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At least 1,099 records · Page 61Linked to original sources
PubMed1995

Breakpoint analysis: precise localization of genetic markers by means of nonstatistical computation using relatively few genotypes.

Placing new markers on a previously existing genetic map by using conventional methods of multilocus linkage analysis requires that a large number of reference families be genotyped. This paper presents a methodology for placing new markers on existing genetic maps by genotyping only a few individuals in a selected subset of the reference panel. We show that by identifying meiotic breakpoint events within existing genetic maps and genotyping individuals who exhibit these events, along with one nonrecombinant sibling and their parents, we can determine precise location for new markers even within subcentimorgan chromosomal regions. This method also improves detection of errors in genotyping and assists in the observation of chromosome behavior in specific regions.

Algorithms↗
PubMed1989

The geometry of the topographic map in striate cortex.

Johnston (1986) proposed that the global geometry of the striate cortical map in primates can be understood with reference to a conic surface in visual space oriented with its base in the plane of the eye and axis along the line of sight. Here, cortical magnification data from the macaque, squirrel and cebus monkeys and distance data from topographic maps of the macaque and owl monkey cortex are used as a further test of this proposal. Though there is a substantial difference in the emphasis placed on foveal vision in the owl monkey and the macaque topographic maps, both can be accommodated by the conic model with a change of parameter. The theory has also been extended in an attempt to model the differential changes in mean cortical receptive field size and inverse magnification with eccentricity found in the macaque. Though cortical receptive fields increase in size with eccentricity when measured on a spherical screen, mean receptive field size should be constant if measured on a tangent planes to a cone with an apical half angle of around 6.4 deg.

Animals↗
PubMed1996

No evidence of association between structural polymorphism at the dopamine D3 receptor locus and alcoholism in the Japanese.

Dopaminergic systems mediate reward mechanisms and are involved in reinforcing self-administration of dependence-forming substances, including alcohol. Studies have reported that polymorphisms of the dopamine D2 receptor, whose structure and function are similar to those of the dopamine D3 receptor, increase the susceptibility to alcoholism. These observations led to the examination of the possible association between a structural polymorphism of the D3 receptor gene and alcoholism. Genotyping results, employing a PCR-RFLP method, showed no difference in allele and genotype frequencies of the D3 BalI polymorphism (Ser9/Gly9) between Japanese alcoholics and controls. Moreover, these frequencies were not altered in alcoholics with inactive aldehyde dehydrogenase-2 (ALDH2), a well-defined negative risk factor for alcoholism. These results strongly suggest that the dopamine D3 receptor is not associated with alcoholism.

Adult↗
PubMed1999

Identification of a novel cytokeratin 19 pseudogene that may interfere with reverse transcriptase-polymerase chain reaction assays used to detect micrometastatic tumor cells.

In many recent publications, it has been claimed that reverse transcriptase-polymerase chain reaction (RT-PCR) assays involving genes with tissue-restricted expression can be used for specific and sensitive detection of cancer cells in blood, bone marrow and lymph nodes. Many different target mRNAs have been evaluated for such purposes. One of the most extensively studied genes, CK19, is predominantly expressed in cells of epithelial origin and normally not at detectable levels in hematopoietic or lymphatic tissues. Based on previous reports on CK19 we wanted to establish a useful assay for detection of micrometastatic cells. RNA and DNA specimens extracted from peripheral blood nucleated cells of healthy volunteers, as well as cell lines positive and negative for CK19 expression, were used in nested RT-PCR assays. Using previously published primers, we found a novel pseudogene that shows a high degree of identity with the CK19 gene sequence, except for differences caused by 3 small deletions and a number of point mutations, resulting in termination codons and frameshifts. The gene has therefore no coding potential. Importantly, published primer sequences and reaction conditions used by several other groups to detect CK19 mRNA may have led to the amplification of this pseudogene. The data illustrate one of the problems that must be addressed in validating RT-PCR assays for micrometastasis detection, and it is suggested that previous work using CK19 as a marker should be reassessed in view of the present finding.

Artifacts↗
PubMed2002

Global analysis of the Brucella melitensis proteome: Identification of proteins expressed in laboratory-grown culture.

