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Results for “second generation sequencing”

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At least 307 records · Page 17Linked to original sources

PubMed2004

A synthetic Rev-independent bovine immunodeficiency virus-based packaging construct.

Replication competent lentivirus (RCL) has been the major safety concern associated with applications of lentivirus-based gene transfer systems for human gene therapy. Minimization and elimination of overlaps between the packaging and the transfer vector constructs are expected to reduce the potential to generate RCL. We previously developed second- and third-generation bovine immunodeficiency virus (BIV)-based gene transfer systems. However, some sequence homologies between the vector and gag/pol packaging constructs remained. In order to minimize the sequence homologies, we recoded gag/pol with codon usage optimized for expression in human cells in this report. Expression of the recoded gag/pol was Rev/RRE independent. Thus, RRE was eliminated from the packaging construct, thereby removing a 312 bp block of homology. In addition, recoding gag/pol minimized overall homologies between the packaging and transfer vector constructs. Vectors generated by the recoded packaging construct with a four plasmid system had titers greater than 1 x 10(6) transducing units per milliliter, equivalent to those of the earlier generation systems. The vectors were functional in vitro and efficiently transduced rat pigment epithelial cells in vivo. Generation of the synthetic packaging construct provides further advances to the safety of lentiviral vectors for clinical applications.

Animals↗

PubMed2000

Regulation of calcium in salivary gland secretion.

Neurotransmitter-regulation of fluid secretion in the salivary glands is achieved by a coordinated sequence of intracellular signaling events, including the activation of membrane receptors, generation of the intracellular second messenger, inositol 1,4,5, trisphosphate, internal Ca2+ release, and Ca2+ influx. The resulting increase in cytosolic [Ca2+] ([Ca2+]i) regulates a number of ion transporters, e.g., Ca2+-activated K+ channel, Na+/K+/2Cl- co-transporter in the basolateral membrane, and the Ca2+-activated Cl- channel in the luminal membrane, which are intricately involved in fluid secretion. Thus, regulation of [Ca2+]i is central to the regulation of salivary acinar cell function and is achieved by the concerted activities of several ion channels and Ca2+-pumps localized in various cellular membranes. Ca2+ pumps, present in the endoplasmic reticulum and the plasma membrane, serve to remove Ca2+ from the cytosol. Ca2+ channels present in the endoplasmic reticulum and the plasma membrane facilitate rapid influx of Ca2+ into the cytosol from the internal Ca2+ stores and from the external medium, respectively. It is well-established that prolonged fluid secretion is regulated via a sustained elevation in [Ca2+]i that is primarily achieved by the influx of Ca2+ into the cell from the external medium. This Ca2+ influx occurs via a putative plasma-membrane-store-operated Ca2+ channel which has not yet been identified in any non-excitable cell type. Understanding the molecular nature of this Ca2+ influx mechanism is critical to our understanding of Ca2+ signaling in salivary gland cells. This review focuses on the various active and passive Ca2+ transport mechanisms in salivary gland cells--their localization, regulation, and role in neurotransmitter-regulation of fluid secretion. In addition to a historical perspective of Ca2+ signaling, recent findings and challenging problems facing this field are highlighted.

Animals↗

PubMed2006

A second-generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects.

A second-generation linkage map was constructed for the silkworm, Bombyx mori, focusing on mapping Bombyx sequences appearing in public nucleotide databases and bacterial artificial chromosome (BAC) contigs. A total of 874 BAC contigs containing 5067 clones (22% of the library) were constructed by PCR-based screening with sequence-tagged sites (STSs) derived from whole-genome shotgun (WGS) sequences. A total of 523 BAC contigs, including 342 independent genes registered in public databases and 85 expressed sequence tags (ESTs), were placed onto the linkage map. We found significant synteny and conserved gene order between B. mori and a nymphalid butterfly, Heliconius melpomene, in four linkage groups (LGs), strongly suggesting that using B. mori as a reference for comparative genomics in Lepidotera is highly feasible.

Animals↗

PubMed2004

[Identification and registration of corn genotypes using molecular markers].

