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Results for “Overlapping PCR”

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At least 487 records · Page 27Linked to original sources

PubMed1997

Identification of a mutation in the MP19 gene, Lim2, in the cataractous mouse mutant To3.

PURPOSE: Lim2, the gene encoding the second most abundant lens specific integral membrane protein, MP19, has recently been proposed as an ideal candidate gene for the cataractous mouse mutant, To3. The aim of this study was to screen the Lim2 gene in the To3 mutant for a genetic lesion that was correlated and consistent with the mutant phenotype. METHODS: Genomic DNA was isolated from both normal mouse parental strains as well as the heterozygous and homozygous To3 cataract mutant. PCR was used to generate overlapping fragments of the entire Lim2 gene from these DNAs. The coding regions, including splice junctions and the translational termination site, of these fragments were then sequenced. RESULTS: A single G -> T transversion was identified within the first coding exon of the Lim2 gene in the To3 mutant DNA. This DNA change results in the nonconservative substitution of a valine for the normally encoded glycine at amino acid 15 of the MP19 polypeptide. CONCLUSIONS: The identified genetic lesion in the Lim2 gene of the cataractous mouse mutant, To3, confirms Lim2 as an ideal candidate gene. Future transgenic experiments should provide proof or disproof of a causative relationship between the identified mutation and the cataractous phenotype. These studies indicate that MP19 may play an important role in both normal lens development and cataractogenesis, and warrants more intense investigation of its role within the ocular lens.

Amino Acid Sequence↗

PubMed1998

[Fluorescence-based semi-automated gene scan with microsatellite markers by multiplex PCR techniques].

OBJECTIVE: To develop a high output and low cost multiplex PCR approach to facilitating large scale gene scan and gene typing with microsatellite markers. METHODS: 5-15 pairs of primers of microsatellite loci were added in one single tube with 5ul reaction volume, containing 10 mmol/L Tris-HCl (pH8.3), 50 mmol/L KCl,0. 1mg/ml gelatin, 3.0 mmol/L MgCl2, 200micromol/L dNTPs (each), 0.25U Taq DNA polymerase, Taq Start antibody and DNA templates. PCR thermocycles were carried out on Perkin Elmer Gene Amp PCR System 9600 with touch-down algorithm (the annealing temperature was decreased by 0.5 C in each cycle) to meet the different demands of different primers. RESULTS: Up to 10-15 loci were labeled by different fluorescents or by the same fluorescent, but their PCR amplification fragments did not overlap in size. Almost all target microsatellite loci were successfully co-amplified in a 5 microliter reaction volume,electrophoresized and analyzed in a single gel lane with Perkin Elmer ABI 373A DNA sequencer, and 9 microsatellite loci were well genotyped. CONCLUSION: This high output and low cost genotyping protocol is applicable to gene mapping, human evolution and forensic analysis.

Genotype↗

PubMed1996

Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels.

Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-3 exons) of any two consecutive target segments. In such cases, amplification from the mutant region of the disease-causing allele fails because binding sites for the PCR primers are missing, but amplification from the normal allele proceeds, yielding only the normal product. To alleviate this problem, we have developed a protocol to reverse transcribe and amplify the entire protein-coding sequence of NF1 as a single PCR product, starting with total RNA from lymphoblast cell lines or from whole blood. The 8.7-kb RT-PCR product was prepared from nine NF1 patients with known deletions or insertions, ranging in size from a 30-bp deletion within 1 exon to a 2.4-kb deletion that removes 12 exons. Agarose gel analysis of the initial products detected deletions as small as 341 bp. Restriction endonuclease digestion with Asel and Fspl, followed by agarose gel electrophoresis, revealed the predicted abnormal bands in all nine patients. All mutant bands were identified readily by observers with no knowledge of the patients' mutations. This simple assay should detect a great variety of insertion/deletion mutations in the NF1mRNA internal to the primer binding sites, including all possible single and multiple exon dropouts and approximately 30% of all previously reported NF1 mutations.

