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Results for “Overlapping PCR”

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At least 307 records · Page 17Linked to original sources

PubMed2000

Characterization of 11 new mutations in COL3A1 of individuals with Ehlers-Danlos syndrome type IV: preliminary comparison of RNase cleavage, EMC and DHPLC assays.

We report on 12 patients with EDS IV in whom clinical diagnosis was confirmed by biochemical analysis of collagen type III, and further proven by mutation analysis of the COL3A1 gene. Four overlapping RT-PCR products covering the coding sequence for the triple-helical domain of type III collagen were analyzed by direct sequencing. So far, we have identified, 4 base changes at donor splice junctions, and 1 base change at an acceptor splice site, which all affect mRNA splicing; 1 genomic deletion, which removes exon 45; and 6 nucleotide changes, which cause substitutions of glycine residues within the triple helix. Eleven of the 12 identified mutations are newly recognized. Furthermore, we report a preliminary comparison of RNase cleavage, EMC and DHPLC assays in mutation detection in the COL3A1 gene.

Adolescent↗

PubMed2003

Clinical and molecular study in congenital muscular dystrophy with partial laminin alpha 2 (LAMA2) deficiency.

Complete laminin alpha2 (LAMA2) deficiency causes approximately half of congenital muscular dystrophy (CMD) cases. Many loss-of-function mutations have been reported in these severe, neonatal-onset patients, but only single missense mutations have been found in milder CMD with partial laminin alpha2 deficiency. Here, we studied nine patients diagnosed with CMD who showed abnormal white-matter signal at brain MRI and partial deficiency of laminin alpha2 on immunofluorescence of muscle biopsy. We screened the entire 9.5 kb laminin alpha2 mRNA from patient muscle biopsy by direct capillary automated sequencing, single strand conformational polymorphism (SSCP), or denaturing high performance liquid chromatography (DHPLC) of overlapping RT-PCR products followed by direct sequencing of heteroduplexes. We identified laminin alpha2 sequence changes in six of nine CMD patients. Each of the gene changes identified, except one, was novel, including three missense changes and two splice-site mutations. The finding of partial laminin alpha2 deficiency by immunostaining is not specific for laminin alpha2 gene mutation carriers, with only two patients (22%) showing clear causative mutations, and an additional three patients (33%) showing possible mutations. The clinical presentation and disease progression was homogeneous in the laminin alpha2-mutation positive and negative CMD patients.

Clubfoot↗

PubMed1995

Efficient strategy for the detection of mutations in acrogeric Ehlers-Danlos syndrome type IV.

cDNA encoding the C-terminal domain (nt2283 to 3714) of type III collagen was amplified by PCR in five overlapping products and examined for mutations in 13 patients with Ehlers-Danlos syndrome type IV (EDS IV) with uncharacterised lesions and in five control patients with known single base mutations. Six different point mutations were detected by denaturing gradient gel electrophoresis (DGGE), in addition to those in the known controls. Four of seven patients who had no point mutations in this region were shown to lack complete exons from their amplified cDNA. Mutations were detected in all patients with typical or acrogeric EDS IV, but only in one of four individuals with the atypical form of the disease.

Base Sequence↗

PubMed2006

Molecular cloning and characterization of SRG-L, a novel mouse gene developmentally expressed in spermatogenic cells.

Full-length cDNA of a novel mouse gene upregulated in late stages of spermatogenic cells was cloned from mouse testis using overlapping RT-PCR and RACE. The mRNA of the gene was expressed mainly in diplotene/pachytene spermatocytes, round and elongating spermatids. We named this gene as SRG-L (Spermatogenesis Related Gene expressed in late stages of spermatogenic cells, GenBank Accession No. AY352586). The tissue-specific analysis showed a higher expression level in testis and spleen. The gene is mapped on chromosome 8q33.1 and contains 18 exons. The full-length of cDNA is 2,843 bp with an open reading frame (ORF) of 2,625 bp that encodes a 104 kDa protein (874 amino acids) with a putative transmembrane region. The bioinformatics analysis revealed that the SRG-L has two conserved regions, transglutaminase-like homologues domain and D-serine dehydratase domain, rich phosphorylation sites and methylation sites. The SRG-L protein was detected in diplotene/pachytene spermatocytes and spermatids by immunohistochemical staining and Western blot. The results suggest that SRG-L may play definite roles regulating differentiation of germ cells during spermatogenesis, particularly during meiosis and spermiogenesis.

Amino Acid Sequence↗

PubMed1995

cDNA sequence analysis of the human brain insulin receptor.

