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Results for “second generation sequencing”

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PubMed1978

Size estimation in paranoid and nonparanoid schizophrenics.

Fifteen paranoid and 15 nonparanoid schizophrenics and 15 normal controls were administered a size estimation task which featured two administrations of nonthematic standard stimuli. The standard stimuli were presented under three conditions of background stimuli: a) surrounded by four smaller stimuli of the same kind; b) surrounded by four larger stimuli of the same kind; c) presented without background stimuli. Standard stimuli were presented at exposure times of 33 and 4000 milliseconds. On the first administration, nonparanoid schizophrenics were found to overestimate size relative to paranoidschizophrenics with normal controls intermediate in performance between the paranoid schizophrenics and nonparanoid schizophrenics, particularly on longer stimulus exposure times. The groups did not differ on the second administration. This replication of the results of earlier investigations suggest that the repeated administration of size estimation procedures in which the effects of sequence and thematic content stimuli were inextricably confounded may have contributed to recent conflicting findings in the size estimation literature. Contrary to predictions generated by Cromwell's stimulus redundancy formation, the paranoid schizophrenics were not more affected by the size of the background stimuli than the nonparanoid schizophrenics.

Adult↗

PubMed2001

Evidence that intragenic recombination contributes to allelic diversity of the S-RNase gene at the self-incompatibility (S) locus in Petunia inflata.

For Solanaceae type self-incompatibility, discrimination between self and nonself pollen by the pistil is controlled by the highly polymorphic S-RNase gene. To date, the mechanism generating the allelic diversity of this gene is largely unknown. Natural populations offer a good opportunity to address this question because they likely contain different alleles that share recent common progenitors. We identified 19 S haplotypes from a natural population of Petunia inflata in Argentina, used reverse transcriptase-polymerase chain reaction to obtain cDNAs for 15 alleles of the S-RNase gene, and sequenced all the cDNAs. Phylogenetic studies revealed that five of these alleles and two previously identified alleles form a major clade, and that the 5' region of S(19) allele was derived from an ancestor allele closely related to S(2), whereas its 3' region was derived from an ancestor allele closely related to S(8). A similar evolutionary relationship was found among S(3), S(12), and S(15) alleles. These findings suggest that intragenic recombination contributed to the generation of the allelic diversity of the S-RNase gene. Two additional findings emerged from the sequence comparisons. First, the nucleotide sequence of the S(1) allele identified in this work is completely identical to that of the previously identified S(1) allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity, S(6) and S(9) alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed.

Alleles↗

PubMed1989

Homologous plasmid recombination is elevated in immortally transformed cells.

The levels of intramolecular plasmid recombination, following transfection of a plasmid substrate for homologous recombination into normal and immortally transformed cells, have been examined by two independent assays. In the first assay, recovered plasmid was tested for DNA rearrangements which regenerate a functional neomycin resistance gene from two overlapping fragments. Following transformation of bacteria, frequencies of recombinationlike events were determined from the ratio of neomycin-resistant (recombinant) colonies to ampicillin-resistant colonies (indicating total plasmid recovery). Such events, yielding predominantly deletions between the directly repeated sequences, were substantially more frequent in five immortal cell lines than in any of three normal diploid cell strains tested. Effects of plasmid replication or interaction with T antigen and of bacterially mediated rejoining of linear molecules generated in mammalian cells were excluded by appropriate controls. The second assay used limited coamplification of a control segment of plasmid DNA, and of the predicted recombinant DNA region, primed by two sets of flanking oligonucleotides. Each amplified band was quantitated by reference to a near-linear standard curve generated concurrently, and recombination frequencies were determined from the ratio of recombinant/control DNA regions. The results confirmed that recombinant DNA structures were generated within human cells at direct repeats in the transfected plasmid and were markedly more abundant in an immortal cell line than in the diploid normal cells from which that line was derived.

Antigens, Viral, Tumor↗

PubMed1992

[Mechanisms of immunodeficiency in HIV infection and ways of overcoming it].

Though antibodies against HIV-1 appearing in the course of infection are successfully used for the diagnostic purposes, their accumulation on the earlier step leads to: firstly, to the rapid generation of the immunodeficiency by different mechanisms and secondly, to inefficiency of immunotherapy. One of the causes for immunodeficiency seems to be antibodies which are induced in the HIV-infected person by the HIV peptides homologous to the MHC class II molecules by their amino acid sequences. 73% of HIV-1 positive sera are shown to react with human B-lymphoma cells expressing surface class II molecule. The binding is caused by the antibodies preventing the murine monoclonal anti-HLA.DR Ab interaction with B-lymphoma. Three amino acid sequences are identified in both alpha- and beta-chain of the HLA.DR antigen, these sequences being homologous to HIV-1 gp120 or gp42 molecules for 50 to 70%. Using synthetic peptides it was shown that HIV-1-infected persons contain antibodies which cross-react to the homologous peptides of the HIV-1 and of the MHC class II. It is supposed that such antibodies shield the class II molecule on the surface of their own antigen-presenting cell which may lead to immunodeficiency caused by the anti-HIV-1 antibody.