Base Sequence↗

PubMed2005

No mutations in TPIT, a corticotroph-specific gene, in human tumoral pituitary ACTH-secreting cells.

BACKGROUND: TPIT is a recently identified transcription factor specific to proopiomelanocortin (POMC)-expressing cells within the pituitary and plays a pivotal role in the embryonal development of POMC lineage. As with other transcription factors, TPIT could theoretically also be involved in corticotroph adenomatous transformation and ACTH hypersecretion and published data indicate that TPIT is present in normal and adenomatous human corticotrophs. OBJECTIVE: The aim of the present study was to corroborate this finding and to seek evidence for mutations in the TPIT coding sequence in human tumoral corticotrophs. DESIGN AND METHODS: Eight human ACTH-secreting pituitary adenomas were collected during surgery, mRNA extracted from primary cultures and reverse transcribed. PCR was performed using 8 different sets of overlapping intron-spanning primers comprising the entire coding sequence of the gene and PCR products analyzed by sequencing. RESULTS: TPIT mRNA was detected in all 8 ACTH-secreting pituitary adenomas without apparent mRNA variants. The entire coding sequence was accounted for, as attested by amplification with all sets of primers. Lastly, sequencing did not reveal differences in the nucleotide arrangement compared with the published sequence. CONCLUSIONS: Aberrant TPIT is unlikely to play a role in corticotroph tumoral trasformation, ie, Cushing's disease, as the entire coding sequence is expressed without any mutation by human pituitary ACTH-secreting adenomas. Conversely, the significance of this transcription factor in tumoral ACTH hypersecretion remains to be clarified.

Adrenocorticotropic Hormone↗

PubMed1994

Identification of human chromosome region 3p14.2-21.3-specific YAC clones using Alu-PCR products from a radiation hybrid.

Deletion of DNA sequences from at least three different regions on the short arm of human chromosome 3 (3p13-14, 3p21 and 3p25) are frequently observed during the development of many solid tumors, including lung cancers and renal cell carcinomas. In order to physically characterize the 3p21 region, we previously identified a radiation fusion hybrid that contained about 20 megabases of DNA from chromosome region 3p14.2-p21.3. In this study total Alu-PCR products from this hybrid were used as a probe to isolate 86 yeast artificial chromosomes (YAC) clones from a 620-kb average insert YAC library (ICRF). Sixty-nine Alu-PCR markers, generated from the YACs, and seven PCR primers were used to screen for overlaps between individual clones. Seven contigs were identified encompassing 32 YAC clones. Based on previous information about localization of the PCR primers, the three largest contigs could be assigned to smaller subregions between 3p14.2 and 3p21.3. By this work a large proportion of the 3p14.2-21.3 region is covered with large-insert YAC clones.

Base Sequence↗

PubMed1995

Amplification of the complete polyomavirus JC genome from brain, cerebrospinal fluid and urine using pre-PCR restriction enzyme digestion.

A method is described for amplification of the complete genome of the human polyomavirus JC (JCV) from progressive multifocal leukuencephalopathy (PML) brain, cerebrospinal fluid (CSF) of PML patients, and from the urine of controls without neurological disease. Efficient amplification with the 'long PCR' method is achieved with primers overlapping the single BamHI or EcoRI site following digestion of the DNA sample with the restriction enzyme BamHI or EcoRI, respectively. Cutting of the supercoiled JCV genome allows full separation of the strands during the denaturation step, and permits primer annealing to compete successfully with reassociation of the genomic DNA. With this method a single PCR amplification allows restriction fragment length polymorphism (RFLP) analysis and direct cycle sequencing of any part of the viral genome. RFLP analysis of JCV amplified from CSF has identified a new mutant sequence. Sequencing of clinical samples is useful for typing of JC virus isolates as Type 1 or Type 2 and for characterization of the JCV regulatory region as archetypal or rearranged.