Brucella melitensis is a facultative intracellular bacterial pathogen that causes brucellosis, a zoonotic disease primarily infecting sheep and goats, characterized by undulant fever, arthritic pain and other neurological disorders in humans. A comprehensive proteomic study of strain 16M was conducted to identify and characterize the proteins expressed in laboratory-grown culture. Using overlapping narrow range immobilized pH gradient strips for two-dimensional gel electrophoresis, 883 protein spots were detected between pH 3.5 and 11. The average isoelectric point and molecular weight values of the detected spots were 5.22 and 46.5 kDa, respectively. Of the 883 observed protein spots, 440 have been identified by matrix-assisted laser desorption/ionization-mass spectrometry. These proteins represent 187 discrete open reading frames (ORFs) or 6% of the predicted 3197 ORFs contained in the genome. The corresponding ORFs of the identified proteins are distributed evenly between each of the two circular B. melitensis chromosomes, indicating that both replicons are functionally active. The presented proteome map lists those protein spots identified to date in this study. This map may serve as a baseline reference for future proteomic studies aimed at the definition of biochemical pathways associated with stress responses, host specificity, pathogenicity and virulence. It will also assist in characterization of global proteomic effects in gene-knockout mutants. Ultimately, it may aid in our overall understanding of the cell biology of B. melitensis, an important bacterial pathogen.

Animals↗
PubMed1991

Molecular analysis of a patient with neurofibromatosis 1 and achondroplasia.

The gene for von Recklinghausen neurofibromatosis (NF1) is on proximal 17q; the location of the gene for achondroplasia (ACH) is unknown. We have begun a molecular analysis of a patient with mental retardation, NF1 and ACH, a clinical presentation suggestive of a contiguous gene syndrome. In addition, this individual has a 47,XYY chromosome constitution. To define a possible chromosome 17 deletion, we investigated the copy number of DNA sequences linked to NF1 with conventional and pulsed-field gel electrophoresis (PFGE). We found no evidence for a deletion on chromosome 17. These results make it unlikely that this patient harbors a single deletion in the NF1 region causing both NF1 and ACH and suggest different mechanisms for the de novo occurrence of 2 autosomal dominant disorders in this individual.

Achondroplasia↗
PubMed1991

Acetylcholine receptor-specific T-lymphocyte clones in the normal human immune repertoire: target epitopes, HLA restriction, and membrane phenotypes.

Potentially autoimmune T-lymphocyte lines specific for the nicotinic acetylcholine receptor of the neuromuscular junction have been isolated previously from patients with myasthenia gravis. We report on the isolation and expansion of T cells specific for the acetylcholine receptor of Torpedo californica or for a recombinant mammalian acetylcholine receptor alpha chain peptide (X4), from the peripheral blood of 11 healthy donors. Two major T-cell epitopes, located between amino acid positions 44-104 and 141-172, were identified using a panel of overlapping mammalian alpha chain fusion proteins. Most T lines recognized the acetylcholine receptor epitopes in the molecular context of HLA-DR molecules. Unexpectedly, all the T. californica acetylcholine receptor-specific T lines obtained from one DR4 (DRw53), DQw3 donor and two DR4, w8 (DRw53), DQw3 donors were restricted by DRw53 product(s). Using DR gene-transfected L cells as antigen presenters, in 4 lines, a close relationship between the recognized epitope and the restricting DR element was revealed. The membrane phenotype of the T. californica acetylcholine receptor-and X4-specific T lines was predominantly CD4+CD8-, with some CD4+CD8+ components. It did not significantly differ from that of control, tuberculin purified protein derivate-specific T lines raised from the same donors. These findings are in harmony with previous ones demonstrating the presence of potentially autoimmune T-lymphocyte clones within normal immune repertoires.

Antigens, CD↗
PubMed1990

Polymorphism and expression of the galactosyltransferase-associated protein kinase gene in normal individuals and galactosylation-defective rheumatoid arthritis patients.

We used restriction endonuclease digestion of leukocyte DNA to assess the structural integrity of an N-acetylglucosamine beta 1----4 galactosyltransferase (GalTase)-associated (GTA) protein kinase gene in rheumatoid arthritis (RA) patients. This analysis provides evidence that the gross structure of the GTA protein kinase gene locus remains intact in patients with defective galactosylation and that this gene locus is polymorphic both in normal individuals and in patients with RA, although no polymorphisms unique to RA patients were observed. Initial data on the expression of this gene indicate that comparable levels of GTA protein kinase messenger RNA are present in the lymphocytes of normal individuals and RA patients, irrespective of whether lymphocytes were obtained from patients with decreased or normal levels of galactosylation.

Acetylglucosamine↗
PubMed1991

A two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studies.

A standard two-dimensional (2-D) protein map of Fischer 344 rat liver (F344MST3) is presented, with a tabular listing of more than 1200 protein species. Sodium dodecyl sulfate (SDS) molecular mass and isoelectric point have been established, based on positions of numerous internal standards. This map has been used to connect and compare hundreds of 2-D gels of rat liver samples from a variety of studies, and forms the nucleus of an expanding database describing rat liver proteins and their regulation by various drugs and toxic agents. An example of such a study, involving regulation of cholesterol synthesis by cholesterol-lowering drugs and a high-cholesterol diet, is presented. Since the map has been obtained with a widely used and highly reproducible 2-D gel system (the Iso-Dalt system), it can be directly related to an expanding body of work in other laboratories.

