to the IFN-tau they produce. Quantitative RNase protection assays of ovine endometrial RNA show that the expression of neither subunit changes greatly during the estrous cycle or pregnancy. These data suggest that the type I IFN receptor, which is expressed by the endometrium and binds IFN-tau, is probably not a structurally unusual form.

Amino Acid Sequence↗
PubMed2002

Identification of a new type 2M von Willebrand disease mutation also at position 1324 of von Willebrand factor.

Type 2M von Willebrand disease (VWD) refers to variants with decreased platelet-dependent function that is not associated with the loss of high molecular weight (HMW) von Willebrand factor (VWF) multimers. This category includes the so-called "phenotype B" responsible for inexistent ristocetin-induced but normal botrocetin-induced binding of VWF to platelet glycoprotein lb. The missense mutation G1324S was identified in the first patient reported to display "phenotype B". We report here on the identification in four members of a French family of a missense mutation also affecting this glycine residue but changing it into an alanine residue. These individuals are heterozygous for this mutation and two of them display an additional quantitative VWF deficiency resulting from a stop codon at position 2470. After transient transfection in Cos-7 cells, the mutated recombinant protein harbouring the G1324A substitution was shown to exhibit normal multimers and inexistent ristocetin-induced but normal botrocetin-induced binding to GPIb, confirming the classification of this new mutation as a type 2M VWD mutation.

Adult↗
PubMed2003

[Egg morphology as an indirect method to identify Anopheles benarrochi, Anopheles oswaldoi and Anopheles rangeli (Diptera: Culicidae)].

In the Department of Putumayo in southern Colombia, malaria transmission has continued in the absence of the 4 traditional Latin American vector species--Anopheles darlingi, Anopheles nuneztovari, Anopheles albimanus or Anopheles trinkae. Human bait collections yielded Anopheles mosquitoes and a morphological variant of Anopheles benarrochi, the adult females of which can easily be misidentified as Anopheles oswaldoi. Species identification of females of Anopheles in the subgenus Nyssorhynchus is generally difficult due to overlapping morphological characters; therefore, progeny of field collected females were link-reared to assess species identity. Herein a robust method is presented to identify the species Anopheles benarrochi, Anopheles oswaldoi and Anopheles rangeli from southern Colombia, using the morphology of the eggs induced from wild-caught females. Eggs of A. rangeli and A. benarrochi were differentiated on the basis of the anterior crown. In A. rangeli, this feature is positioned apically with high walls. In A. benarrochi, anterior crown is positioned more ventrally with comparatively shorter walls. No crown is present in A. oswaldoi. These differences are clear with the aid of a dissecting microscope and make accurate species determination possible even in field conditions. Egg morphology is shown to be an accurate, albeit indirect, method for the taxonomic determination for the three southern Colombian species and may also be useful in other regions of Latin America where the morphological variant of A. benarrochi is sympatric with A. oswaldoi.

Animals↗
PubMed2005

Contribution of PCR-based methods to diagnosis and management of imported malaria.

Since the first description, in 1990, of the diagnosis of Plasmodium falciparum infection by polymerase-chain-reaction (PCR), the role of this kind of molecular method in laboratory diagnosis of imported malaria is still a topical question. Various molecular assays have been used, the first of which was hybridization using labeled probes in 1984. When compared to thick blood smear, this test displayed a sensitivity ranging from 65% to 81% and specificity was close to 100%. The next technical improvement was the introduction of the so-called polymerase chain reaction (PCR), the principle of which was described in 1985. In 1993, a PCR-based assay detecting all four Plasmodium species was published, followed by different variants of this method. By the turn of the century, novel real-time PCR slashed workaround time, which dropped from 2 1/2 hours to less than 1 hour. Moreover, automatic reading with no human action on PCR products reduced the risks of contamination. The first application of real-time PCR to the diagnosis of malaria was published in 2001. PCR-based assays were found to be more sensitive than all conventional methods. Variations in sensitivity were probably due to different medical practices as well as to the proportion of various types of subjects (travelers under chemoprophylaxis, immigrants from malaria-endemic areas) in the population undergoing malaria diagnosis. The target of the primers was also of crucial importance: for the detection of P. falciparum, the most efficient assays amplified either the gene SSUrRNA, or Pf155/RESA, or Cox 1. Specificity of PCR results is guaranteed by the nature of the target for primers or probes, as determined by the studies of the Plasmodium genome whose results are available in GenBank. PCR use often corrected the results of Plasmodium species identification by microscopy and PCR-based methods were found to be the most efficient for the detection of mixed infections. Concerning the diagnosis of imported malaria, it appears clearly that PCR should be considered as second-line method which can be especially interesting, as a negative result rules out malaria in febrile patients. However, the use of PCR assays appears to be restricted to health centers, such as University Hospitals, for whom malaria identification is an important and routine problem. In the future, the detection of mutations related to drug resistance could be used to orient anti-malarial therapy.

