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Results for “second generation sequencing”

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PubMed1996

Nucleotide sequences of the hepatitis C virus core region in patients without anti-core antibody.

Second-generation assays for detection of hepatitis C virus (HCV) infection that include reactivity of antibodies to core, NS3, NS4 are used because of their high sensitivity. Among these antibodies, anti-core antibody seems to be the most sensitive. However, there are some patients without anti-core antibodies, although HCV RNA is detectable by reverse transcription-polymerase chain reaction and branched DNA assay. The mechanism for the absence of anti-core antibody on its own is unclear. We therefore determined the nucleotide and deduced amino acid sequences of the core region obtained from two anti-core antibody-negative patients with HCV RNA (genotype 1b) and compared them with those of four anti-core antibody-positive patients and a previously reported sequence. Amino acids spanning 1-47, which seemed to exist in major B cell epitopes, were found to be completely conserved among these patients. Furthermore, the predictive binding motif to HLA DR4 (a.a 81-90) was completely conserved in both of the anti-core antibody-negative patients. There were various mutations in the residual amino acids spanning 49-108, but specific mutations could not be found in anti-core antibody-negative patients. These data indicate that the absence of anti-core antibody in two patients is not due to the presence of some formerly unknown viral variants, but due to a possible defect in the host's immune system.

Amino Acid Sequence↗

PubMed1998

Multiple novel transcripts for apolipoprotein(a)-related gene II generated by alternative splicing in tissue- and cell type-specific manners.

Various Kringle 4 (K4) sequences were identified in human genomic clones and genomic DNAs amplified by PCR. These K4s were homologous to those found in the apo(a) gene and thus termed apo(a)-related genes (ARGs). The same sequences were obtained when human peripheral leukocytes were analyzed by reverse transcription-PCR in order to study the expression mode of the ARGs. It was of note that multiple transcripts with three optional exons for an ARG (ARGII) were detected in leukocytes, indicating that they were generated by alternative splicing. All these transcripts possessed the first half of the second K4 sequence, which had been reported to be skipped. The variant products of ARGII are expected to contain an additional region of either 44, 66, or 100 unique amino acids at the C-terminus of a single K4 unit. When normal human tissues and cultured tumor cells were analyzed, the multiple ARGII transcripts were detected at varying levels. The presence of the cellular state-specific alternative splicing machinery may provide not only redundancy but also diversity in the structure/function of ARGII.

Alternative Splicing↗

PubMed1986

Two distinct but overlapping antibody binding sites in the pre-S(2) region of HBsAg localized within 11 continuous residues.

The fine specificity of the humoral immune response to the pre-S(2) region of the hepatitis B surface antigen was studied. It was demonstrated that the murine antibody response to the pre-S(2) region is focused on residues 133 through 143, and two distinct but overlapping epitopes were identified within 11 continuous residues. One epitope, defined by p133-139, is group specific, and the other epitope, defined by p137-143, is influenced by a subtype-dependent amino acid substitution at residue 141. However, the influence of residue 141 was "covert" in that it was only detected when synthetic antigens of 19 amino acids or smaller were used as the solid-phase ligand. The minimum size of both epitopes (p133-139 and p137-143) was seven amino acids. The physical and chemical form of the immunogen (i.e., protein vs peptide; conjugated vs free peptide) influenced antibody fine specificity. In quantitative antibody inhibition studies it was demonstrated that antibodies with nonoverlapping as well as overlapping fine specificities were capable of mutual inhibition. Finally, human HBV-infected, patient sera were shown to possess anti-pre-S(2) region antibodies that recognized sequences in common with the murine antisera. These results have implications relevant to the design of synthetic and recombinant second generation HBV vaccines and diagnostic reagents.

Amino Acid Sequence↗

PubMed1996

Absence of extensive genetic heterogeneity of hepatitis C virus in antibody-negative chronic hepatitis C.