In plant genetics and breeding, second-generation molecular markers allow detailed characterization of plant genotypes. Unique genotypes at ten simple sequence repeat (SSR) loci were established for 40 maize accessions by means of PCR. For every locus, SSR analysis revealed heterozygotes among simple hybrids, which made it possible to identify the parental forms with a high probability of exclusion of nonparental forms. A system was proposed for registration of maize genotypes in the form of genetic formulas reflecting the allelic state of microsatellite loci, in order to catalog, preserve, and effectively employ the existing maize gene pool in breeding.

Base Sequence↗

PubMed1993

Gene transfer and cardiovascular disorders.

Within the past four years, basic recombinant techniques (such as molecular cloning, sequencing, site-directed mutagenesis, PCR, and transfection) have been combined to yield a "second generation" of recombinant DNA technology with experimental potential which could barely have been envisioned only a decade ago. This review will focus upon the genesis and cardiovascular application of two recent developments in gene transfer technology: gene targeting by homologous recombination and direct in vivo gene transfer. Gene targeting evolved from transgenic mouse technology but is distinguished by its ability to precisely disrupt or "knock-out" specific genes in the murine genome. This not only provides decisive answers to functional questions, but also produces accurate models of human genetic disorders. In vivo gene transfer provides for the direct introduction of genetic information into living tissues. In vivo gene transfer not only facilitates basic research by providing a simple and direct way to analyze gene structure and function in intact animals, but may also find direct clinical application in the treatment of genetic and acquired disorders such as familial hypercholesterolemia and restenosis.

Animals↗

PubMed1998

A transgenic strategy for analyzing the regulatory regions of the human prostate-specific antigen gene: potential applications for the treatment of prostate cancer (Review).

Prostate-specific antigen (PSA) has been used clinically as a marker for the diagnosis and staging of prostate cancer due to its specific expression in prostate epithelial cells. In addition to its medical importance, its complex hormonal and tissue-specific regulation makes it an attractive model to study gene regulation. Two approaches have been applied to the identification of regulatory regions which confer this specific expression pattern. In vitro analysis of the regulatory regions of the human PSA gene using promoter reporter constructs and tumor cell lines has revealed a number of the DNA sequences involved in the hormone-dependent expression of PSA. We have pursued an alternative in vivo approach using transgenic animal technology, which is the focus of this review. Using this second approach, a transgenic mouse was generated using a 14 kilobase (kb) region of the human PSA gene encompassing the coding region and intervening sequences as well as 6 kb of upstream sequence and 2 kb of downstream sequence. This genomic DNA clone confers a PSA expression pattern in mice which appears to be very similar if not identical to that of humans, allowing us to investigate tissue-specificity and developmental regulation of PSA expression. In addition, these mice, for which PSA is a self-antigen, provide a model to test the feasibility and efficacy of PSA-directed immunotherapy for prostate cancer. The further identification of the PSA regulatory regions important for tissue-specificity may ultimately allow the design of new therapeutics for the treatment of prostate cancer.

Animals↗

PubMed2006

Scalable generation of high-titer recombinant adeno-associated virus type 5 in insect cells.

We established a method for production of recombinant adeno-associated virus type 5 (rAAV5) in insect cells by use of baculovirus expression vectors. One baculovirus harbors a transgene between the inverted terminal repeat sequences of type 5, and the second expresses Rep78 and Rep52. Interestingly, the replacement of type 5 Rep52 with type 1 Rep52 generated four times more rAAV5 particles. We replaced the N-terminal portion of type 5 VP1 with the equivalent portion of type 2 to generate infectious AAV5 particles. The rAAV5 with the modified VP1 required alpha2-3 sialic acid for transduction, as revealed by a competition experiment with an analog of alpha2-3 sialic acid. rAAV5-GFP/Neo with a 4.4-kb vector genome produced in HEK293 cells or Sf9 cells transduced COS cells with similar efficiencies. Surprisingly, Sf9-produced humanized Renilla green fluorescent protein (hGFP) vector with a 2.4-kb vector genome induced stronger GFP expression than the 293-produced one. Transduction of murine skeletal muscles with Sf9-generated rAAV5 with a 3.4-kb vector genome carrying a human secreted alkaline phosphatase (SEAP) expression cassette induced levels of SEAP more than 30 times higher than those for 293-produced vector 1 week after injection. Analysis of virion DNA revealed that in addition to a 2.4- or 3.4-kb single-stranded vector genome, Sf9-rAAV5 had more-abundant forms of approximately 4.7 kb, which appeared to correspond to the monomer duplex form of hGFP vector or truncated monomer duplex SEAP vector DNA. These results indicated that rAAV5 can be generated in insect cells, although the difference in incorporated virion DNA may induce different expression patterns of the transgene.

