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PubMed2002

The degenerate primer design problem.

A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly-degenerate primers for a set of genomic sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.

Algorithms↗
PubMed2001

Expression of P-170 glycoprotein sensitizes lymphoblastoid CEM cells to mitochondria-mediated apoptosis.

Multidrug resistance caused by P-glycoprotein (P-170) is a phenomenon by which cells exposed to a single drug acquire resistance to other structurally and functionally unrelated drugs. This is a widespread phenomenon described in vivo in the management of infectious as well as non-infectious diseases. Several in vitro models have been developed in order to evaluate physiopathological properties of P-170. Among these are P-170-expressing variants of the human T-lymphoblastoid CEM cell line called VBL100. As a general rule, drug resistance normally results in resistance to apoptosis induction. By contrast, a paradoxical activity is exerted in this cell model by the cytokine tumour necrosis factor-alpha (TNF-alpha), which is capable of inducing apoptosis in P-170-expressing variants better than in wild-type (wt) cells. In the present study we partially address the mechanisms underlying this activity. In fact, the susceptibility of VBL100 cells to TNF-alpha appears to be specifically due to the depolarization of their mitochondrial membrane, a key factor for apoptotic induction. The same was observed with staurosporine, a specific mitochondrion-mediated proapoptotic chemical probe. Conversely, other proapoptotic stimuli, such as Fas/CD95 or the anti-cancer drug etoposide, did induce significant cell death in wild type cells only. Thus, schematically, mitochondrially dependent stimuli appeared to be more effective in VBL100-cell killing, while 'physiological' stimuli showed the opposite behaviour. Importantly, under steady-state conditions, VBL100 cells displayed per se a mitochondrial membrane hyperpolarization that appeared strictly related to their high susceptibility to specific apoptotic stimuli. In conclusion, the study of a well-established cell model such as that represented by the wt/VBL CEM lymphoid cell line seems to suggest that the multidrug resistance phenotype can specifically sensitize cells towards 'unphysiological', mitochondria-associated cell death cascade or, in the same fashion, it could shift cells from type I (mainly plasma membrane-associated) towards type II (mainly mitochondrial membrane-associated) phenotype.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1982

A papillary endobronchial tumor with a transitional cell pattern.

An endobronchial papillary tumor in a 75-year-old reformed cigarette smoker exhibited the light microscopic features of a transitional cell neoplasm. The constituent cells showed cytologic features of malignancy; in addition, there were microfoci of mucosal invasion. Electron microscopy showed tonofilaments and numerous desmosomes. There were no ultrastructural features similar to those seen in tumors of urothelial origin, and the similarity with the latter was only at the light microscopic level, the tumor being a variant of a squamous carcinoma. Previous descriptions of so-called transitional cell neoplasms of the lower bronchial tree included a cytologically benign lesion an one showing carcinoma in situ. The present case indicated that the spectrum of these neoplasms includes lesions that show microinvasion. Therefore, exophytic papillary endobronchial tumors should be distinguished as a group of distinct variants of squamous carcinoma.

Aged↗
PubMed2001

Preserved speech variants of the Rett syndrome: molecular and clinical analysis.

Mutations in the MECP2 gene cause the severe neurodevelopmental disorder called Rett syndrome. Preliminary evidence suggests that MECP2 may be involved in a broader phenotype than classical Rett syndrome including preserved speech variants (PSV). Here we report clinical and mutation analysis of 18 PSV patients. Ten of them had a MECP2 mutation (55%). The clinical features of these girls have been characterized and two subgroups defined. All of them had slow recovery of verbal and praxic abilities, evident autistic behavior, and normal head circumference. Six were overweight, often obese, had kyphosis, coarse face, and mental age of two-to-three years, and were able to speak in sentences; four had normal weight, mental age not beyond one-to-two years, and spoke in single words and two-word phrases. The course of the disorder was in stages as in classic Rett syndrome. Hand-washing was present in the first years of life but often subsequently disappeared. Significantly, all mutations found in PSV are either missense or late truncating mutations. In particular, we did not find the four early truncating hot spots: R168X, R255X, R270X, R294X. These results suggest that early truncating mutations lead to a poor prognosis (classic Rett), while late truncating and missense mutations lead either to classic Rett or PSV. We hypothesize that a missense or late truncating mutation is necessary but not sufficient to produce a PSV, based on the presence of one (or more) modifier genes whose product may interact in a epistatic manner with MeCP2 protein.