Brain tissue mRNA was amplified using polymerase chain reaction (PCR) with eight overlapping sets of primers that span the cDNA coding sequence for the human placental insulin receptor. Only the A isoform (lacking exon 11) of the receptor was detected. No difference was found in the predicted amino acid sequence of brain derived insulin receptor cDNA compared with the receptor from human placenta. A silent polymorphism was detected at nucleotide position 1698 (amino acid 523), confirming that mRNA corresponding to both alleles of the human brain receptor was sequenced. Our findings indicate that the unique glycosylation properties of brain insulin receptors do not stem from differences in primary structure, but rather are due to tissue-specific differences in post-translational processing.

Amino Acid Sequence↗

PubMed1997

Mouse TCOF1 is expressed widely, has motifs conserved in nucleolar phosphoproteins, and maps to chromosome 18.

Mutations in the human TCOF1 gene have been identified in patients with Treacher Collins Syndrome (Mandibulofacial Dysostosis), an autosomal dominant condition affecting the craniofacial region. We report the isolation of the entire mouse Tcof1 coding sequence (3960 bp) by performing a computer-based search for mouse cDNA clones homologous to TCOF1 and generating overlapping RT-PCR products from mouse RNA. Tcof1 is a 1320 amino acid protein of 135 kd with 61.4% identity to TCOF1 and displays repeating motifs enriched for serine- and acidic amino acid-rich regions with potential phosphorylation sites and putative nuclear localization signals. Tcof1 maps to the mouse chromosome 18 region syntenic with human chromosome 5q32-->q33 which contains the TCOF1 locus. Northern blot hybridization indicates Tcof1 expression is ubiquitous in adult tissues and in the embryonic stage, is elevated at 11 dpc when the branchial arches and facial swellings are present in mouse. Our results are consistent with TCOF1 mutations leading to the Treacher Collins syndrome phenotype.

Amino Acid Sequence↗

PubMed2001

Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2.

Amyotrophic lateral sclerosis is a progressive neurodegenerative disease that manifests as selective upper and lower motor neuron degeneration. The autosomal recessive form of juvenile amyotrophic lateral sclerosis (ALS2) has previously been mapped to the 1.7-cM interval flanked by D2S116 and D2S2237 on human chromosome 2q33-q34. We identified three novel full-length transcripts encoded by three distinct genes (HGMW-approved symbols ALS2CR1, ALS2CR2, and ALS2CR3) within the ALS2 critical region. The intron-exon organizations of these genes as well as those of CFLAR, CASP10, and CASP8, which were previously mapped to this region, were defined. These genes were evaluated for mutations in ALS2 patients, and no disease-associated sequence alterations in either exons or intron-exon boundaries were observed. Sequence analysis of overlapping RT-PCR products covering the whole coding sequence for each transcript revealed no aberrant mRNA sequences. These data strongly indicate that ALS2CR1, ALS2CR2, ALS2CR3, CFLAR, CASP10, and CASP8 are not causative genes for ALS2.

Adaptor Proteins, Signal Transducing↗

PubMed1999

Molecular cloning and characterization of MSRV-related sequences associated with retrovirus-like particles.

New sequences have been obtained by successive overlapping RT-PCR extensions from the pol region of a retroviral RNA (multiple sclerosis-associated retroviral element, MSRV) amplified in retrovirus-like particles from patients with multiple sclerosis. gag and pol sequences are related to type C oncoviruses, whereas the env sequence is closer to type D. A tryptophan-like (W) tRNA primer-binding site was identified downstream of the RU5 region in the 5'LTR, and the U3R region cloned in the 3'LTR exhibited potent promoter activity. MSRV clones define a novel family of endogenous elements, HERV-W. From our data, HERV-W RNAs are copackaged in extracellular particles which might be produced by replication-competent or transcomplemented HERV-W copies or by an exogenous member of the HERV-W family.

Amino Acid Sequence↗

PubMed2003

Transformation of Azospirillum brasilense Cd with an ACC deaminase gene from enterobacter cloacae UW4 fused to the Tet r gene promoter improves its fitness and plant growth promoting ability.

It has been reported that PGPB, containing ACC deaminase, can cleave the plant ethylene precursor ACC and thereby lower ethylene concentration in a developing or stressed plant, protecting it against the deleterious effects of stress ethylene and facilitating the formation of longer roots. In a previous work we have demonstrated expression of the ACC deaminase gene ( acdS) from Enterobacter cloacae UW4 under the control of the lac promoter in Azospirillum brasilense Cd. With the inference that a construct including the ACC deaminase gene under the control of a constitutive promoter weaker than the lac promoter might impose less metabolic load on Azospirillum and improve its fitness, it was decided to clone acdS under the control of a tetracycline resistance gene promoter. The ACC deaminase structural gene was fused to the Tet(r) gene promoter by overlap extension using PCR, cloned in pRK415, and transferred into A. brasilense Cd. The resulting transformants showed lower ACC deaminase activity than those with the lac promoter controlled acdS gene. However, acdS under the control of the Tet(r) gene promoter imposed lesser metabolic load on Azospirillum brasilense Cd. The result was significantly increased IAA synthesis and greater bacterial growth rate, as well as increased ability to survive on the surface of tomato leaves and to promote the growth of tomato seedlings.