Alkaline Phosphatase↗

PubMed1997

Expression of an F1/V fusion protein in attenuated Salmonella typhimurium and protection of mice against plague.

A novel approach to making fusions of F1 and V antigens, which may be incorporated into a live recombinant vaccine for plague, was developed. The nucleotide sequences encoding Yersinia pestis V antigen (lcrV) and the mature form of F1 antigen (caf1) were amplified by PCR with primers which included tails. At the 3' end of caf1 and the 5' end of lcrV, the tails encoded one of three six- or eight-amino acid linkers or their complementary sequences. The DNA overlap in each linker region was used to prime a second PCR to generate three F1/V fusions, which were cloned into pUC18. The resulting plasmids expressed fusion proteins consisting of F1 and V antigens, separated by the linkers Gly-Ser-Ile-Glu-Gly-Arg, Ser-Ala-Pro-Gly-Thr-Pro or Ser-Ala-Pro-Gly-Thr-Pro-Ser-Arg. As shown by Western blotting of bacterial cell lysates with anti-V and anti-F1 sera, the level of expression and degree of degradation of the three fusion proteins was similar. To investigate the immunogenicity of F1/V, one of the plasmids, placFV6 which encoded the Gly-Ser-Ile-Glu-Gly-Arg linker, was electroporated into the attenuated Salmonella typhimurium strain SL3261 (aroA). Mice receiving two intravenous doses of 5 x 10(6) cfu SL3261/placFV6 developed serum anti-V and anti-F1 IgG titres, with similar IgG1:IgG2a isotype ratios, and T cell responses specific for V and F1 antigens. Six weeks after vaccination, mice were challenged subcutaneously with 7.4 x 10(2) or 7.4 x 10(4) LD50s of Y. pestis strain GB, and a significant degree of protection was demonstrated. These results demonstrate the potential of co-expressing Y. pestis antigens as fusion proteins to develop a live recombinant vaccine against plague.

Amino Acid Sequence↗

PubMed1997

Imaging of shifted stimulated echoes and multiple spin echoes.

It is shown that a repetitive pulse sequence consisting of two 90 degrees pulses and gradients in a 1:2 ratio around the second 90 degrees pulse generates interscan shifted stimulated echoes (SSTEs) and intrascan multiple spin echoes (MSEs). Separation of these two types of signals is accomplished using specific gradient crusher schemes. The intensity of the SSTEs is an order of magnitude larger than that of the MSEs and determines the signal contrast if both effects are selected simultaneously. The SSTE sequence generates improved contrast between gray and white matter, even at high field, which is explained in terms of increased inverse T1-weighting for the interscan echo. The MSE image has low signal to noise and no detectable contrast. The effect of interscan diffusion weighting is also discussed.

Animals↗

PubMed2005

Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues.

Tissue-specific cDNA library sequences (expressed sequence tags, or EST) yield a detailed snapshot of gene expression and are useful in developing second-generation molecular resources (i.e., microarrays) for gene expression profiling. The objective of this study was to develop and characterize an intestine-specific cDNA library to examine the transcriptome of the bovine gut and identify expressed genes that influence ruminant nutrition and health. We describe BARC-8BOV, a normalized cDNA library developed from mRNA isolated from four distinct intestinal locations (duodenal, jejunal and ileal small intestine, colon) of Holstein dairy cattle resulting in 19,110 5'-EST deposited into the NCBI GenBank EST database. Assembly and clustering of these 19,110 clone sequences yielded 11,208 unique elements (3,419 contigs and 7,789 singletons) with an average length of 695 base pairs. Analysis strongly suggests normalization and tissue pooling were effective at increasing the discovery rate of new bovine sequence. A total of 1,123 sequence elements not previously identified in cattle, but with similarity to known genes in other animal species, were identified and shown to be involved in numerous critical biological processes. An additional 745 transcripts were not previously represented as EST in nucleotide or protein databases, and further analysis of these could lead to the identification of gut-specific transcript variants of known genes or potentially the discovery of novel bovine genes. Of the 11,208 assembled sequences, 11,034, or 98.4%, match sequences present in the bovine DNA trace archive at NCBI, and add to a bovine EST database previously lacking significant gut tissue representation. Ultimately, these data will also contribute in efforts to annotate the bovine genome.