Animals↗
PubMed1993

Quantitation of hepatitis C virus RNA in serum of asymptomatic blood donors and patients with type C chronic liver disease.

We describe a method for quantifying hepatitis C virus RNA in serum. This competitive assay combines reverse transcription and polymerase chain reaction and is based on coamplification of the target RNA with known amounts of synthetic mutated RNA. We tested serum samples from 104 hepatitis C virus carriers (9 asymptomatic blood donors and 95 patients with type C chronic liver disease) to determine the relationship between the replicative level of hepatitis C virus and various stages of the carrier states. The amount of circulating hepatitis C virus RNA ranged from 10(4) to 10(9.5) genomes/ml serum. The titer of hepatitis C virus RNA (logarithmic transformed copy numbers of RNA per milliliter of serum) was lower in asymptomatic blood donors (5.4 +/- 2.0) and in patients with chronic persistent hepatitis (7.3 +/- 1.1) than in patients with chronic active hepatitis (7.9 +/- 0.8), cirrhosis (7.8 +/- 0.7) or hepatocellular carcinoma (7.9 +/- 0.7). The titer of hepatitis C virus RNA was significantly lower in carriers younger than 40 yr old and correlated positively with the logarithmic transformed serum ALT level. Logistic regression showed that age and titer of hepatitis C virus RNA correlated independently with the stages of liver disease. These results showed that the replicative level of hepatitis C virus is higher in advanced liver disease and that elevation of viral replication may play an important role in liver injury and progression of liver disease. This competitive assay is useful in evaluating the state of viral replication in hepatitis C virus infection.

Alanine Transaminase↗
PubMed1992

Illegitimate transcription of phenylalanine hydroxylase for detection of mutations in patients with phenylketonuria.

Illegitimately transcribed phenylalanine hydroxylase mRNA was amplified using the polymerase chain reaction from both fibroblasts and Epstein-Barr virus-transformed lymphocytes. This method was used to study mutations of this gene in patients with phenylketonuria and known point mutations were easily detected. Illegitimate transcription was successful for studying splicing defects and it was found that the previously described mutation which changes G to A at the 5' donor site of intron 7 causes exon 7 to be spliced out.

Amino Acid Sequence↗
PubMed1994

Analysis of the CFTR gene in the Spanish population: SSCP-screening for 60 known mutations and identification of four new mutations (Q30X, A120T, 1812-1 G-->A, and 3667del4).

In order to determine the spectrum of CF mutations in the Spanish population, we have analysed 40 unrelated Spanish CF patients, with at least one chromosome negative for mutations delta F508, G542X, and N1303K. Exons 1-7,10-14a,15,16,17b,18-21 of the CFTR gene were studied by Single Strand Conformation Polymorphism (SSCP) analysis, using 60 known CF mutations as controls. SSCP screening allowed us to detect 28 different mutations in 52 CF chromosomes, and to identify four new mutations (Q30X in exon 2, A120T in exon 4, 1812-1G-->A in intron 11 and and 3667del4 in exon 19). Further analysis of the four new mutations in a total of 950 Spanish CF chromosomes showed a final frequency of 0.4%, 0.1%, 0.1%, and 0.1% for 1812-1G-->A,Q30X, A120T, and 3667del4, respectively. No mutations were detected in exons 1, 3, 14a, 16, and 18. We have also detected 10 intragenic polymorphisms and DNA sequence variants and have analysed their frequencies in our population. The total of 28 mutations identified in the 80 CF chromosomes highlight the molecular heterogeneity of CF in the Spanish population.

Base Sequence↗
PubMed1992

A new gene, BCM, on chromosome 16 is fused to the interleukin 2 gene by a t(4;16)(q26;p13) translocation in a malignant T cell lymphoma.

A t(4;16)(q26;p13.1) chromosome translocation found in tumour cells from a patient with a T cell lymphoma was shown to rearrange the interleukin 2 gene, normally located on chromosome band 4q26, with sequences from chromosome band 16p13.1. A cDNA library of tumour cells was screened with an interleukin 2 gene-specific probe. Three clones were isolated, which consisted, from 5' to 3', of the three first exons of the interleukin 2 gene followed by a 16p13 in-frame sequence encoding 181 amino acids. A probe derived from this sequence detected a 1.2 kb transcript in various cell lines exhibiting mature B lymphoid cell features, but this was not detected in other cell lines representative of other haematopoietic lineages, or in other organs. For this reason, the novel gene was termed BCM for B cell maturation. The open reading frame of BCM normal cDNA predicted a 184 amino acid protein with a single transmembrane domain which had no homology with any protein sequence stored in data banks. Our data indicate that BCM is a new gene whose expression coincides with B cell terminal maturation.