Hepatitis C virus (HCV) carriers usually have antibodies to HCV; however, there are viremic individuals without these antibodies. To investigate whether variations of the viral genome are responsible for this discrepancy, the nucleotide and deduced amino acid sequences of HCV capsid and nonstructural regions obtained from 15 viremic patients were examined. These 15 patients were infected with type 1b HCV, and 10 did not have antibody to HCV assayed with second-generation tests. The nucleotide homology of the 5 seropositive and 10 seronegative patients with the HCV prototype sequence were 91.6% and 91.9%, respectively, in the capsid region. There was no apparent difference in the deduced amino acid sequences between the two groups of patients studied (94% vs. 95%). The nucleotide and amino acid sequences of a part of the nonstructural region 3 also showed similar results. These findings suggest that absence of antibodies against both capsid and nonstructural peptides in HCV carriers is not caused by genetic heterogeneity of the viral epitopes.

Adult↗

PubMed1997

Permeabilization and fusion of uncharged lipid vesicles induced by the HIV-1 fusion peptide adopting an extended conformation: dose and sequence effects.

The peptide HIV(arg), corresponding to a sequence of 23 amino acid residues at the N-terminus of HIV-1 gp41 (LAV1a strain), has the capacity to destabilize negatively charged large unilamellar vesicles. As revealed by infrared spectroscopy, the peptide associated with those vesicles showed conformational polymorphism: in the absence of cations the main structure was a pore-forming alpha-helix, whereas in the presence of Ca2+ the conformation switched to a fusogenic, predominantly extended beta-type structure. Here we show that an extended structure can also be involved in electrically neutral vesicle destabilization induced by the HIV-1 fusion peptide when it binds the vesicle from the aqueous phase. In the absence of cations, neutral liposomes composed of phosphatidylcholine, phosphatidylethanolamine, and cholesterol (molar ratio 1:1:1) selected for an extended structure that became fusogenic in a dose-dependent fashion. At subfusogenic doses this structure caused the release of trapped 8-aminonaphtalene-1,3,6-trisulfonic acid sodium salt/p-xylenebis(pyridinium)bromide from liposomes, indicating the existence of a peptide-mediated membrane destabilizing process before and independent of the development of fusion. When compared to HIV(arg), the fusion activity of HIV(ala) (bearing the R22 --> A substitution) was reduced by 70%. Fusogenicity was completely abolished when a second substitution (V2 --> E) was included to generate HIV(ala-E2), a sequence representing the N-terminus of an inactive gp41. However, the three sequences associated with vesicles to the same extent, and the three adopted a similar extended structure in the membrane. Whereas 1-(4-trimethylaminophenyl)-6-phenyl-1,3,5-hexatriene emission anisotropy was unaffected by the three peptides, DPH emission anisotropy in membranes was increased only by the fusogenic sequences. Taken together, our observations strongly argue that it is not an alpha-helical but an extended structure adopted by the HIV-1 fusion peptide what actively destabilizes cholesterol-containing, electrically neutral membranes. Moreover, membrane destabilization is modulated by the amino acid sequence in the extended structure. The effect displayed by the aforementioned V2 --> E substitution suggests that the fusion process described here could be reflecting a physiologically relevant phenomenon.

Amino Acid Sequence↗

PubMed1987

The mechanism of transduction of proto-oncogene c-src by avian retroviruses.

Chicken c-src sequences have been transduced by avian leukosis viruses (ALV) and by partial src-deletion (td) mutants of Rous sarcoma virus in several independent events. Analyses of the recombination junctions in the genomes of src-containing viruses and the c-src DNA have shed light on the mechanism of transduction, which involves at least two steps of recombination. The initial recombination between a viral genome and the 5' region of c-src appears to occur at the DNA level. This step does not require extensive homology and can be mediated by stretches of sequences with only partial homology. The 5' recombination junction can also be formed by splicing between viral and c-src sequences. The second recombination is presumed to occur between the transducing ALV or td viral RNA and the viral-c-src hybrid RNA molecule generated from the initial recombination. This step involving recombination at the 3' ends of those molecules restores the 3' viral sequences essential for replication to the viral-c-src hybrid molecule. High frequency of c-src transduction by partial td mutants suggests that the second recombination is greatly enhanced when there is sequence homology between the transducing virus and the 3' region of c-src. Incorporation of the c-src sequences into an ALV genome results in greatly elevated expression of the gene. However, increased expression of c-src alone is insufficient to activate its transforming potential. Structural changes in c-src are necessary to convert it into a transforming gene. The changes can be as small as single nucleotide changes resulting in single amino aid substitutions at certain positions. Mutations can occur rapidly during viral replication after c-src is incorporated into the viral genome. Therefore, it is most likely that transduction of c-src by ALV is followed by subsequent mutation and selection for the sarcomagenic virus. In the case of transduction by td viruses that retain certain src sequences, joining of these sequences with the transduced c-src apparently is sufficient to activate its transforming potential.