Adolescent↗
PubMed1988

A new class of Paramecium surface proteins anchored in the plasma membrane by a glycosylinositol phospholipid. Membrane anchor of Paramecium cross-reacting glycoproteins.

Treatment of paramecia with ethanol or Triton X-100 solubilizes a major membrane protein, namely the surface antigen (SAg), and a set of glycopeptides in the range 40-60 kDa, which cross-react with the SAg. We demonstrate that these glycopeptides, called 'cross-reacting glycoproteins' (CRGs), are distinct molecules from the SAg. First, after purification of CRGs from ethanolic extracts of Paramecium primaurelia expressing the 156G SAg, the amino acid composition of a given CRG was found to be different from, and incompatible with, that of the 156G SAg. Secondly, we showed that the CRGs, although not immunologically detectable, are present in fractions containing the myristoylated form of the 156G SAg. The treatment of these fractions by phosphatidylinositol-specific phospholipases C enables us to reveal the CRGs through the unmasking of two distinct epitopes. One is the 'cross-reacting determinant' (CRD), initially described for the variant surface glycoproteins (VSGs) of Trypanosoma; the other determinant, called 'det-2355', is specific to the SAg and to the CRGs. Our results suggest that (1) phosphatidylinositol is covalently linked to the CRGs and (2) the CRD and the det-2355 are localized in the same region of the CRGs. We propose that the CRGs are a new set of surface proteins anchored in the cell membrane of Paramecium via a glycosylinositol phospholipid, in the same way as the SAgs.

Amino Acids↗
PubMed1987

Pigmented dermatofibrosarcoma protuberans. Report of two cases as a variant of dermatofibrosarcoma protuberans with partial neural differentiation.

Two cases of so-called Bednár tumor are reported. The histopathological finding of a typical storiform pattern composed of fusiform tumor cells resembled dermatofibrosarcoma protuberans (DFSP) except for the presence of melanin-containing cells scattered within the lesion. Ultrastructurally, the predominant tumor cells in case 1 possessed extensive cytoplasmic processes, convoluted nuclei, and intercellular junctions, but lacked basal lamina. Melanocytic tumor cells contained melanosomes and were surrounded by basal lamina. Immunohistochemical examinations revealed a positive reaction for S-100 protein and neuron-specific enolase in the pigment-laden cells. Consequently, these two tumors were considered to be a variant of DFSP with partial neural differentiation.

Adult↗
PubMed2005

Molecular mechanisms of cation transport by the renal Na+-K+-Cl- cotransporter: structural insight into the operating characteristics of the ion transport sites.

Two variants of the renal Na(+)-K(+)-Cl(-) cotransporter (NKCC2), called NKCC2A and NKCC2F, display marked differences in Na(+), Rb(+), and Cl(-) affinities, yet are identical to one another except for a 23-residue membrane-associated domain that is derived from alternatively spliced exons. The proximal portion of these exons is predicted to encode the second transmembrane domain (tm2) in the form of an alpha-helix, and the distal portion, part of the following connecting segment (cs1a). In recent studies, we have taken advantage of the A-F differences in kinetic behavior to determine which regions in tm2-cs1a are involved in ion transport. Functional characterizations of chimeras in which tm2 or cs1a were interchanged between the variants showed that both regions are important in specifying ion affinities, but did not allow delineating the contribution of individual residues. Here, we have extended these structure-function analyses by studying additional mutants in which variant residues between A and F were interchanged individually in the tm2-cs1a region (amino acid number 216, 220, 223, 229, or 233 in NKCC2). None of the substitutions were found to affect K(m (C1-)), suggesting that the affinity difference for anion transport is conveyed by a combination of variant residues in this domain. However, 2 substitutions in the tm2 of F were found to affect cation constants specifically; interestingly, one of these mutations (residue 216) only affected K(m (Rb+)) while the other (residue 220) only affected K(m (Na+)). We have thus identified two novel residues in NKCC2 that play a key role in cation transport. Because such residues should be adjacent to one another on the vertical axis of the tm2 alpha-helix, our results imply, furthermore, that the ion transport sites in NKCC2 could be physically linked.

Animals↗
PubMed1975

[Isolation of Drosophila melanogaster cell lines of different genotypes and study of multiplication of two variants of sigma rhabdovirus in those lines (author's transl)].