Amino Acid Sequence↗
PubMed1992

Haloperidol prevents induction of the hsp70 heat shock gene in neurons injured by phencyclidine (PCP), MK801, and ketamine.

The non-competitive NMDA receptor antagonists, PCP (phencyclidine), MK801, and ketamine produce psychosis in humans and abnormal vacuoles in posterior cingulate and retrosplenial rat cortical neurons. We show that PCP (> or = 5 mg/kg), MK801 (> or = 0.1 mg/kg), and ketamine (> 20 mg/kg) induce hsp70 mRNA and HSP70 heat shock protein in these vacuolated, injured neurons, and PCP also induces hsp70 in injured neocortical, piriform, and amygdala neurons. The PCP, MK801, and ketamine drug induced injury occurs in 30 day and older rats, but not in 0-20 day old rats, and is prevented by prior administration of the antipsychotic drugs haloperidol and rimcazole. Since haloperidol and rimcazole block dopamine and sigma receptors, and since M1 muscarinic cholinergic receptor antagonists also prevent the injury produced by PCP, MK801, and ketamine, future studies will be needed to determine whether dopamine, sigma, M1, or other receptors mediate the injury.

Amygdala↗
PubMed2005

Inverted repeat of a large segment unveiled on the right arm of Saccharomyces cerevisiae chromosome II.

By means of gene disruption analyses, Saccharomyces cerevisiae strain YPH499 was shown to have two, and only two, copies of ATP3 that encodes the gamma-subunit of H+-dependent ATP synthase and locates on the right arm of chromosome II. Linkage analyses of the two distinguishably marked copies of ATP3 indicated that the distance between them was about 43 cM. Since YBR030W, an ORF proximal to ATP3 by a distance of 17 kbp, was also found to be duplicated, we marked them with two distinguishable nutritional markers, which were also distinguishable from those used for marking the two copies of ATP3, and achieved four-point linkage analyses; CEN2 marked with an appropriate nutritional marker gene was included as a reference point. And, the following linkage map was deduced: CEN2- [11 cM]-YBR030Wa- [8 cM]-ATP3a-[47 cM]-ATP3b- [55 cM]-YBR030Wb. From this map, we suspected that a segment spanning at least YBR030W-ATP3 would be inversely duplicated on the right arm of chromosome II. We then carried out chromosome fragmentation analyses, using several laboratory strains including YPH499, and obtained data in accord with our speculation for all strains, although the distance between the two copies of ATP3 varied from 48 kbp to 192 kbp among the strains examined.

ATP Synthetase Complexes↗
PubMed1993

Prior arterial injury enhances luciferase expression following in vivo gene transfer.

We determined the time course of gene expression following DNA/Lipofectin transfection of normal or previously injured arterial segments using direct intraluminal infusion following surgical exposure. Constructs possessing the firefly luciferase cDNA regulated by Simian virus 40, Rous sarcoma virus, or alpha-actin promoter were incubated together with Lipofectin for 30 minutes. Arterial segments were assayed for luciferase activity following harvest at 2-21 days. Without prior injury, luciferase activity was only 2.5-fold greater than background two days following gene transfer. Arterial injury three days before gene transfer resulted in luciferase activity 12.5-fold over background levels. This observation has clinical implications with regard to gene therapy following angioplasty, a procedure that is associated with endothelial cell denudation and smooth muscle cell proliferation. Maintenance of gene expression for several days could ameliorate the early smooth muscle migration and proliferation following arterial injury.

Actins↗
PubMed1993

Neuropeptide-Y Y1 receptor gene polymorphism: cross-sectional analyses in essential hypertension and obesity.

Neuropeptide Y increases blood pressure and appetite, disorders of which have a genetic component. The present study examined the neuropeptide-Y Y1 receptor gene (NPYY1R) for involvement in essential hypertension (HT) and obesity. Frequency of alleles of the only known variant, involving a point mutation in intron 1, was determined by PCR and PstI digestion. Minor allele frequency was 0.37 in 75 HT offspring of two HT parents, compared with 0.35 in 86 normotensives (NTs) ( chi 2 = 0.11; P = 0.73). In obese and lean HTs frequency was 0.40 and 0.35 (chi 2 = 0.51; P = 0.46); and was 0.38 and 0.34 in obese and lean NTs (chi 2 = 0.16; P = 0.69). In conclusion, variant(s) in linkage disequilibrium with the NPYY1R RFLP are not involved in HT or obesity.

Alleles↗