Azospirillum brasilense↗

PubMed1997

Alu-splice PCR: a simple method to isolate exon-containing fragments from cloned human genomic DNA.

We have developed a simple, straightforward procedure to isolate exons from cloned human genomic DNA. The method is PCR based and relies upon the conservation of splice-site sequences and the frequency of Alu repeat elements in the genome to capture coding sequences. We designed two different sets of primers: a primer from each end of the Alu element and primers with the 5' or 3' splice-site consensus sequences. Putative exons were amplified by PCR using YAC DNA as starting material. We applied Alu-splice PCR to two overlapping YACs, 72H9 and 860G11, from human chromosome 21. Sequence and northern analysis of 37 initial clones resulted in the identification of five novel exons.

Amino Acid Sequence↗

PubMed1998

Comparative sequence analysis of open reading frames 2 to 7 of the modified live vaccine virus and other North American isolates of the porcine reproductive and respiratory syndrome virus.

To elucidate changes associated with the attenuated virulence in a modified live porcine reproductive and respiratory syndrome (PRRS) vaccine (Boehringer Ingelheim Animal Health, St. Joseph, MO), derived from an American prototype ATCC virus VR-2332, nucleotide sequence of 3' genome covering open reading frames (ORFs) 2 to 7 coding regions from the vaccine virus was determined by RT-PCR with two overlapping fragments. Comparisons showed 98 base changes (94 substitutions, 3 deletions, and 1 addition) out of 3318 nucleotides between the vaccine virus and its parental virus. There were 15, 26, 17, 29, 9, and 6 base substitutions in ORFs 2, 3, 4, 5, 6, and 7, respectively, resulting in 5, 13, 8, 13, 2, and 3 amino acid (a.a.) substitutions in their deduced proteins, respectively. Most of these a.a. substitutions were also present in 17 known virulent/wild type PRRS virus isolates from North America. However, there were 1, 4, 1, and 1 unique a.a. substitutions in the vaccine virus ORFs 2, 3, 4, and 5 deduced proteins, respectively. These unique amino substitutions may be responsible for the attenuated virulence in the vaccine virus.

Amino Acid Sequence↗

PubMed1998

Synthesis of biologically active cDNA clones of cymbidium mosaic potexvirus using a population cloning strategy.

Biologically active cDNA clones of cymbidium mosaic potexvirus (CymMV) were synthesized using a population cloning strategy. Three populations of overlapping RT-PCR products encompassing the entire viral RNA of CymMV were ligated into pBluescriptKS+ with T7 RNA polymerase promoter fused to the 5' extreme of the viral cDNA. Capped-RNA in vitro transcripts were infectious. This is the first report of successful synthesis of biologically active CymMV clones. Unlike the conventional methods, population cloning maximizes the probability of obtaining biologically active cDNA clones.

DNA, Complementary↗

PubMed1995

Genomic and cDNA cloning of a novel mouse lipoxygenase gene.

A novel 12- and 15-lipoxygenase related gene was isolated from a mouse strain 129 genomic phage library in a screen with a human 15-lipoxygenase cDNA probe. The complete genomic sequence revealed 14 exons and 13 introns covering 7.3 kb of DNA. The splice junctions were verified from the cDNA sequences of a series of overlapping RT-PCR products. This novel mouse lipoxygenase gene was found to contain an open reading frame encoding 662 amino acids. The cDNA sequence is 68% identical to the mouse leukocyte type 12-lipoxygenase and 65% identical to the mouse platelet type 12-lipoxygenase cDNA. Nucleotide identities to the human 15-lipoxygenase cDNA and the human platelet type 12-lipoxygenase cDNA are 70% and 67%, respectively. The deduced amino acid sequence is 60% identical to the mouse platelet and leukocyte type 12-lipoxygenase sequences and the human 15- and 12-lipoxygenase sequences. This novel mouse lipoxygenase gene was found to be transcribed predominantly in epidermal tissue and named Aloxe.

Amino Acid Sequence↗

PubMed1993

Use of recombinant gp135 to study epitope-specific antibody responses to maedi visna virus.

The envelope glycoprotein gp135 of the ovine lentivirus maedi visna virus (MVV) is the main target for neutralising antibody in vivo, however little is known about the specific regions of gp135 which elicit this neutralising response. We have used the polymerase chain reaction (PCR) to generate overlapping fragments of the gp135 gene which have been expressed as fusion proteins in the yeast Ty-VLP system. These fusion proteins have been used to analyse the antibody response to gp135 in MVV infected sheep and we are able to identify at least three distinct regions of gp135 to which antibodies are directed. The approach described in this paper provides a rapid and simple method of generating overlapping fusion proteins with which to carry out epitope mapping studies.