Base Sequence↗

PubMed2006

Partially degraded RNA from bladder washing is a suitable sample for studying gene expression profiles in bladder cancer.

OBJECTIVES: To determine the impact of different levels of RNA degradation on gene expression measurements and to ascertain if the gene expression profile obtained from bladder washing (BW) correlates to that obtained from the related bladder tumour (BT). METHODS: BT and BW RNAs from the same patient were heat shocked to obtain three RNA degradation states, which were compared with intact RNAs from healthy bladders by using complementary DNA (cDNA) microarrays. All samples were amplified by means of a T3N9-based transcription method. In addition, four of the differentially expressed genes in microarrays related to bladder cancer (KRT20, IGF2, GSN, and CCL2) were analyzed in 36 tumoural and 14 control BW samples by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). RESULTS: A high percentage of overlapping differentially expressed genes were detected between BT arrays (85-91%) and between BW arrays (78-93%). Furthermore, the similarity between BW and BT arrays was relatively high and independent of the RNA degradation state (52-60%). Finally, expression differences for the four selected genes were confirmed in the vast majority of extended BW samples tested by qRT-PCR. CONCLUSIONS: Our results showed that partially degraded RNA samples analyzed by cDNA microarrays yielded gene expression profiles comparable to those obtained using intact RNA. Moreover, BW RNA exhibited gene expression patterns similar to those identified in the BT, indicating that BW is an appropriate sample for studying gene expression profiles of BT using cDNA microarrays. In addition, qRT-PCR results further support the suitability of BW for gene expression profiling and its potential use for routine diagnostics.

Chemokine CCL2↗

PubMed2001

Polyphasic investigation of the diversity within Lactobacillus plantarum related strains revealed two L. plantarum subgroups.

The diversity of 140 strains related to Lactobacillus plantarum was investigated using a polyphasic approach combining two molecular techniques: randomly amplified polymorphic DNA fingerprinting (RAPD) and Southern hybridisation with a pyr probe on BglI digests of chromosomal DNA, as well as phenotypic characterization. The RAPD technique allowed us to classify a subset of 60 representative strains into four groups. One group belonged to Lactobacillus paraplantarum, the second to Lactobacillus pentosus and the two remaining groups to L. plantarum (G(L)p1 and G(L)p2). The Southern hybridisation technique (F. Bringel, M.-C. Curk and J.-C. Hubert, Int. J. Syst. Bacteriol. 46: 588-594, 1996) revealed nine groups of profiles (I to IX). Results indicated an excellent convergence between RAPD and hybridisation classifications for more than 93% (56/60) of the strains studied. When we compared the fermentation patterns of the L. plantarum strains, three differences were found. Melezitose fermentation was not fermented by the G(L)p2 RAPD group, unlike the G(L)p1 RAPD group which included L. plantarum type strain NCIMB11974T. Second, alpha-methyl-D-mannoside was fermented by a majority of the strains of the G(L)p1 RAPD group but by none of the strains in the G(L)p2 RAPD group. Third, dulcitol was catabolized by nearly half of the strains of the G(L)p2 RAPD group but by none of the strains in the G(L)p1 RAPD group. Molecular diversity within L. plantarum was confirmed using Southern profiles, PCR amplification and subsequent sequencing of these PCR products. A 773 bp sequence overlapping the pyrDF genes showed high homology: at least 97% identical in L. plantarum strains (V to IX) and 99.9% identical in hybridisation groups VII and VIII. The same G-T transversion which destroyed the pyrF BglI site was found in 11 strains (hybridisation groups VI, VII and VIII). DNA rearrangements were identified downstream from the pyr genes, by PCR amplification and Southern hybridisation profile analysis in three strains of hybridisation groups VIII and IX, two of which also harboured the G-T transversion.

Blotting, Southern↗

PubMed1995

[Abnormality of PMP-22 gene in Japanese patients with Charcot-Marie-Tooth disease--comparison between Southern blot and polymerase chain reaction analysis in the detection of PMP-22 gene duplication].