Strains of sigma virus which are called P- do not multiply in Drosophila strains called Paris, homozygous for the Pp allele of gene ref(2)P. Adsorption is normal and the virus is not destroyed. It seems that the viral function concerned is an early one. P+ variants isolated from a P- population do multiply in flies from the Paris strain. Three continuous cell lines homozygous for the Pp allele and one homozygous for the Po allele were isolated. Several attempts to infect those cell lines with P- and P+ variants of sigma virus were done. Cultures homozygous for the Pp allele reacted differently whether infection was initiated with P+ or P- viral strains, while cultures homozygous Po/Po gave the same result with both viral strains. Similarity between results obtained with two independent P- viral strains leads to the conclusion that the ref (2) P gene is active in cells from continuous cell lines; its Pp allele does not allow multiplication of P- viral types. An interpretation of the slight multiplication observed with concentrated inoculum is discussed.

Animals↗
PubMed1983

Reactive perforating collagenosis of diabetes mellitus and renal failure.

We believe that the disease we are reporting is associated with diabetes, particularly in patients on renal dialysis, and the perforation is initiated by scratching. Decreasing pruritus is the only needed treatment as the lesions tend to resolve on their own. While this entity has been called Kyrle's disease, it more correctly is reactive perforating collagenosis, both clinically and histologically. Whether this is a variant of what Kyrle originally described is not clear. We propose that this entity be called reactive perforating collagenosis of diabetes and renal failure.

Adult↗
PubMed2003

MD simulations of anthrax edema factor: calmodulin complexes with mutations in the edema factor "switch a" region and docking of 3'-deoxy ATP into the adenylyl cyclase active site of wild-type and mutant edema factor variants.

Bacillus anthracis, a spore-forming infectious bacterium, produces an exotoxin, called the edema factor (EF), that functions in part by disrupting internal signalling pathways. When complexed with human host cell calmodulin (CaM), EF becomes an active adenylyl cyclase, producing the internal signal substance cyclic-AMP in an uncontrolled fashion. Recently, the crystal structures for uncomplexed EF and EF:CaM complexes in the presence and absence of a substrate analog (3'-deoxy-ATP), were reported. EF mutational studies have implicated a number of residues important in CaM binding and/or in the generation of the adenylyl cyclase active site, formed by the movements of the EF switch A, B and C regions upon CaM binding. Here we report on the results of molecular dynamics (MD) simulations on two EF:CaM complexes, one containing wild-type EF and the other containing EF in which a cluster of residues in the switch A region (L523, K525, Q526 and V529) have been mutated to alanine. The switch A mutations cause a large increase in the flexibility of the switch C region, the rupture of a number of EF-CaM interactions, an expansion of the carboxyl-terminal domain of CaM, and a change in the Ca(2+) ion binding abilities of the CaM that is in complex with EF. The results indicate the importance of the mutated switch A residues in maintaining a compact EF:CaM complex that appears to be a prerequisite for the generation of a fully-functional adenylyl cyclase active site. The effects of mutating key residues (K346, K353, H577, E588, D590 and N639) in the active site region of EF (to alanine) on the ability of EF to bind the 3'-deoxy-ATP substrate analog were also examined. Active-site residue substitutions at positions 583 (N583A) and 577 (H577A) were found to be particularly disruptive for the placement of the adenine ring moiety into the position found in the x-ray crystal structure of the ligand-protein complex.

Adenylyl Cyclases↗
PubMed2000

Factors influencing the salience of temporal cues in the discrimination of synthetic Japanese monkey (Macaca fuscata) coo calls.

If temporal position of a frequency inflection is the most salient communication cue in Japanese macaque smooth early and smooth late high coos, then macaques should perceive coos differing only along the early-late dimension as belonging to different classes. The perceived similarity of synthetic coos and temporally reversed variants were evaluated, using multidimensional scaling of macaque discrimination latencies. Original calls and calls temporally reversed in the frequency domain could be discriminated if the peak was near a call endpoint but not if the frequency peak in the original call was near the coo midpoint. Perceived similarity of such calls was inversely related to the amount of frequency modulation. Temporal reversals of amplitude contours were also conducted. Although macaques are quite sensitive to amplitude increments, reversal of the relatively flat amplitude contours of these calls did not affect discrimination responses.

Animals↗
PubMed1986

Electrotypes and formal genetics of red cell glutathione peroxidase (GPX1) in the Djuka of Surinam.