Animals↗

PubMed2005

vALId: validation of protein sequence quality based on multiple alignment data.

The validation of sequences is essential to perform accurate phylogeny and structure/function analysis. However among the thousands of protein sequences available in the public databases, most have been predicted in silico and have not systematically undergone a quality verification. It has recently become evident that they often contain sequence errors. To address the problem of automatic protein quality control, we have developed vALId, an interactive web interfaced software. Taking advantage of high quality multiple alignments of complete protein sequences (MACS), vALId first warns about the presence of suspicious insertions, deletions (indels) and divergent segments, and second, proposes corrections based on transcripts and genome contigs. In a first evaluation test, hundreds of indels and divergent segments were randomly generated in a manually refined MACS. The sensitivity (Sn) and specificity (Sp) of indel detection were excellent (0.96) while the mean Sn(0.49) and Sp(0.56) of divergent segment delineation depended on the percent identity between sequence neighbors. In a second test, 6195 sequences in 100 MACS corresponding to different functional and structural protein families were analyzed. 65% of the sequences were in silico predictions and 44% of eukaryote predicted proteins were partially incorrect with at least one suspicious indel or divergent segment.

Algorithms↗

PubMed2000

Utilizing fowlpox virus recombinants to generate defective RNAs of the coronavirus infectious bronchitis virus.

Coronavirus defective RNAs (D-RNAs) have been used as RNA vectors for the expression of heterologous genes and as vehicles for reverse genetics by modifying coronavirus genomes by targetted recombination. D-RNAs based on the avian coronavirus infectious bronchitis virus (IBV) D-RNA CD-61 have been rescued (replicated and packaged into virions) in a helper virus-dependent manner following electroporation of in vitro-generated T7 transcripts into IBV-infected cells. In order to increase the efficiency of rescue of IBV D-RNAs, cDNAs based on CD-61, under the control of a T7 promoter, were integrated into the fowlpox virus (FPV) genome. The 3'-UTR of the D-RNAs was flanked by a hepatitis delta antigenomic ribozyme and T7 terminator sequence to generate suitable 3' ends for rescue by helper IBV. Cells were co-infected simultaneously with IBV, the recombinant FPV (rFPV) containing the D-RNA sequence and a second rFPV expressing T7 RNA polymerase for the initial expression of the D-RNA transcript, subsequently rescued by helper IBV. Rescue of rFPV-derived CD-61 occurred earlier and with higher efficiency than demonstrated previously for electroporation of in vitro T7-generated RNA transcripts in avian cells. Rescue of CD-61 was also demonstrated for the first time in mammalian cells. The rescue of rFPV-derived CD-61 by M41 helper IBV resulted in leader switching, in which the Beaudette-type leader sequence on CD-61 was replaced with the M41 leader sequence, confirming that helper IBV virus replicated the rFPV-derived D-RNA. An rFPV-derived D-RNA containing the luciferase gene under the control of an IBV transcription-associated sequence was also rescued and expressed luciferase on serial passage.

Animals↗

PubMed2002

Effect of glycosylation on MUC1 humoral immune recognition: NMR studies of MUC1 glycopeptide-antibody interactions.

