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Results for “Overlapping PCR”

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PubMed2026

Identification of a novel HIV-1 circulating recombinant form (CRF209_cpx) and its descendant unique recombinant form (URF) CRF209_cpx/B among MSM in Guangdong, southern China.

BACKGROUND: The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. METHODS: Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. RESULTS: Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. CONCLUSIONS: The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

HIV-1↗

PubMed2005

Codon optimization of papillomavirus genes.

Early and late genes of human and animal papillomaviruses show a codon composition seemingly unfavorable for expression in mammalian cells. It remains unclear how the viruses manage to achieve high levels of late gene expression during the viral life cycle. One possible solution could be that the availability of certain t-RNAs changes with progressing stages of cellular differentiation. Previous studies have demonstrated that modification of codon usage of papillomavirus late (L1 and L2) and early genes (E7) can overcome poor expression of these proteins both in transient and in stable expression systems. This was shown not only for human but also for plant cells. Two strategies can be employed to alter codon usage: elimination of only those codons that are rarely used in a particular expression system, or exchange of all possible codons by the ones most frequently used. Currently, there are two protocols for codon modification--a template-less polymerase chain reaction (PCR)-based protocol, in which very long overlapping oligodeoxynucleotides are used in an overlap-extension reaction, or a ligase chain reaction, in which shorter oligodeoxynucleotides are fused together after an annealing procedure. Both methods are presented and discussed.

Amino Acids↗

PubMed1992

[Identification of a 3' splice site mutation in the thyroglobulin gene in a case of congenital familial goiter].

A case of congenital familial goiter with impaired thyroglobulin (Tg) synthesis has been reported. The patient is the fifth in a family of six children, three of whom have a goiter. The parents are cousins. The patient's thyroid function tests showed low T4 (1.0 microgram g/dl) and free T4 (0.2 ng/dl), normal or slightly increased T3 (1.8 ng/ml) and free T3 (7.4 pg/ml), and high TSH (57 micrograms U/ml). Serum Tg was 5.1 ng/ml (normal less than 30). The thyroidal 123I-uptake was 59.8% before and 54.5% after perchlorate test. Gel filtration with Bio-Gel A 5m demonstrated the presence of albumin-like protein probably iodinated as a major protein in the thyroid and very low content of Tg which was smaller than the normal 19S Tg. Histologically microfollicular adenoma and negative Tg immunostaining were the dominant findings. Segregation of Tg alleles in the family was studied by Southern blotting with a probe revealing a diallelic RFLP. The results demonstrated that the affected siblings had received the same alleles from both parents and were homozygous for the RFLP. Northern blotting analysis of the goiter RNA with a Tg probe revealed that, whereas the amount of Tg mRNA was normal, its size seemed slightly reduced. PCR amplification of Tg mRNA as six overlapping cDNA fragments demonstrated that a 200bp fragment was missing from the 5' region of the goiter mRNA. Subcloning and sequencing of the cDNA fragments, and of the patient's genomic DNA amplified from this region, revealed that this aberrant splicing is due to a cytosine to guanine transversion at position minus 3 in the acceptor splice site of intron 3. The presence in exon 4 of a putative donor tyrosine residue (tyr 130) involved in thyroid hormone formation provides a coherent explanation of the hypothyroid status of the patient. To our knowledge, this is the first identified mutation responsible for congenital familial goiter in humans.

Adult↗

PubMed1998

Type 2 rice metallothionein-like gene has two introns.

A type 2 rice metallothionein-like gene was isolated from root by PCR and sequenced. The PCR fragment was designated as pcr1460, which overlaps with OsMT-2, a cDNA sequence previously characterized, with the presence of two additional segments, 583 and 613 bp in length. These segments are recognized as introns which divide the coding sequence into three exons, 65, 78 and 106 base pairs in length. The sequences flanking the introns conform with the GT/AG rule for splice junctions, and one exonic open reading frame can be identified in each of the introns. The observation that MT-like gene has two introns is the first of such a finding obtained from monocotyledonous plants.

Amino Acid Sequence↗

PubMed2000

Cloning, sequencing, and expression of the hepatitis E virus (HEV) nonstructural open reading frame 1 (ORF1).