Acquired Immunodeficiency Syndrome↗

PubMed2002

Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase.

The spontaneous occurrence of resistance to the herbicide glyphosate in weed species has been an extremely infrequent event, despite over 20 years of extensive use. Recently, a glyphosate-resistant biotype of goosegrass (Eleusine indica) was identified in Malaysia exhibiting an LD(50) value approximately 2- to 4-fold greater than the sensitive biotype collected from the same region. A comparison of the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) activity by glyphosate in extracts prepared from the resistant (R) and sensitive (S) biotypes revealed an approximately 5-fold higher IC(50)(glyphosate) for the (R) biotype. Sequence comparisons of the predicted EPSPS mature protein coding regions from both biotypes revealed four single-nucleotide differences, two of which result in amino acid changes. One of these changes, a proline to serine substitution at position 106 in the (R) biotype, corresponds to a substitution previously identified in a glyphosate-insensitive EPSPS enzyme from Salmonella typhimurium. Kinetic data generated for the recombinant enzymes suggests that the second substitution identified in the (R) EPSPS does not contribute significantly to its reduced glyphosate sensitivity. Escherichia coli aroA- (EPSPS deficient) strains expressing the mature EPSPS enzyme from the (R) biotype exhibited an approximately 3-fold increase in glyphosate tolerance relative to strains expressing the mature EPSPS from the (S) biotype. These results provide the first evidence for an altered EPSPS enzyme as an underlying component of evolved glyphosate resistance in any plant species.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

PubMed2002

Bead injection for surface enhanced Raman spectroscopy: automated on-line monitoring of substrate generation and application in quantitative analysis.

The technique of bead injection has been adapted for surface enhanced Raman scattering (SERS) to substantially improve precision, long term stability and sensitivity of SERS detection in analytical chemistry. For this purpose a fully automated flow system comprising a dedicated flow-cell has been developed and tested. With the developed flow-cell, which contains two inlet and two outlet channels, it is possible to retain, perfuse and discharge minute amounts of polymer beads while monitoring all steps by Raman spectroscopy. First, beads carrying cation exchanger moieties were retained in the flow-cell and subsequently perfused with a silver nitrate and a hydroxylamine solution using one inlet of the flow cell. By this sequence homogeneous SERS active silver layers were formed on the beads. The uniformity of the achieved silver layer was studied by secondary electron microscopy. For measurement, the analyte was then introduced from the second inlet channel such that the interaction between the activated SERS beads and analyte occurred in close proximity and within the focus of the laser excitation beam. Due to the complete computer control of all experimental steps, including bead entrapment, SERS layer generation, sample introduction and final bead removal, highly reproducible conditions for SERS were achieved. The method was developed using 9-aminoacridine as a test molecule. Quantitative studies were carried out for 9-aminoacridine and acridine showing linear calibrations from 1-100 nmol l(-1) and 50-1,000 nmol l(-1), respectively, using a sample volume of 200 microl each. Typical relative standard deviations were 4.7% for 9-aminoacrine and 5.8% for acridine.

Journal Article↗

PubMed2000

Polymorphism in oestrogen response element associated with variation in plasma angiotensinogen concentrations in healthy pregnant women.