Alpharetrovirus↗

PubMed1997

Genomic sequence of the RA27/3 vaccine strain of rubella virus.

The sequence of the genome of the RA27/3 vaccine strain of rubella virus (RUB) was determined. In the process, several discrepancies between the previously reported genomic sequences of two wild RUB strains (Therien and M33) were resolved. The genomes of all three strains contain 9762 nucleotides (nts), exclusive of the 3' poly A tract. In all three strains, the genome contains (5' to 3'), a 40 nt 5' untranslated region (UTR), an open reading frame (ORF) of 6348 nts that encodes nonstructural proteins, a 123 nt UTR between the two genomic ORFs, a 3189 nt ORF that encodes the structural proteins, and a 62 nt 3' UTR. The 5' end of the subgenomic RNA was found to correspond to a uridine residue at nt 6436 of the genomic RNA. At the nucleotide level, the sequence of the three strains varied by 1.0 to 2.8%, while at the amino acid level, the sequence varied by 1.1 to 2.4% over both ORFs. The RA27/3 sequence will be of use in identification of the determinants of its attenuation, in vaccine production control and in development of second generation RUB vaccines based on recombinant DNA technology.

Amino Acid Sequence↗

PubMed1998

Cloning and tissue distribution of novel splice variants of the rat GABAB receptor.

We have identified two novel splice variants of the metabotropic gamma-aminobutyric acid receptor (GABABR1), designated GABABR1c and GABABR1d, when screening a rat cerebellum cDNA library. GABABR1c has an amino acid sequence identical to GABABR1b, a member of GABABR1 isoforms, and an additional 93-bp insertion that generates an additional 31-amino-acid sequence in the fifth transmembrane region of GABABR1b. Thus, GABABR1c may have a structural variation in the second extracellular loop and fifth transmembrane region. GABABR1d also has an amino acid sequence identical to GABABR1b and an additional insertion of 566 bp that generates a divergent amino acid sequence in the carboxylterminal end. Reverse-transcription polymerase chain reaction analysis showed that in various rat tissues GABABR1c mRNA was ubiquitously expressed and GABABR1d mRNA in forebrain, cerebellum, eye, kidney, and urinary bladder. GABABR1 isoforms may function not only in the central nervous system but also in various peripheral tissues.

Alternative Splicing↗

PubMed1991

Enzymatic multiplex DNA sequencing.

The problem of reading DNA sequence films has been reformulated using an easily implemented, multiplex version of enzymatic DNA sequencing. By utilizing a uniquely tagged primer for each base-specific sequencing reaction, the four reactions can be pooled and electrophoresed in a single lane. This approach has been previously proposed for use with fluorescently labelled probes (1), and is analogous to the principle used in four-dye fluorescence sequencing except that the signals are resolved following electrophoresis (2). After transfer to a nylon membrane, images are obtained separately for each of the four reactions by hybridization using oligonucleotide probes. The images can then be superimposed to reconstitute a complete sequence pattern. In this way the correction of gel distortion effects and accurate band registration are considerably simplified, as each of the four base-specific ladders require very similar corrections. The methods therefore provide the basis for a second generation of more accurate and reliable film reading programs, as well as being useful for conventional multiplex sequencing. Unlike the original multiplex protocol (3), the approach described is suitable for small projects, as multiple cloning vectors are not used. Although more than one vector can be utilized, only a library of fragments cloned into any single phage, phagemid or plasmid vector is actually required, together with a set of tagged oligonucleotide primers.

Base Sequence↗

PubMed1993

Response of the 23Na-NMR double-quantum filtered signal to changes in Na+ ion concentration in model biological solutions and human erythrocytes.