MUC1 mucin is a large transmembrane glycoprotein, of which the extracellular domain is formed by a repeating 20 amino acid sequence, GVTSAPDTRPAPGSTAPPAH. In normal breast epithelial cells, the extracellular domain is densely covered with highly branched complex carbohydrate structures. However, in neoplastic breast tissue, the extracellular domain is underglycosylated, resulting in the exposure of a highly immunogenic core peptide epitope (PDTRP in bold above) as well as the normally cryptic core Tn (GalNAc), STn (sialyl alpha2-6 GalNAc), and TF (Gal beta1-3 GalNAc) carbohydrates. In the present study, NMR methods were used to correlate the effects of cryptic glycosylation outside of the PDTRP core epitope region to the recognition and binding of a monoclonal antibody, Mab B27.29, raised against the intact tumor-associated MUC1 mucin. Four peptides were studied: a MUC1 16mer peptide of the sequence Gly1-Val2-Thr3-Ser4-Ala5-Pro6-Asp7-Thr8-Arg9-Pro10-Ala11-Pro12-Gly13-Ser14-Thr15-Ala16, two singly Tn-glycosylated versions of this peptide at either Thr3 or Ser4, and a doubly Tn-glycosylated version at both Thr3 and Ser4. The results of these studies showed that the B27.29 MUC1 B-cell epitope maps to two separate parts of the glycopeptide, the core peptide epitope spanning the PDTRP sequence and a second (carbohydrate) epitope comprised of the Tn moieties attached at Thr3 and Ser4. The implications of these results are discussed within the framework of developing a glycosylated second-generation MUC1 glycopeptide vaccine.

Amino Acid Sequence↗

PubMed1986

Localization and DNA sequence analysis of the C gene of bacteriophage Mu, the positive regulator of Mu late transcription.

The C gene of bacteriophage Mu, required for transcription of the phage late genes, was localized by construction and analysis of a series of deleted derivatives of pKN50, a plasmid containing a 9.4 kb Mu DNA fragment which complements Mu C amber mutant phages for growth. One such deleted derivative, pWM10, containing only 0.5 kb of Mu DNA, complements C amber phages and transactivates the mom gene, one of the Mu late genes dependent on C for activation. The DNA sequence of the 0.5 kb fragment predicts a single long open reading frame coding for a 140 amino acid protein. Sequence analysis of DNA containing a C amber mutation located the base change to the second codon of this reading frame. Generation of a frameshift mutation by filling in a BglII site spanning codon 114 of this reading frame resulted in the loss of C complementation and transactivation activity. These results indicate that this open reading frame encodes the Mu C gene product. Comparison of the predicted amino acid sequence of the C protein with those of other transcriptional regulatory proteins revealed some similarity to a region highly conserved among bacterial sigma factors.

Amino Acid Sequence↗

PubMed2002

Deficient dimerization of human immunodeficiency virus type 1 RNA caused by mutations of the u5 RNA sequences.

The human immunodeficiency virus type 1 (HIV-1) virion contains two copies of genomic RNA that are noncovalently attached along a region at their 5' ends, in which two contact sites have been observed by electron microscopy. One of these sites is believed to be the stem-loop 1 (SL1) sequence which serves as the dimerization initiation site (DIS), and the other site, closer to the 5' end of the viral RNA, may involve the R or U5 RNA sequences. In this study, we present biochemical evidence showing that alteration of the U5 RNA sequence in the context of full-length viral RNA leads to diminished dimerization of virion RNA. In particular, two stretches of GU-rich sequences, which are located at nucleotides (nt) 99 to 108 and nt 112 to 123 within U5, were either deleted or substituted with exogenous sequences. The mutated viruses thus generated all exhibited deficient RNA dimerization. This dimerization deficit was not corrected by second-site mutations that preserved local RNA structures, such as the poly(A) hairpin, and was overcome to only a limited extent by compensatory mutations within Gag; these mutations were identified after long-term culture of the relevant mutant viruses in permissive cell lines and were able to restore viral infectiousness and RNA packaging to wild-type levels. Therefore, these GU sequences do not regulate RNA dimerization by the formation of local secondary structures nor by the maintenance of efficient viral RNA packaging; instead, they may mediate direct RNA-RNA interactions in the dimer structure. In contrast, mutation of palindrome 5'-AAGCUU-3', which resides within R and crowns the poly(A) hairpin, did not affect either RNA dimerization or RNA packaging.

5' Untranslated Regions↗

PubMed1992

Enzyme immunoassays for anti-hepatitis C virus antibodies improved specificity and analytical sensitivity by combination of three different recombinant viral proteins in second generation tests.