OBJECTIVE: To investigate the hypothesis that the genotype at nucleotide A(-20)C in the 5' flanking region of the angiotensinogen gene, which lies within a sequence with high homology to an oestrogen response element, affects plasma angiotensinogen levels in pregnancy. DESIGN: Prospective observational study METHODS: Seventy-two healthy pregnant women were recruited in the second half of pregnancy from hospital and primary care antenatal clinics in Nottingham, UK. Plasma angiotensinogen concentrations were measured by radioimmunoassay of angiotensin I generated from endogenous angiotensinogen in the presence of excess human renin. DNA was extracted from peripheral venous blood, and angiotensinogen genotype determined at A(-20)C, G(-6)A and Met235Thr. Associations between genotype and plasma angiotensinogen concentration were assessed by analysis of variance. RESULTS: Women homozygous for the -20C allele had the lowest mean plasma angiotensinogen concentration of 1.7 +/- 0.3micromol/l. Women homozygous for -20A had significantly higher plasma angiotensinogen concentrations (2.6 +/- 0.1 micromol/l), and intermediate levels (2.0 +/- 0.1 micromol/l) were observed in women heterozygous for A(-20)C (P = 0.002, ANOVA). The polymorphisms at nucleotide -6 and codon 235 were in almost complete linkage disequilibrium, and nucleotide -20C was found only in a subset of -6A/235Thr alleles. Conclusion The low plasma angiotensinogen levels associated with the -20C/-6A/235Thr haplotype in pregnant women contrast with the high concentrations associated with the 235Thr allele in the non-pregnant state. A possible explanation lies in the presence of a motif with high homology to an oestrogen response element between the TATA box and transcription initiation site. Previous in vitro studies of reporter gene constructs have demonstrated thatthe A(-20)C polymorphism affects oestrogen responsiveness. The results of this study support the hypothesis that the oestrogen response element of the angiotensinogen gene is of functional importance in pregnancy, and that oestrogen responsiveness in pregnancy is influenced by the genotype at nucleotide - 20.

Alleles↗

PubMed1992

Nucleotide sequence of the third cytokine LD78 gene and mapping of all three LD78 gene loci to human chromosome 17.

Cytokine LD78 is a member of a newly identified cytokine superfamily. We cloned the third human gene for the LD78, termed LD78 gamma and the sequence analysis showed that it is a 5'-truncated pseudogene. Exons 2 and 3 and the intron between them are highly homologous to those of the LD78 beta gene, hence, the gamma gene was probably derived from the beta gene. Southern blot analysis of human x mouse somatic hybrid cell DNAs and in situ hybridization experiments mapped all the three gene loci on human chromosome 17q21.1-q21.3. Analysis of DNAs from family members supports our previous finding that the beta and gamma genes on each of the paired chromosome 17 vary in copy number and that the LD78 alpha gene is presumably a single copy. In our analyses of cosmid clones, the LD78 beta gene and the second gene for AT744, which is also a member of the superfamily are closely linked in a head-to-head arrangement. The mechanism of generation of the three LD78 genes is discussed.

Base Sequence↗

PubMed2006

Complex spatio-temporal dynamics of fMRI BOLD: A study of motor learning.

Many studies have investigated the temporal properties of BOLD signal responses to task performance in regions of interest, often noting significant departures from the conventionally modelled response shape, and significant variation between regions. However, these investigations are rarely extended across the whole brain nor incorporated into the routine analysis of fMRI studies. As a result, little is known about the range of response shapes generated in the brain by common paradigms. The present study finds such temporal dynamics can be complex. We made a detailed investigation of BOLD signal responses across the whole brain during a two minute motor-sequence task, and tracked changes due to learning. The multi-component OSORU (Onset, Sustained, Offset, Ramp, Undershoot) linear model, developed by Harms and Melcher (J.Neurophysiology, 2003), was extended to characterise responses. In many regions, signal transients persisted for over thirty seconds, with large signal spikes at onset often followed by a dip in signal below the final sustained level of activation. Training altered certain features of the response shape, suggesting that different features of the response may reflect different aspects of neuro-vascular dynamics. Unmodelled, this may give rise to inconsistent results across paradigms of varying task durations. Few of the observed effects have been thoroughly addressed in physiological models of the BOLD response. The complex, extended dynamics generated by this simple, often employed task, suggests characterisation and modelling of temporal aspects of BOLD responses needs to be carried out routinely, informing experimental design and analysis, and physiological modelling.

Brain↗

PubMedDate not supplied

Generation of a variant of human interleukin-4 by alternative splicing.

A second species of interleukin-4 (IL-4) mRNA was identified using both a reverse transcription-polymerase chain reaction and an RNase protection assay. This novel IL-4 mRNA was 48 base pairs smaller than IL-4 mRNA, which is the size of IL-4 exon 2. Sequence data of cloned cDNA demonstrated that this variant contained IL-4 exons 1,3 and 4, with exon 1 spliced directly to exon 3 in an open reading frame. The entire protein encoding region of this variant, named IL-4 delta 2, was identical to IL-4 except for the omission of exon 2. IL-4 delta 2 mRNA was detected in all human peripheral blood mononuclear cells tested and in purified CD3+ T cells. Amounts of both IL-4 and IL-4 delta 2 mRNAs increased upon T cell activation, although IL-4 mRNA increased to a greater extent than IL-4 delta 2 mRNA did. Human IL-3, IL-5, IL-13, and granulocyte macrophage-colony stimulating factor did not use alternative splicing to delete exon 2. We speculate that IL-4 delta 2 may regulate IL-4 function.