We investigated the duplication of the PMP-22 gene in 23 Japanese patients with Charcot-Marie-Tooth disease (CMT) by Southern blot and PCR analysis. To detect duplication of the PMP-22 gene region, PMP-22 cDNA and a polymorphic marker, VAW409R3, located in the region flanking the PMP-22 gene, were used as probes for Southern blot analysis. A marker, 6G1, also located in the PMP-22 flanking region, was amplified using the quantitative PCR method. The signal intensity of the 2.8-kb and 2.7-kb bands of MspI digests probed with VAW409R3 was different in patients with duplication. The ratio of these two bands, measured by densitometry, ranged from 1.75 to 2.13 in the patients with duplication and from 1.01 to 1.15 in those without duplication and in normal controls. The signal ratio of PMP-22 to the reference marker SF85 of BamHI digests ranged from 1.15 to 1.33 in the patients with duplication and from 0.96 to 1.04 in those without duplication, when compared with normal controls assigned a value of 1.0. The ranges of the intensity in these two groups were narrow, but did not overlap. The signal ratio of the PCR products of 6G1 to reference marker D1S80 on quantitative PCR analysis was also measured. The ratio ranged between 1.67 and 2.23 with duplication and between 1.29 and 1.74 without duplication according to the results of Southern blot analysis. However, some patients exhibited overlapping signal intensity in the duplication and non-duplication ranges. Thus, these three methods each has its own advantages and disadvantages in regard to detecting duplication.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

PubMed2006

Immunohistochemistry of primary malignant neuroepithelial tumors of the kidney: a potential source of confusion? A study of 30 cases from the National Wilms Tumor Study Pathology Center.

Ewing sarcoma/peripheral primitive neuroectodermal tumor (pPNET) is a rare primary tumor of the kidney with morphologic features similar to those of other primitive tumors. Previous studies have shown that these tumors frequently stain positively with immunostains against CD99 and FLI-1 and negatively with stains against WT-1, suggesting that these markers may be used for the distinction between Wilms tumor and pPNET. We present 30 cases of primary malignant neuroepithelial tumor with immunohistochemical profiles and reverse transcriptase polymerase chain reaction (RT-PCR) analysis and show that immunophenotypic overlap exists between Wilms tumor and pPNET. A subset of 30 neuroepithelial tumors from the National Wilms Tumor Study originally categorized as putative pPNETs of the kidney was stained with FLI-1, WT-1, and thyroid transcription factor-1. Bicolor fluorescence in situ hybridization studies were performed on 19 of the cases. Other data on these tumors were available from a previous study (Am J Surg Pathol 2001;25:133). Of 7 primary tumors that had the EWS/FLI-1 fusion transcript by RT-PCR, 6 exhibited strong immunopositivity for FLI-1. Nine that were negative by RT-PCR stained positively with the FLI-1 stain. Five fusion-negative cases stained with both FLI-1 and WT-1. Three fusion-negative cases were negative for FLI-1 but positive for WT-1. Five fusion-negative cases were negative for both FLI-1 and WT-1. Of the 30 cases, 29 were positive for CD99. Seven cases that were negative for the EWS-FLI-1 fusion by RT-PCR were positive by fluorescence in situ hybridization. All cases were negative for thyroid transcription factor-1. Reliance upon immunohistochemistry as the sole means of ancillary diagnosis in renal pPNET can lead to confusing results. We recommend molecular fusion studies for clarification of primitive renal tumors with unexpected immunophenotypic results.

Adult↗

PubMed2003

Characterization of the CYP4A11 gene, a second CYP4A gene in humans.