Double quantum filtered (DQF) 23Na-NMR signals were evaluated as a function of [Na+] at constant temperature in two model systems (bovine serum albumin (BSA) and Ficoll 400) and in human red blood cells (RBCs). In model systems, the ratio of double quantum filtered to single quantum (SQ) signal intensities was independent of [Na+], even over a wide range of Na+/K+ ratios. Varying the DQF preparation time affected only the DQF signal intensity. In contrast, in human red blood cells (RBCs) the shape and phase of the DQF intracellular Na+ signal (Na+in) varied as a function of preparation time. Similar observations in cartilage [Eliav, U., Shinar, H. and Navon, G. (1992) J. Magn. Reson. 28, 223-229] have been attributed to the generation of a second- and a third-rank tensor by the DQF pulse sequence, resulting from Na+ ion ordering. By using a DQF sequence which isolates the second-rank tensor only, this component was found to originate from the intracellular Na+ ion pool in human RBCs, as well as from interactions of Na+ ions with the extracellular face of the plasma membrane. The residual quadrupolar splitting for the signal originating from the former environment was shown to be less than the SQ linewidth, explaining its absence in SQ spectra, and this was confirmed by two-dimensional DQF 23Na-NMR experiments. By isolating the contribution from the third-rank tensor exclusively, the ratio of DQF:SQ signal intensities for Na+in in human RBCs was shown to be constant over a 4-fold change in [Na+in] produced by addition of an ionophore (nystatin). This indicates that such changes in physiological state do not alter the efficiency of DQF signal generation in human RBCs.

Animals↗

PubMed1995

Selection and characterization of RNAs replicated by Q beta replicase.

RNAs replicated by Q beta replicase were isolated from two random sequence RNA populations (one 56 nucleotides in length, the second 83) using a replication/dilution protocol. The selected molecules were cloned and sequenced, generating data set of 54 replicatable RNAs bound with higher affinity to Q beta replicase than did the random populations from which they were selected. Deletion analyses on two of the molecules indicated that internal regions of the RNAs were responsible for the specific binding of Q beta replicase. Truncated molecules representing the minimized RNA binding sites could inhibit replication of the full-length molecules, apparently by obstructing their binding to the replicase. The binding regions of the two RNAs were dominated by extended runs of pyrimidines. Similar C/U-rich regions existed in 85% of the sequences in the data set as well as in all of the previously published replicatable sequences. Mutation of the polypyrimidine domain of one of the replicatable sequences reduced the affinity of the molecule for Q beta replicase by 10-fold and completely abolished its ability to be replicated.

Base Sequence↗

PubMed2003

Correlation of subcellular compartmentalization of HPMA copolymer-Mce6 conjugates with chemotherapeutic activity in human ovarian carcinoma cells.

PURPOSE: Intracellular targets sensitive to oxidized damage generated by photodynamic therapy (PDT) utilizing N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-mesochlorin e6 monoethylenediamine (Mce6) conjugates was explored to aid in the design of second generation PDT delivery systems. METHODS: Low temperature, metabolic inhibitor, and nuclear localization sequences (NLS(FITC)) were used to achieve desired subcellular localization that was evaluated by confocal analysis and subcellular fractionation. Mce6 was bound to HPMA copolymer conjugates via non-degradable dipeptide linkers (P-GG-Mce6, P-NLS(FITC)-GG-Mce6) or lysosomally degradable tetrapeptide spacers (P-GFLG-Mce6, P-NLS(FITC)-GFLG-Mce6). Chemotherapeutic efficacy was assessed by the concentration that inhibited growth by 50% (IC50), cell associated drug concentration (CAD) and confocal microscopy. RESULTS: P-GFLG-Mce6 possessed enhanced chemotherapeutic activ ity compared to P-GG-Mce6 indicating enzymatically released Mce6 was more active than copolymer-bound Mce6. Lysosomes appeared less sensitive to photodamage as observed by a higher IC50. Nuclear-directed HPMA copolymer-Mce6 conjugates (P-NLS(FITC)-GG-Mce6, P-NLS(FITC)-GFLG-Mce6) possessed enhanced chemotherapeutic activity. However, control cationic HPMA copolymer-Mce6 conjugates containing a scrambled NLS (P-scNLS(FITC)-GG-Mce6) or amino groups (P-NH2-GG-Mce6) also displayed increased chemotherapeutic activity. CONCLUSIONS: Nuclear delivery was observed for P-NLS(FITC)-GG-Mce6 and P-NLS(FITC)-GFLG-Mce6 indicating NLS was a feasible approach for nuclear delivery. Due to the cationic nature of NLS, increased membrane binding of PDT systems incorporating cationic nuclear targeting moieties must be addressed.