Samples of venous blood from 239 male and 476 female adults including 41 pairs of parents and 123 of their children belonging to a Surinam population called the Djuka or Bush Negroes of West African origin were screened for electrophoretic variants of red cell glutathione peroxidase (GPX1) in Cellogel. The results confirmed an earlier hypothesis that at least a part of the GPX1 variation mainly, if not exclusively, observed in the Africans and people of African origin living elsewhere, is determined by two codominant alleles (called GPX1*1 and GPX1*2), at an autosomal locus. The frequency of GPX1*2 allele in the Djuka was estimated to be .054. A rare variant provisionally designed as GPX1 Djuka (thought to be a heterozygote due to a third allele called GPX1*3 and the GPX1*1) was found in two apparently unrelated individuals. Catalytically, the product of GPX1*2 appears to be about twice more active than that of GPX1*1. For heuristic purposes, it was proposed and discussed that GPX1*2 is a South-Saharan African allele and is amenable for natural selection.

Adult↗
PubMed1996

Moyamoya disease associated with persistent primitive trigeminal artery variant in identical twins.

Identical twin cases of moyamoya disease associated with persistent primitive trigeminal artery variant are presented. Both of the children suffered from the cerebrovascular occlusive disease called "moyamoya disease," but there existed a remarkable time lag in the manifestation of their first clinical symptoms. Coexistence of persistent primitive trigeminal artery variant and high occurrence of moyamoya disease in identical twins suggest some congenital factors in the development of this disease. However, the time lag of the first clinical manifestation between the twins suggests certain acquired factors may also play a role in the manifestation of this disease.

Brain Ischemia↗
PubMed1993

Affinity maturation of human growth hormone by monovalent phage display.

We describe a selection procedure for construction of very high affinity variants of human growth hormone (hGH) for binding to the extra cellular domain of its receptor (called the hGHbp). Five different libraries of mutated hGH genes (each containing approximately 2 x 10(5) protein variants) were created by randomly mutating four different codons at residues that were shown to be important for receptor binding by structural or functional criteria. Mutated proteins were displayed as single copies from their respective filamentous phagemid particles and sorted in vitro for binding to the immobilized hGHbp. Phagemid particles that bound the immobilized hGHbp were eluted and propagated. After three to seven rounds of binding enrichments, hGH variants were isolated that contained 2 to 4 mutations and exhibited three- to sixfold improvements in binding affinity. Because of the limits of DNA transfection efficiency in creating the library we could not sample thoroughly mutations at more than four codons at once. Nonetheless, the free energy effects for these mutations acted cumulatively. Thus, by combining affinity enhanced mutants from libraries independently sorted we created an hGH variant with 15 substitutions that bound approximately 400-fold more tightly to the hGHbp than wild-type hGH. The affinity enhancements occurred predominantly by slowing the off-rate of the hormone (> 60-fold), and partly through increasing the on-rate (up to 4-fold). Residues that were shown to be important for binding by alanine-scanning were most highly conserved after binding selection, and interestingly many of them could be further improved. Thus, we found it most effective to randomly mutate the residues that were shown to modulate affinity by alanine-scanning, and to combine the selectants from separate libraries that exhibit the highest affinities. The selection procedure and mutagenesis strategy provides a framework for affinity maturation of protein-protein complexes.

Amino Acid Sequence↗
PubMed1986

Identification of a mouse serum protein increased by administration of an antitumor polysaccharide, PSK, as a variant of mouse transferrin and some of its biological activities.

One of the so-called LC components, the content of which is increased in the serum of PSK (antitumor polysaccharide) treated mice, was purified by repeated ion-exchange column chromatography on DEAE-Sephadex A-50. The purified protein, designated as LC-2, was identified as a variant of mouse transferrin, which is a serum beta 1-globulin having an iron-binding capacity. The absorption spectrum and ultraviolet circular dichroism (CD) curve of LC-2 were identical with those of mouse transferrin. The molecular weight, isoelectric point and amino acid composition of LC-2 were in good agreement with the results obtained previously for mouse transferrin. However, the carbohydrate content of LC-2 was different from that of mouse transferrin. This protein restored the depressed spleen cell response of tumor-bearing mice to concanavalin A (Con A) and promoted the metabolism of proteose-peptone induced peritoneal macrophages obtained from tumor-bearing mice. Furthermore, it had weak but definite antitumor activity against Sarcoma 180 cells in vivo.

Animals↗
PubMed2003

Energetic characteristics of the new transthyretin variant A25T may explain its atypical central nervous system pathology.