Animals↗

PubMed1993

Primary structure of the canine CD4 antigen.

After PCR amplification two overlapping cDNA clones encoding the dog homologue of the human CD4 glycoprotein were identified. This internal fragment of the mature protein including the complete extracellular domains, consists of 1297 bp with a deduced amino acid sequence of 432 residues. The dog CD4 molecule differs from the corresponding protein of other species including human in the second domain. We found nine extra residues in the beginning of that domain, a cysteine at position 138, usually involved in a disulfide bridge, is substituted by tryptophan, and three new glycosylation sites are present.

Amino Acid Sequence↗

PubMed1995

Recombinant histatins: functional domain duplication enhances candidacidal activity.

Histatin 3 (Hst3) is a 32-amino-acid (aa) His-rich protein with antimicrobial activity found in human salivary secretions. To explore further the structure/function relationship of Hst, we utilized a bacterial system for the efficient production of recombinant Hst3 (re-Hst3) and Hst variants. Previously, we demonstrated that the middle portion of Hst3 (aa 13-24) contains the functional domain responsible for killing Candida albicans. Using PCR and splice overlap extension, a Hst variant (re-Hst3rep) was made in which the functional domain was repeated in tandem. Using the pRSET bacterial expression system, re-Hst3 and the variant re-Hst3rep were produced as chimeric fusions and were isolated from bacterial sonicates by affinity chromatography. Affinity purified fusion proteins were digested with CNBr and re-Hst were separated from their fusion partners by reverse-phase high-performance liquid chromatography. The activity of re-Hst3 and re-Hst3rep was compared to that of native Hst3 from human salivary secretions in the C. albicans killing assay. The LD50 values for candidacidal activity of native Hst3, re-Hst3 and re-Hst3rep were 7.2, 6.8 and 4.1 nmol/ml, respectively. At lower concentrations re-Hst3rep was five times more active than native Hst3 or re-Hst3 and at even lower concentrations re-Hst3rep exhibited significant candidacidal activity while native Hst3 and re-Hst3 were inactive. These results demonstrate an expression system for production of biologically active functional Hst and Hst variants and shows that repetition of the functional domain of Hst3 enhances candidacidal activity.

Amino Acid Sequence↗

PubMed2006

Transcriptional regulation of the rainbow trout CYP19a gene by FTZ-F1 homologue.

In rainbow trout, there are at least two CYP19 genes (CYP19a and CYP19b). They encode distinct P450arom isozymes that are differentially expressed in the ovary and brain. To understand the transcriptional regulation of the rainbow trout CYP19a (rtCYP19a) gene in the ovary, we isolated its 5'-flanking region. The presence of potential FTZ-F1-binding sites prompted us to isolate the cDNA encoding a rainbow trout FTZ-F1 homologue (rtFTZ-F1) and analyze its effect on the rtCYP19a gene transcriptional activity. RT-PCR analysis showed overlapping expression of the rtCYP19a and rtFTZ-F1 genes in the ovary. Transient transfection studies in Chinese hamster ovary-derived CHO-K1 cells revealed that the region from -247 to -105, which contains three potential FTZ-F1-binding sites, was required for rtFTZ-F1-mediated transcriptional activation of the rtCYP19a gene. Among the three potential binding sites, the two from -150 to -142 and from -118 to -110 showed strong affinities for rtFTZ-F1 in gel shift assays, and base substitutions in either site almost abolished the transcriptional activation by rtFTZ-F1. Taken together, these results demonstrate that rtFTZ-F1 plays an important role in the transcriptional regulation of the rtCYP19a gene in the ovary.

Amino Acid Sequence↗

PubMed2006

Quadruple antigenic epitope peptide producing immune protection against classical swine fever virus.

Research on epitope-based vaccines is a current focus in the development of new vaccines against classical swine fever virus (CSFV). The present study aimed to engineer a quadruple antigenic epitope peptide of the CSFV immunogen E2 glycoprotein by splice overlap extension (SOE) PCR, expressed in E. coli fused with glutathione S-transferase (GST), and named rGST-4E. Enzyme-linked immunosorbent assay (ELISA) and Western blot analysis showed that purified rGST-4E had an excellent immunoreactivity with swine anti-CSFV serum and rabbit anti-E2 serum. Animal vaccination trials showed that the rGST-4E was more immunogenic than mono-epitope peptide and was able to produce effective immune protection in rabbits against challenge with hog cholera lapinized virus, and in pigs against challenge with virulent CSFV. These data show that the recombinant repeated epitope peptide could be considered a potential epitope-based vaccine for prevention of the disease.

Animals↗