Alternative Splicing↗

PubMed1996

Woot, an active gypsy-class retrotransposon in the flour beetle, Tribolium castaneum, is associated with a recent mutation.

A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposen into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor approximately 25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.

Amino Acid Sequence↗

PubMed1985

Structural and evolutionary relationships among five members of the human gamma-crystallin gene family.

We have characterized five human gamma-crystallin genes isolated from a genomic phage library. DNA sequencing of four of the genes revealed that two of them predict polypeptides of 174 residues showing 71% homology in their amino acid sequence; the other two correspond to closely related pseudogenes which contain the same in-frame termination codon at identical positions in the coding sequence. Two of the genes and one of the pseudogenes are oriented in a head-to-tail fashion clustered within 22.5 kilobases. All three contain a TATA box 60 to 80 base pairs upstream of the initiation codon and a highly conserved segment of 44 base pairs in length immediately preceding the TATA box. The two genes and the two pseudogenes are similar in structure: each contains a small 5' exon encoding three amino acids followed by two larger exons that correspond exactly to the two similar structural domains of the polypeptide. The first intron varies from 100 to 110 base pairs, and the second intron ranges from 1 to several kilobases, rendering an overall gene size of 1.7 to 4.5 kilobases. At least one of the two pseudogenes appears to have been functional before inactivation, suggesting that their identical mutation was generated by gene conversion.

Amino Acid Sequence↗

PubMed1987

Sequence and structural organization of murine cytomegalovirus immediate-early gene 1.

In murine cytomegalovirus, abundant immediate-early transcription originates from 0.769 to 0.815 map units of the genome. This region contains the immediate-early gene (gene ieI) which encodes pp89, a phosphoprotein active in transcriptional regulation. In this paper we report on the precise location, structural organization, and sequence of gene ieI. The predominant ieI transcript, a 2.75-kilobase mRNA, is generated by splicing and composed of four exons. The precise termini of the 2.75-kilobase mRNA and the positions of the exons were determined by nuclease digestion experiments with either 5' or 3' end-labeled DNA fragments or in vitro transcribed cRNA probes. Exons of 300, 111, 191, and 1,703 nucleotides are separated by introns of 825, 95, and 122 nucleotides. The first AUG is located in the second exon of 111 nucleotides, and a single open reading frame of 1,785 nucleotides predicts a protein of 595 amino acids with a calculated molecular weight of 66,713. The N-terminal region of the protein contains sequences similar to a consensus sequence of histone 2B proteins. The regulatory function of pp89 and the role of this protein as an immunodominant antigen are discussed in relation to the amino acid sequence.

Amino Acid Sequence↗

PubMed2003

Artificial-infection protocols allow immunodetection of novel Borrelia burgdorferi antigens suitable as vaccine candidates against Lyme disease.

Vaccination with recombinant outer surface protein A (OspA) from Borrelia burgdorferi provides excellent antibody-mediated protection against challenge with the pathogen in animal models and in humans. However, the bactericidal antibodies are ineffective in the reservoir host, since OspA is expressed by spirochetes only in the vector, but rarely, if at all, in mammals. Using an artificially generated immune serum (anti-10(8) spirochetes) with high protective potential for prophylactic and therapeutic treatment, we have now isolated from an expression library of B. burgdorferi (strain ZS7) three novel genes, zs7.a36, zs7.a66 and zs7.a68. All three genes are located, together with ospA/B, on the linear plasmid lp54, and are expressed in vitro and in ticks. At least temporarily two of them, ZS7.A36 and ZS7.A66, are also expressed during infection. The respective natural antigens are poorly immunogenic ininfected normal mice but elicited antibodies in Lyme disease patients. We show that recombinant preparations of ZS7.A36, ZS7.A66 and ZS7.A68 induce functional antibodies in rabbits capable of protecting immunodeficient mice against subsequent experimental infection. These findings suggest that all three recombinant antigens represent potential candidates for a "second generation" vaccine to prevent and/or cure Lyme disease.

Animals↗

PubMed1996

Functional studies of single-site variants in the calmodulin-binding domain of RC3/neurogranin in Xenopus oocytes.