The detection of hepatitis C virus infection currently relies on a "virology without a virus" approach. So far, only viral nucleic acid has been isolated and sequenced by the methods of genetic engineering. The resulting viral sequence was then used to "design" proteins for diagnostic use as antigens in enzyme immunoassays (EIA). A first-generation EIA (EIA I), which uses a non-structural hepatitis C virus protein as antigen, detected 26 (0.6%) reactive sera out of a total of 4350 blood donors. An inhibition test using recombinant hepatitis C virus antigen, and EIAs using other, both synthetic and recombinant hepatitis C virus peptides were used as a specificity enhancing measure and as confirmatory tests, respectively. Only 7 of these reactives (0.16%, inhibition test) and 5 (0.11%, peptide EIA) were confirmed positive. Of the 26 initially reactive donor sera, 5 sera (0.11%) reacted positive in a second-generation anti-hepatitis C virus antibody EIA (EIA II), which uses two different recombinant non-structural hepatitis C virus proteins and one recombinant core protein. Seventeen (77%) of 22 haemophiliacs reacted positive in EIA I, and 19 (86%) did so in EIA II. There were no false positives in this cohort. Twenty-eight (19%) out of 148 liver disease patients showed a positive reaction in EIA I, and 31 (21%) were reactive in EIA II. Based on the results of the peptide enzyme immunoassay, 1 serum of this group was false positive in EIA I, while none of the sera of this group were false positive in EIA II.(ABSTRACT TRUNCATED AT 250 WORDS)

Antigens, Viral↗

PubMed1997

Case report: Clinical and virological analyses of a patient positive for hepatitis C virus-RNA by branched DNA assay but negative for anti-hepatitis C virus antibodies.

Infection with hepatitis C virus (HCV) is usually diagnosed by the presence of antibodies against fusion proteins or peptides derived from different regions of the HCV genome. However, a subgroup of patients with HCV viraemia are seronegative for antibody against hepatitis C virus (anti-HCV) by conventional antibody assays. We analysed serum samples from a patient with liver cirrhosis who tested negative for anti-HCV by a second-generation assay, but positive for HCV-RNA by reverse transcription polymerase chain reaction (RT-PCR) and branched DNA signal amplification. To identify possible mutations that could explain the failure of detection of anti-HCV by second-generation assay, PCR-amplified DNA fragments of the core region derived from the serum were cloned and sequenced. Nucleotide (nt) and amino acid (aa) sequence analyses (nt 1-486, aa 1-162) showed no mutations revealing stop codons, frame-shifts, deletions or insertions, but the presence of two amino acid substitutions (aa 75 and 91) when compared with HCV-J, a prototype strain of genotype 1b isolated from a Japanese patient. One of these two mutations (aa 75) was situated in the second hydrophilic domain of the core peptide, but analysis of the hydropathy profile showed only a little change. The two mutations were identical to those identified in other Japanese HCV isolates. The serum immunoglobulin level and T and B cell counts were normal in our patient. Our data suggest that the absence of anti-HCV in this patient was not due to mutations of major epitopes of HCV. Low-dose prednisolone administration just after transfusion may have induced immunological tolerance against HCV in this patient.

Aged↗

PubMed2004

Enantioselective total synthesis of FR900482.

The development of two approaches for the enantioselective total synthesis of FR900482 is described. A precursor for the formation of the benzazocine ring was assembled effectively by a modification of the Sonogashira coupling of an aryl triflate with a chiral acetylene unit derived from tartaric acid and the subsequent novel ketone formation via conjugate addition of pyrrolidine to the o-nitrophenylacetylene derivative. The first-generation approach to the key pentacyclic intermediate of our racemic total synthesis utilizes an intramolecular Mitsunobu reaction of an omega-hydroxynitrobenzenesulfonamide to form the benzazocine ring and a stepwise sequence to construct the hydroxymethyl group at the C(7) position. The key intermediate could be synthesized in optically pure form via formation of the characteristic hydroxylamine hemiacetal and a stereoselective epoxide formation. In the second-generation approach, the N-hydroxybenzazocine ring could be constructed directly from an omega-formylnitrobenzene derivative by intramolecular reductive hydroxylamination. The crucial stereoselective hydroxymethylation and the formation of the hydroxylamine hemiacetal could be performed efficiently by a one-pot sequence. After leading to the pentacyclic key intermediate, the total synthesis of (+)-FR900482 was accomplished by a modification of our protocol established in the racemic total synthesis. Stereochemical issues involved in the hydroxymethylation at the C(7) position and formation of the hydroxylamine hemiacetal are also discussed in detail.

Antineoplastic Agents↗