Comparison between the cDNA sequence of CYP4A11 and that deduced from a published genomic clone suggested the presence of an additional CYP4A gene in humans, CYP4A22. PCR amplification of genomic DNA yielded overlapping clones covering 13kb of genomic DNA and extending from 1003bp upstream from CYP4A11 translation initiation to 135bp upstream of the mRNA polyadenylation signal. Sequence and Southern blot analysis showed the presence in humans of two highly homologous CYP4A genes, CYP4A11 and CYP4A22. These two genes share 96% sequence identity and have similar intron/exon sizes and distribution. Short nucleotide insertions (< or =10bp) in introns 1, 3, 9, and 11, and deletions (< or =18bp) in introns 4, 6, and 11 differentiate the two genes. RT-PCR amplification of human kidney RNA followed by restriction fragment analysis showed that CYP4A11 is the predominant isoform expressed in kidney.

Base Sequence↗

PubMed1998

Non-stoichiometric reduced complexity probes for cDNA arrays.

A method is presented in which the reduced complexity and non-stoichiometric amplification intrinsic to RNA arbitrarily primed PCR fingerprinting (RAP-PCR) is used to advantage to generate probes for differential screening of cDNA arrays. RAP-PCR fingerprints were converted to probes for human cDNA clones arrayed as Escherichia coli colonies on nylon membranes. Each array contained 18 432 cDNA clones from the IMAGE consortium. Hybridization to approximately 1000 cDNA clones was detected using each RAP-PCR probe. Different RAP-PCR fingerprints gave hybridization patterns having very little overlap (<3%) with each other or with hybridization patterns from total cDNA probes. Consequently, repeated application of RAP-PCR probes allows a greater fraction of the message population to be screened on this type of array than can be achieved with a radiolabeled total cDNA probe. This method was applied to RNA from HaCaT keratinocytes treated with epidermal growth factor. Two RAP-PCR probes detected hybridization to 2000 clones, from which 22 candidate differentially expressed genes were observed. Differential expression was tested for 15 of these clones using RT-PCR and 13 were confirmed. The use of this cDNA array to analyze RAP-PCR fingerprints allowed for an increase in detection of 10-20-fold over the conventional denaturing polyacrylamide gel approach to RAP-PCR or differential display. Throughput is vastly improved by the reduction in cloning and sequencing afforded by the use of arrays. Also, repeated cloning and sequencing of the same gene or of genes already known to be regulated in the system of interest is minimized. The procedure we describe uses inexpensive arrays of plasmid clones spotted as E.coli colonies to detect differential expression, but these reduced complexity probes should also prove useful on arrays of PCR-amplified fragments and on oligonucleotide chips. Genesobserved in this manuscript: H11520, U35048, R48633, H28735, M13918, H12999, H05639, X79781, M31627, H23972, AB000712, R75916, U66894, AF067817.

DNA, Complementary↗

PubMed1993

Efficiency of various strategies and materials to generate new markers: saturating the region 5q11.2-q13.3 with 30 new randomly distributed clones.

Several different strategies and materials were used for saturating the region 5q11.2-q13.3 with new, randomly distributed markers: isolation of human clones from three chromosome-5-specific libraries (a BssHII endclone phage library from the somatic cell hybrid H64 and two total genomic phage libraries from radiation hybrids IH12 and IH132), as well as Alu-PCR from chromosome-5-specific radiation hybrids with overlapping fragments in the region around the spinal muscular atrophy locus, followed either by direct isolation of Alu-PCR products or hybridization of Alu-PCR products to chromosome-5-gridded cosmid libraries. 253 human phage and cosmid clones were mapped to various parts of chromosome 5 by deletion mapping to somatic cell hybrid panels. 30 of these clones were mapped into the region 5q11.2-q13.3, 9 of which are flanking rate cutting BssHII-sites, known to be, often, starting points for genes. They represent excellent starting material for the development of new polymorphic markers and sequence-tagged sites, for YAC screening and building of contigs, as well as for direct isolation of genes.

Animals↗

PubMed2004

Molecular basis and hematologic characterization of deltabeta-thalassemia and hereditary persistence of fetal hemoglobin in Thailand.