Single-site variants in the calmodulin-binding domain of RC3/neurogranin were heterologously expressed in Xenopus oocytes to examine their effects on serotonin-evoked currents. RC3 variants serine36 -->alanine (Ser36-->Ala), serine36-->glycine (Ser36-->Gly), and phenylalanine37-->tryptophan (Phe37-->Trp), which bind calmodulin but are deficient in protein kinase C (PKC) phosphorylation, display serotonin-evoked Ca(2+)-dependent Cl- currents in oocytes similar to control oocytes. A serine36-->aspartate (Ser36-->Asp) variant, which does not bind calmodulin and mimics the PKC-phosphorylated state of RC3, significantly enhances serotonin-evoked currents in a manner similar to wild-type. The results suggest that RC3 not only regulates the availability of free calmodulin in a dendritic spine but also, when phosphorylated, independently stimulates G-protein coupled second messenger pathways that generate inositol 1,4,5-trisphosphate (IP3), diacylglycerol (DAG) and intracellular Ca2+.

Amino Acid Sequence↗

PubMed2003

Generation of an infectious clone of VR-2332, a highly virulent North American-type isolate of porcine reproductive and respiratory syndrome virus.

A full-length cDNA clone of the prototypical North American porcine reproductive and respiratory syndrome virus (PRRSV) isolate VR-2332 was assembled in the plasmid vector pOK(12). To rescue infectious virus, capped RNA was transcribed in vitro from the pOK(12) clone and transfected into BHK-21C cells. The supernatant from transfected monolayers were serially passaged on Marc-145 cells and porcine pulmonary alveolar macrophages. Infectious PRRSV was recovered on Marc-145 cells as well as porcine pulmonary macrophages; thus, the cloned virus exhibited the same cell tropism as the parental VR-2332 strain. However, the cloned virus was clearly distinguishable from the parental VR-2332 strain by an engineered marker, a BstZ17I restriction site. The full-length cDNA clone had 11 nucleotide changes, 2 of which affected coding, compared to the parental VR-2332 strain. Additionally, the transcribed RNA had an extra G at the 5' end. To examine whether these changes influenced viral replication, we examined the growth kinetics of the cloned virus in vitro. In Marc-145 cells, the growth kinetics of the cloned virus reflected those of the parental isolate, even though the titers of the cloned virus were consistently slightly lower. In experimentally infected 5.5-week-old pigs, the cloned virus produced blue discoloration of the ears, a classical clinical symptom of PRRSV. Also, the seroconversion kinetics of pigs infected with the cloned virus and VR-2332 were very similar. Hence, virus derived from the full-length cDNA clone appeared to recapitulate the biological properties of the highly virulent parental VR-2332 strain. This is the first report of an infectious cDNA clone based on American-type PRRSV. The availability of this cDNA clone will allow examination of the molecular mechanisms behind PRRSV virulence and attenuation, which might in turn allow the production of second-generation, genetically engineered PRRSV vaccines.

Animals↗

PubMed2005

Second-generation, highly abbreviated route for elaboration of the oxetane D-ring in a fully functionalized taxane.

A six-step conversion of oxirane 3 to oxetane 9 is reported. The synthetic route takes particular advantage of the acid-catalyzed ring opening of 3 to allyl alcohol 4 in a polar reaction medium and of the heightened capability of the OsO4.TMEDA complex to effect the efficient stereocontrolled dihydroxylation of this intermediate. The overall yield of the new sequence is 33%.

Bridged-Ring Compounds↗

PubMed1999

Recurrent and new hepatitis C virus infection after liver transplantation.

Chronic infection with the hepatitis C virus (HCV) is the most common reason for liver transplantation. We examined the results of laboratory tests for HCV on a cohort of patients who received a liver transplant between 1990 and 1994 at three large centers. Seven hundred twenty-two recipients and 604 donors were tested for antibody to HCV (anti-HCV) using a second-generation enzyme-linked immunoassay (EIA-2), followed by recombinant immunoblot (RIBA-2) and HCV RNA confirmation by reverse-transcription polymerase chain reaction (RT-PCR) (with genotyping and viral quantification). Diagnosis of posttransplantation infection required detection of serum HCV RNA that could be genotyped by sequencing or was repeatedly positive despite being unsequenceable. Twenty-five percent of transplantation candidates were seropositive for anti-HCV. Approximately 86% of anti-HCV-positive, 93% of RIBA-positive, and 97% of HCV RNA-positive candidates developed infection after transplantation. Pretransplantation HCV RNA was superior to RIBA-2 for predicting posttransplantation infection. Whereas HCV genotype was identified in nearly all candidates and changed little after transplantation, serum viral levels rose markedly after transplantation. Fifteen donors were either anti-HCV- or HCV RNA-positive. Recipients of grafts from donors with HCV RNA all developed infection, whereas infection was not detected in recipients of grafts from donors with anti-HCV but without detectable HCV RNA. The rate of new infection fell significantly (P =.02) after the introduction of EIA-2 screening of blood. Donor and candidate markers for HCV predict posttransplantation infection.

Cohort Studies↗