Hepatitis E virus (HEV) causes enterically transmitted epidemic and sporadic viral hepatitis affecting millions of people in the developing world. Different geographical isolates of HEV show a high degree of homology at the nucleotide and amino acid levels. The approximately 7.2 kb RNA genome has three open reading frames of which ORF1 is predicted to code for the viral nonstructural polyprotein. The expression, processing and properties of the nonstructural ORF1 polyprotein have not been reported so far. In this study, the complete HEV ORF1 was reconstructed from overlapping fragments amplified by polymerase chain reaction (PCR) of total RNA isolated from the bile fluid of a rhesus monkey experimentally infected with HEV isolate from an epidemic. The complete assembled ORF1 was sequenced using HEV specific primers. The ORF1 polyprotein was expressed in E. coli, in a cell free translation system and in HepG2 cells, and was characterized by western blotting and immunoprecipitation using acute phase patient serum as well as polyclonal antibodies raised against defined parts of the ORF1 polyprotein. The nonstructural polyprotein of HEV was expressed as a 186 kDa protein. No processing was observed into discrete units, either in-vitro based on a kinetic analysis, or in HepG2 cells based on immunoprecipitation.

Animals↗

PubMed2001

Identification of a proviral structure in human breast cancer.

Involvement of a virus similar to mouse mammary tumor virus (MMTV) in human breast cancer has long been postulated but never demonstrated. We have detected by PCR a 660-bp sequence similar to the env gene of MMTV but not to the known endogenous viruses, in 38% of human breast cancers examined (Wang et al., Cancer Res., 55: 5173-5179, 1995). This sequence was expressed in 66% of the env-positive tumors as detected by reverse transcription-PCR (Wang et al., Clin. Cancer Res., 4: 2565-2568, 1998). In this article we report the amplification of a whole proviral structure from each of two human breast carcinomas that were env positive. Using nested extra-long PCR and primers from specific MMTV sequences, overlapping env-long terminal repeat (LTR), LTR-gag, gag-pol, and pol-env segments were successfully amplified. The 9.9-kb provirus is 95% homologous to MMTV but only 57% to human endogenous retrovirus K10 in 3.5 kb of the gag and pol genes. The provirus displays typical features of a replication competent virus, plus the open reading frame for the superantigen and the glucocorticoid responsive element. Fluorescence in situ hybridization with a 2.7-kb env-LTR sequence of an env-positive breast cancer cell line revealed that the sequence is inserted in several chromosomes but not in chromosomes from normal breast cells. The origin of the MMTV-like sequences is uncertain. Because they are undetectable in normal tissues, because the similarity between the two isolates is high (96%), and because they maintain open reading frames, they appear to be exogenous.

Breast Neoplasms↗

PubMed2001

Enzymatic mutation detection method evaluated for detection of p53 mutations in cDNA from breast cancers.

BACKGROUND: Rapid, reproducible, and easily run methods with high sensitivity and specificity are required for mutation screening of clinical samples. We evaluated the Enzymatic Mutation Detection (EMD(TM)) method by analysis of archival cDNA from 203 breast cancer patients and comparison with results of cDNA-based sequencing of the tumor suppressor gene p53. METHODS: The EMD technology uses the T4 endonuclease VII, which cleaves double-stranded DNA at sites where a DNA mismatch is present because of mispairing or an insertion/deletion of nucleotides. The EMD analyses were carried out by dividing the p53 gene into two overlapping fragments that were analyzed separately. After PCR amplification, the fragments were hybridized with wild-type p53 and subsequently exposed to the EMD enzyme. Cleavage products were analyzed and scored using an ALF(TM) automated DNA sequencer and ALFwin Fragment Analyzer software (VER: 1.02). RESULTS: The EMD technique had sensitivities of 45% and 64% and specificities of 83% and 84% for the two fragments, respectively. Patients with EMD-positive, wild-type p53 tumors had a survival similar to that of patients with EMD-negative, wild-type p53 tumors. Node-positive patients with p53 mutated tumors according to sequencing had a statistically significantly worse overall survival than those with p53 wild-type tumors (P = 0.016), whereas this difference in survival was not detected when p53 status was determined with EMD (P = 0.47). CONCLUSIONS: EMD had insufficient sensitivity for consideration in screening for the p53 gene in this archival material. Sequencing must still be considered as the standard procedure.