Transthyretin (TTR) is a tetrameric protein that must misfold to form amyloid fibrils. Misfolding includes rate-limiting tetramer dissociation, followed by fast tertiary structural changes that enable aggregation. Amyloidogenesis of wild-type (WT) TTR causes a late-onset cardiac disease called senile systemic amyloidosis. The aggregation of one of > 80 TTR variants leads to familial amyloidosis encompassing a collection of disorders characterized by peripheral neuropathy and/or cardiomyopathy. Prominent central nervous system (CNS) impairment is rare in TTR amyloidosis. Herein, we identify a new A25T TTR variant in a Japanese patient who presented with CNS amyloidosis at age 42 and peripheral neuropathy at age 44. The A25T variant is the most destabilized and fastest dissociating TTR tetramer published to date, yet, surprising, disease onset is in the fifth decade. Quantification of A25T TTR in the serum of this heterozygote reveals low levels relative to WT, suggesting that protein concentration influences disease phenotype. Another recently characterized TTR CNS variant (D18G TTR) exhibits strictly analogous characteristics, suggesting that instability coupled with low serum concentrations is the signature of CNS pathology and protects against early-onset systemic amyloidosis. The low A25T serum concentration may be explained either by impaired secretion from the liver or by increased clearance, both scenarios consistent with A25T's low kinetic and thermodynamic stability. Liver transplantation is the only known treatment for familial amyloid polyneuropathy. This is a form of gene therapy that removes the variant protein from serum preventing systemic amyloidosis. Unfortunately, the choroid plexus would have to be resected to remove A25T from the CSF-the source of the CNS TTR amyloid. Herein we demonstrate that small-molecule tetramer stabilizers represent an attractive therapeutic strategy to inhibit A25T misfolding and CNS amyloidosis. Specifically, 2-[(3,5-dichlorophenyl)amino]benzoic acid is an excellent inhibitor of A25T TTR amyloidosis in vitro.

Amyloid Neuropathies, Familial↗
PubMed2005

Cystic hypersecretory carcinoma: rare and poorly recognized variant of intraductal carcinoma of the breast. Report of five cases.

AIMS: To report five cases of a rare variant of intraductal carcinoma of the breast, so-called cystic hypersecretory carcinoma. The clinical and pathological characteristics of the lesion are described, along with a review of the literature. METHODS AND RESULTS: The patients were females aged between 53 and 78 years (average 66.8 years). The size of the lesions ranged between 70 and 80 mm in largest dimension. In two cases, the development of high-grade invasive ductal carcinoma was observed; in one additional case there was recurrence of high-grade in-situ carcinoma after 3 years. This emphasizes the importance of correct diagnosis of this potentially aggressive lesion. Strong over-expression of HER-2/neu protein was observed in three cases, including the two with an invasive component. Protein p53 was variably positive in all cases. Steroid receptor immunohistochemistry yielded variable results with only one case being positive for both oestrogen and progesterone receptors. Interestingly, in most cases (4/5) staining for androgen receptors was observed. CONCLUSIONS: Cystic hypersecretory ductal carcinoma of the breast is a rare distinctive variant of ductal carcinoma in situ. It has the potential for invasive growth and the development of metastases.

Aged↗
PubMed2004

Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene.

The difficulty of fine localizing the polymorphisms responsible for genotype-phenotype correlations is emerging as an important constraint in the implementation and interpretation of genetic association studies, and calls for the definition of protocols for the follow-up of associated variants. One recent example is the 3435C>T polymorphism in the multidrug transporter gene ABCB1, associated with protein expression and activity, and with several clinical conditions. Available data suggest that 3435C>T may not directly cause altered transport activity, but may be associated with one or more causal variants in the poorly characterized stretch of linkage disequilibrium (LD) surrounding it. Here we describe a strategy for the follow-up of reported associations, including a Bayesian formalization of the associated interval concept previously described by Goldstein. We focus on the region of high LD around 3435C>T to compile an exhaustive list of variants by (1) using a relatively coarse set of marker typings to assess the pattern of LD, and (2) resequencing derived and ancestral chromosomes at 3435C>T through the associated interval. We identified three intronic sites that are strongly associated with the 3435C>T polymorphism. One of them is associated with multidrug resistance in patients with epilepsy (chi2 = 3.78, P = 0.052), and sits within a stretch of significant evolutionary conservation. We argue that these variants represent additional candidates for influencing multidrug resistance due to P-glycoprotein activity, with the IVS 26+80 T>C being the best candidate among the three intronic sites. Finally, we describe a set of six haplotype tagging single-nucleotide polymorphisms that represent common ABCB1 variation surrounding 3435C>T in Europeans.

ATP Binding Cassette Transporter, Subfamily B, Mem↗