Cell Line, Tumor↗

PubMed2002

Insight into the potential for DNA idiotypic fusion vaccines designed for patients by analysing xenogeneic anti-idiotypic antibody responses.

DNA vaccines induce immune responses against encoded proteins, and have clear potential for cancer vaccines. For B-cell tumours, idiotypic (Id) immunoglobulin encoded by the variable region genes provides a target antigen. When assembled as single chain Fv (scFv), and fused to an immunoenhancing sequence from tetanus toxin (TT), DNA fusion vaccines induce anti-Id antibodies. In lymphoma models, these antibodies have a critical role in mediating protection. For application to patients with lymphoma, two questions arise: first, whether pre-existing antibody against TT affects induction of anti-scFv antibodies; second, whether individual human scFv fusion sequences are able to fold consistently to generate antibodies able to recognize private conformational Id determinants expressed by tumour cells. Using xenogeneic vaccination with scFv sequences from four patients, we have shown that pre-existing anti-TT immunity slows, but does not prevent, anti-Id antibody responses. To determine folding, we have monitored the ability of nine DNAscFv-FrC patients' vaccines to induce xenogeneic anti-Id antibodies. Antibodies were induced in all cases, and were strikingly specific for each patient's immunoglobulin with little cross-reactivity between patients, even when similar VH or VL genes were involved. Blocking experiments with human serum confirmed reactivity against private determinants in 26-97% of total antibody. Both immunoglobulin G1 (IgG1) and IgG2a subclasses were present at 1.3 : 1-15 : 1 consistent with a T helper 2-dominated response. Xenogeneic vaccination provides a simple route for testing individual patients' DNAscFv-FrC fusion vaccines, and offers a strategy for production of anti-Id antibodies. The findings underpin the approach of DNA idiotypic fusion vaccination for patients with B-cell tumours.

Animals↗

PubMed2002

Heavy-metal complexation by de novo peptide design.

From poisoning caused by lead-based paint on domestic buildings to groundwater contamination by naturally occurring arsenic deposits in India, heavy-metal toxicity is a global health problem. Contaminated ground water and acute cases of heavy-metal poisoning are treated with chelators to remove the heavy metals from the contaminated site or person. This review discusses the effort to generate heavy-metal chelators through peptide de novo design. De novo design entails the design of a primary sequence that will precisely fold into a predetermined secondary and tertiary protein structure. The first-generation peptide chelator used to initiate this investigation is the three-stranded coild coil containing Cys. Cys provides a potential trigonal binding site with soft thiolate ligands, which has been proposed to provide specific interactions with heavy metals. This hypothesis derives from the observation that similar sites on natural proteins show selectivity for heavy metals over other essential metals, such as Zn or Mg. A description of two systems, the TRI series and the IZ-AC peptide, is given, highlighting the interaction of these peptides with Hg, Cd, As and Pb. Arguments are also presented for the potential use of three-helix bundles as a second-generation design.

Amino Acid Sequence↗

PubMed2003

3' RACE walking along a large cDNA employing tiered suppression PCR.

Large genes present particular cloning difficulties, especially when expressed at relatively low levels. We describe a novel method, termed 3' rapid amplification of cDNA ends (RACE) walking, for the rapid determination of unknown 3' flanking sequence of a large cDNA. The technique is a derivative of the anchored PCR 5' RACE procedure but includes a specific and limited second-strand cDNA synthesis and a tiered "panhandle" suppression of nonspecific products. The method generated 900 bp of new sequence for the large tammar wallaby ATRY gene in two easy steps, in which standard 3' RACE and PCR-based cDNA library walking proved unsuccessful. This robust approach represents a new tool for isolating unknown sequence under challenging cloning scenarios such as poor library representation, long coding regions, long 3' untranslated regions, and difficult template regions.