Breast Neoplasms↗

PubMed2005

Sporadic methicillin resistance in community acquired Staphylococcus aureus in Mozambique.

This study reports the drug resistance and clonal relationship of 24 Staphylococcus aureus community acquired isolates from patients attending Maputo Central Hospital, Mozambique, during one year (2002-2003). All the isolates produced beta-lactamase, six strains were resistant to tetracycline alone, three were resistant to erythromycin alone and one was resistant to trimethoprim-sulfamethoxazole; 11 were susceptible to all other drugs tested. Only one strain showed a multiple resistance pattern, including methicillin resistance. To investigate the clonal relationships we applied the ERIC AP-PCR and the SmaI PFGE RFLP methods. Overlapping drug resistances with these two molecular profiles, no significant correlation was obtained. The emergence of methicillin resistance in a multiple resistant strain is of great concern for resistance spreading surveillance in Mozambique.

Anti-Bacterial Agents↗

PubMed1995

Absence of point mutations in the extracellular domain of the alpha subunit of the GM-CSF receptor in a series of patients with acute myeloid leukemia (AML).

The GM-CSF receptor belongs to the cytokine receptor superfamily. The high-affinity receptors of this class are lacking intrinsic tyrosine kinase domains. The GM-CSF receptor consists of alpha and beta subunits. The beta subunit is shared with the receptors of IL-3 and IL-5. In addition to the membrane bound forms the receptors have been found to possess soluble isoforms. Since retroviral infection of the human GM-CSF dependent cell line, TF-1, leads to factor independent growth by increased expression of the GM-CSF receptor alpha chain in a subgroup of infected clones, we were interested in studying the role of this chain in human AML. Further considering that a point mutation in the extracellular domain of the erythropoietin receptor, also a member of the cytokine receptor superfamily, resulted in constitutive activation of a murine cell line, we investigated the possibility that a point mutation of the GM-CSF receptor was responsible for autonomous growth of AML cells. We sequenced a segment of the receptor coding for the extracellular domain of the alpha subunit. cDNA was prepared from peripheral blood or bone marrow cells from 24 patients with AML, from four patients with MDS and from three human myeloid cell lines. The region of interest was amplified with two rounds of PCR reactions with nested primers, covering five overlapping fragments, and directly sequenced using a non-radioactive technique. No point mutations were found in the investigated samples. Thus, point mutations in this segment of the GM-CSF receptor gene do not seem to play an important role in the transformation process of human acute leukemia.

Base Sequence↗

PubMed2005

HPLC and chemometric assisted spectrophotometric methods for simultaneous determination of diprophylline, phenobarbitone and papaverine hydrochloride.

Three methods are developed for the simultaneous determination of diprophylline (DP), phenobarbitone (PH) and papaverine hydrochloride (PP). The chromatographic method depends on a high performance liquid chromatographic (HPLC) separation on a reversed-phase C18 column with a mobile phase consisting of 0.02 M potassium dihydrogen phosphate, pH 3.5--acetonitrile (55:45 v/v). Quantitation was achieved with UV detection at 210 nm based on peak area. The other two chemometric methods applied were principal component regression (PCR) and partial least squares (PLS-1). These approaches were successfully applied to quantify the three drugs in the mixture using the information included in the UV absorption spectra of appropriate solutions in the range 215-245 nm with the intervals Delta lambda = 0.2 nm. The calibration PCR and PLS-1 models were evaluated by internal validation (prediction of compounds in its own designed training set of calibration), by cross-validation (obtaining statistical parameters that show the efficiency for a calibration fit model) and by external validation over laboratory-prepared mixtures and pharmaceutical preparations. The PCR and PLS-1 methods require neither any separation step, nor any priori graphical treatment of the overlapping spectra of the three drugs in a mixture. The results of PCR and PLS-1 methods were compared with HPLC method obtained in pharmaceutical formulation and a good agreement was found.

Bronchodilator Agents↗

PubMed1991

Generation of a 1.5-kb cDNA fragment of the hepatitis C virus genome by overlap extension.