Automation↗
PubMed1986

[Descriptive and immunohistochemical study of ghost cell keratinization in the calcifying odontogenic cyst].

The calcifying odontogenic cyst (COC) or Gorlin cyst is a rare and benign lesion most often intraosseous, although an appreciable number of cases are peripheral. Two histologic entities are described, one being cystic and the other neoplastic. The cystic type may occur as three variants. The occurrence of ghost cells, although shared with calcifying epithelioma of Malherbe, craniopharyngioma and other odontogenic tumors, represents the most conspicuous feature of the COC. Ghost cells are so called because they stain only faintly with common dies, including eosin. Although seldom studied, it is claimed that ghost cells are keratinized. However, this hypothesis is not universally accepted since electron microscopic studies give evidence that ultrastructural features of ghost cells differ from what is observed during the keratinizing process of the epidermis and oral mucosae. The present study, dealing with one case of COC, combines two complementary techniques: one a Rhodamine B keratin specific staining method and the other an immunohistochemical technique based on the use of a primary antiserum directed against high molecular weight keratins. With the Rhodamine B method, ghost cells and orthokeratinized cells of control gingiva are strongly stained while intermediate cells of the COC are less prominent. On the other hand, with the immunohistochemical technique, intermediate mediate cells of the COC are less prominent. On the other hand, with the immunohistochemical technique, intermediate cells of the COC and high level cells of control epithelium react strongly. Ghost cells of the COC are only faintly labelled and orthokeratinized cells of the control gingiva remain unlabelled. In combination with previous histochemical studies, these results confirm the occurrence of a keratinizing process.(ABSTRACT TRUNCATED AT 250 WORDS)

Fluorescent Dyes↗
PubMed1989

[Malignant fibrous histiocytoma of the kidney].

Malignant fibrous histiocytoma formerly called malignant fibroxanthoma is a pleomorphous sarcoma with partial fibroblastic and histiocytic differentiation. When its primary localization is in the kidney, it cannot be differentiated from some forms of "sarcomatoid variants of renal carcinomas" described in 1983 by Tomer and Farrow. The present authors described a malignant fibrous histiocytome of the left kidney in a 63-year-old man, who died from generalization 11 months after operation.

Histiocytoma, Benign Fibrous↗
PubMed1997

[Liver resections and operations in portal hypertension viewed via the experience of our practice].

After listing the indications for liver resection, the operative technique used is discussed with a special reference to an original modification implemented in practice. The case material is made of 52 liver resections and 6 lobectomies with a favourable outcome. In one lobectomy with subtotal proximal resection jejunogastroplasty is performed, supplemented by isolated antireflux anisoperistaltically interposed invagination esophagojejunostomy, duplicated by suturing its two portions. Application of catheter, inserted into the recanalized umbilical vein, is described under the heading of locoregional chemotherapy. In carcinomas involving the confluence of hepatic ducts a variant of Rodney Smith's operation is used while in hepatocholedochus resection plastic repair is done over Kerr drainage. In portal hypertension, after discussing the various methods existing, attention is called to the indirect shunts: splenectomy with omentoreno- and omentoparietopexy, Charsky and fenestration of Glisson's capsule using electric knife and argon with omentohepato- and hepatoparietopexy, as well as implantation of the recanalized v. umbilicalis into m. rectus abdominis dexter. In 15 cases operated on by parenchyma stimulating procedures, survivorship ranging from 3 to 26 years is achieved. For the purpose of prophylaxis against cholangiohepatitis and cirrhosis the following operations are performed: 68 papillotomies and plastic repairs over balloon catheter, passed through the choledochus and papilla, using an electric knife, 12 choledochoduodenostomies type "frog mouth", and 11 deperitonizations-desympathizations with a successful cure being attained.

Anastomosis, Surgical↗