Animals↗

PubMed1993

Post-transfusional anti-HCV-negative non-A non-B hepatitis (II) serological and polymerase chain reaction analysis for hepatitis C and hepatitis B viruses.

Hepatitis C virus (HCV) is a major etilogical agent of post-transfusional and sporadic acute and chronic hepatitis in various geographical areas. However, anti-HCV seroconversion was uncommon in a recent study of patients with post-transfusional hepatitis in Paris, France (N. Asar et al., companion paper). The aim of the present study was to detect viral markers, in particular HCV RNA and hepatitis B virus (HBV) DNA, in these patients. A combination of second-generation assays for anti-HCV antibodies and the polymerase chain reaction were used to identify HCV RNA and HBV DNA sequences in serum samples collected before and after transfusion from patients who developed non-A, non-B hepatitis. Eighteen cases of acute, post-transfusional, non-A, non-B hepatitis were identified in the prospective clinical survey. Only three of these 18 subjects developed anti-HCV antibodies in second-generation tests. HCV RNA was identified in the serum of these three subjects but in none of the others. Two patients who were anti-HCV-negative had polymerase chain reaction evidence of HBV DNA. Known viral markers were not identified in 13 of the 18 patients with acute post-transfusional non-A, non-B hepatitis. These results raise the issue of HCV strains or 'non-A, non-B, non-C' viruses not identified by current HCV and HBV markers and implicated in post-transfusional hepatitis in France.

Base Sequence↗

PubMed2026

Scion-based drought stress memory affects potato response to water deficit.

A scion-based stress memory signal, which was derived from drought-primed potato plants, was transmitted to new potato plants generated through vegetative reproduction. This affected potato tuber yield. Drought is one of the most significant threats to agricultural productivity worldwide. The cultivated potato (Solanum tuberosum L.) is a crop species that is sensitive to drought stress. This study investigated the impact of scion-based drought stress memory on tuber yield, physiological parameters, gene expression, and DNA methylation in the vegetative progeny of grafted plants. The tuber progeny plants remembered the drought stress signal transmitted from the drought-primed scion. Significant changes were observed in the expression of genes, primarily those related to photosynthetic metabolic pathways, as well as those associated with chromatin remodeling, DNA repair, and the plant's response to abiotic stresses. The gene expression landscape corresponded with variability in chlorophyll fluorescence parameters. In the first and the second generation of vegetatively propagated plants, scion-based memory had a positive effect on tuber yield. This was achieved by buffering the decline in yield caused by drought, as compared to plants grown under control conditions. Whole-genome bisulfite sequencing analysis revealed no correlation between changes in DNA methylation and gene expression. Drought-induced alterations in DNA methylation were erased in the second progeny generation. We propose that there is a direct causal relationship between scion-based memory of drought stress and photosynthetic efficiency, as well as potato tuber productivity.

Solanum tuberosum↗

PubMed1992

Protein-DNA interactions at a yeast replication origin.

An understanding of the protein-DNA interactions in vivo at origins of DNA replication in eukaryotes is essential to delineate the mechanism of initiation of DNA synthesis and its control in the cell cycle. In the yeast Saccharomyces cerevisiae, a family of sequences known as autonomously replicating sequences (ARSs) function as origins of bidirectional DNA replication on plasmids and, in several instances, also in their normal chromosomal location. Here we use nucleotide resolution genomic footprinting to investigate the association of proteins with ARS1. Nuclease protection patterns indicate that at least two different cellular factors interact with functional elements in ARS1. The first seems to be ARS-binding factor 1. The second seems to be a novel protein that generates extensive protection over the essential ARS consensus sequence and phased DNaseI-sensitive sites across a functionally important flanking sequence. Hypersensitivity of this region to cleavage by copper phenanthroline indicates that it is under torsional strain, analogous to that produced at transcriptional start sites by assembly of an initiation complex. The protection in situ is similar to that generated by the origin recognition complex (ORC) protein.

Base Sequence↗