Hepatitis C virus (HCV) is a recently identified RNA virus responsible for most of non-A, non-B hepatitis. Genetic analysis of HCV sequences and their encoded proteins has been hampered by the difficulty in obtaining cDNA fragments of sufficient lengths: construction of cDNA library requires technical expertise while amplification by the polymerase chain reaction (PCR) usually yields fragments of less than 400 base pairs. In this report we have generated a 1.5-kb HCV cDNA fragment by overlap extension of smaller PCR fragments and by ligation through restriction sites. Sequencing of the cloned fragment confirmed the absence of significant sequence alteration produced by this procedure. Overlap extension may represent an easy method for generating relatively large HCV cDNA clones for the expression of HCV-encoded proteins.

Base Sequence↗

PubMed1998

Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis.

We developed a new approach to DNA sequence analysis that uses fluorogenic reporter molecules--molecular beacons--and demonstrated their ability to discriminate alleles in real-time PCR assays of genomic DNA. A set of overlapping molecular beacons was used to analyze an 81-bp region of the Mycobacterium tuberculosis rpoB gene for mutations that confer resistance to the antibiotic rifampin. In a blinded study of 52 rifampin-resistant and 23 rifampin-susceptible clinical isolates, this method correctly detected mutations in all of the resistant strains and in none of the susceptible strains. The assay was carried out entirely in sealed PCR tubes and was simple to perform and interpret. This approach can be used to analyze any DNA sequence of moderate length with single base pair accuracy.

Antibiotics, Antitubercular↗

PubMed2003

Mutation analysis of feline Niemann-Pick C1 disease.

Niemann-Pick C (NPC) disease is an autosomal recessive neurovisceral lysosomal storage disorder that results in defective intracellular transport of cholesterol. The major form of human NPC (NPC1) has been mapped to chromosome 18, the NPC1 gene (NPC1) has been sequenced and several mutations have been identified in NPC1 patients. A feline model of NPC has been characterized and is phenotypically, morphologically, and biochemically similar to human NPC1. Complementation studies using cultured fibroblasts from NPC affected cats and NPC1 affected humans support that the gene responsible for the NPC phenotype in this colony of cats is orthologous to human NPC1. Using human-based PCR primers, initial fragments of the feline NPC cDNA were amplified and sequenced. From these sequences, feline-specific PCR primers were generated and designed to amplify six overlapping bands that span the entire feline NPC1 open reading frame. A single base substitution (2864G-C) was identified in NPC1 affected cats. Obligate carriers are heterozygous at the same allele and a PCR-based assay was developed to identify the geneotype of all cats in the colony. The mutation results in an amino acid change from cysteine to serine (C955S). Several of the mutations identified in people occur in the same region. Marked similarity exists between the human and feline NPC1 cDNA sequences, and is greater than that between the human and murine NPC1 sequences. The human cDNA sequence predicts a 1278aa protein with a lysosomal targeting sequence, several trans-membrane domains and extensive homology with other known mediators of cholesterol homeostasis.

Amino Acid Sequence↗

PubMed1994

Differential expression of five somatostatin receptor subtypes, SSTR1-5, in the CNS and peripheral tissue.

Somatostatin regulates endocrine and exocrine secretion, acts as a neurotransmitter/neuro-modulator and possesses antiproliferative properties. These diverse physiological effects are mediated by G-protein coupled receptors of which at least five subtypes have been cloned (SSTR1-5). Here, we have investigated the tissue distribution pattern of mRNAs encoding the five SRIF receptor subtypes in the adult rat by RT-PCR analysis and in situ hybridization histochemistry. All five receptor subtypes were found to be expressed simultaneously in brain and pituitary by RT-PCR. Besides, the in situ hybridization results clearly show a distinct but overlapping expression pattern of SSTR1-5 mRNA in the central nervous system as was found by RT-PCR for the periphery. Such distinct SRIF receptor expression may contribute to the selective biological functions of the receptor subtypes.

Animals↗

PubMed1990

Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction.

Gene Splicing by Overlap Extension or "gene SOEing" is a PCR-based method of recombining DNA sequences without reliance on restriction sites and of directly generating mutated DNA fragments in vitro. By modifying the sequences incorporated into the 5'-ends of the primers, any pair of polymerase chain reaction products can be made to share a common sequence at one end. Under polymerase chain reaction conditions, the common sequence allows strands from two different fragments to hybridize to one another, forming an overlap. Extension of this overlap by DNA polymerase yields a recombinant molecule. This powerful and technically simple approach offers many advantages over conventional approaches for manipulating gene sequences.

Amino Acid Sequence↗

PubMed1999

CHOP/GADD153 and methionyl-tRNA synthetase (MetRS) genes overlap in a conserved region that controls mRNA stability.

The transcription factor CHOP is involved in the regulation of the cell division cycle and the control of programmed cell death in response to cellular stress. CHOP expression has been linked with several forms of cancer. A reciprocal translocation between the CHOP and TLS RNA-binding protein gene results in myxoid liposarcoma and amplifications of the CHOP gene are associated with solid tumors including several types of sarcomas. Here we report the mapping of the methionyl tRNA synthetase (MetRS) gene to the identical 12q13 locus where the CHOP gene had previously been mapped. PCR analysis demonstrates a tail-to-tail overlap of both genes over a 55-bp region. As a result the two mRNAs share a 3' UTR complementary sequence allowing an in vivo interaction between the two mRNAs. An AU-rich regulatory element (ARE) known to control mRNA stability resides in the overlapping sequence. To test for functional significance of the ARE a luciferase reporter plasmid containing the 3'UTR of CHOP was constructed. Transfection experiments in NIH-3T3 cells show that CHOP 3'UTR confers a significantly lower activity than a control reporter or a reporter in which the region overlapping the MetRS mRNA is deleted. The conservation of this overlapping of the CHOP and MetRS genes and the role of their complementary sequence in the control of mRNA stability suggest the existence of a functional link between the expression of these two genes.

3' Untranslated Regions↗

PubMed2005

Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production.

We describe a computer program, Assembly PCR Oligo Maker, created to automate the design of oligodeoxynucleotides for the PCR-based construction of long DNA molecules. This program is freely available at http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html and has been specifically designed to aid in the construction of DNA molecules that are to be used for the production of RNA molecules by in vitro synthesis with T7 RNA polymerase. The input for Assembly PCR Oligo Maker is either the desired DNA sequence to be made or an RNA sequence. If RNA is the input, the program first determines the DNA sequence necessary to produce the desired RNA molecule. The program then determines the sequences of all the oligodeoxynucleotides necessary for a two-step assembly PCR-based synthesis of the desired DNA molecule. The oligodeoxynucleotide sequences outputted are designed to have a uniform melt temperature and are checked for regions of overlap outside of the desired priming regions necessary for the PCR reaction. The validity of the program was verified experimentally by synthesizing a 191-nt long DNA molecule using the DNA sequences suggested by the program.

DNA↗

PubMed2001

Real-time TaqMan PCR as a specific and more sensitive alternative to the branched-chain DNA assay for quantitation of simian immunodeficiency virus RNA.

We developed a rapid and highly reproducible assay based on real-time PCR (TaqMan, Applied Biosystems, Foster City, CA) to quantitate simian immunodeficiency virus (SIV) RNA in plasma samples. This assay was compared with the current branched-chain DNA assay (Bayer, Emeryville, CA). Results obtained with the real-time TaqMan PCR assay were comparable to those obtained with the branched-chain DNA assay in overlapping ranges of sensitivities (r = 0.9429, p < 0.05). However, the real-time TaqMan PCR assay was capable of detecting as few as 50 copies of RNA/ml, whereas branched-chain DNA was only sensitive to 1,500 copies of RNA/ml. Therefore, several animals that tested negative by branched-chain DNA were positive by realtime TaqMan PCR. Two false positive tests were also recorded for the branched-chain DNA test. False negative and positive tests were confirmed by cell culture isolation and conventional nested RT-PCR. The SIV TaqMan assay detected a wide range of wild-type, cloned, and recombinant SIV strains with similar amplification efficiency, including SIVmac251, SIVmac239, SIVmac239 containing the 184V mutation in RT, SIV1A11, SIVmac239 delta3, SIVmac-M4, and chimeras (SHIVs) containing specific HIV-1 genes, such as reverse transcriptase (RT-SHIV) or Env (SHIV-E). In conclusion, the high sensitivity, increased specificity, wide dynamic range, simplicity, and reproducibility of the real-time SIV RNA quantitation allow the screening of large numbers of samples and make this method especially suitable for measuring both viral DNA and RNA levels during vaccine and therapy studies.

Animals↗