BACKGROUND AND OBJECTIVES: Hereditary persistence of fetal hemoglobin (HPFH) and deltabeta-thalassemia are heterogeneous disorders characterized by increased levels of Hb F in adult life. The distinction between these two conditions is not always possible from routine hematologic analyses. This study investigated the hematologic and molecular characteristics of high HbF determinants in Thailand, and describes a rapid DNA-based assay to facilitate diagnosis in a routine laboratory. DESIGN AND METHODS: A multiplex allele-specific polymerase chain reaction (PCR) system for rapid detection of three common DNA deletions causing (deltabeta)0-thalassemia and HPFH in South-east Asians was developed and used to examine the molecular basis for the high Hb F phenotypes in 273 unrelated Thai individuals. Hematologic data were recorded and correlated to the molecular findings. RESULTS: The multiplex PCR system was validated and results were completely concordant with those of other established methods. DNA analysis identified GgAg(deltabeta)0-thalassemia in 148 cases (54.2%), deletional HPFH-6 in 83 (30.4 %) and the deletion-inversion Ggamma(Agammadeltabeta)0-thalassemia in 22 (8.1 %) cases, while another 20 (7.3 %) subjects remained uncharacterized. Genotype-phenotype relationships are discussed. INTERPRETATION AND CONCLUSIONS: These data emphasize the high frequencies of deltabeta-thalassemia and HPFH in Thailand and the need for differential diagnostic methods since the hematologic parameters associated with the conditions are very similar and overlap. The multiplex allele-specific PCR approach should prove useful in complementing routine Hb analysis for the differential diagnosis of these three common causes of high Hb F determinants and should facilitate a program of hemoglobinopathy screening in the region.

Adolescent↗

PubMed2005

[RAPD-PCR analysis of ground squirrels from the Tobol-Ishim interfluve: evidence for interspecific hybridization between ground squirrel species Spermophilus major and S. erythrogenys].

Populations of two ground squirrel species, Spermophilus major and S. erythrogenys, from the interfluvial area of the Tobol and Ishim rivers, where their ranges overlap, have been examined using RAPD-PCR. We have identified 253 loci, which included taxon-specific markers for S. major and S. erythrogenys as well as markers for geographic populations. Estimation of genetic diversity and construction of phylogenetic relationships were performed using software programs POPGENE, TEPGA, and TREECON. In all, based on morphological traits, animals from the Tobol-Ishim interfluve were assigned to the two parental morphotypes and showed similar levels of genetic variability (H, n(a), n(e)). However, the total polymorphism level proved to be higher in ground squirrels with the major morphotype (P = 40.32%, P95 = 27.27%) than in animals with the erythrogenys morphotype (P = 32%, P95 = 22.13%). Nevertheless, the number of rare alleles was high in both cases, constituting about 70% of the total number. By contrast, interpopulation differentiation was considerably higher in S. major (6 = 0.50) than in S. erythrogenys (delta = 0.41). The genetic differentiation between local samples from the Tobol-Ishim interfluvial area was lower than that between the parental species. A significant part of the genetic diversity of the species examined and animals from the zone of overlapping ranges was accounted for by intrapopulation variability. Animals from the northern and southern parts of the Tobol-Ishim interfluve were characterized by the core traits of S. major and S. erythrogenys, respectively, falling into two distinct clusters in the UPGMA and NJ reconstructions. In addition to three hybrid individuals, identified by the bioacoustic method, three hybrid animals were distinguished using RAPD analysis. These animals earlier were thought to be "pure" species and formed their own clusters in phylogenetic reconstructions. Thus, the RAPD-PCR results directly showed the existence of stable hybridization (20% genetic hybrids) between S. major and S. erythrogenys in the Tobol-Ishim interfluvial area, which is more extensive than inferred previously from morphological and bioacoustic data.

Animals↗

PubMed2005

Characterization of novel non-clonal intrachromosomal rearrangements between the H4 and PTEN genes (H4/PTEN) in human thyroid cell lines and papillary thyroid cancer specimens.

The two main forms of RET rearrangement in papillary thyroid carcinomas (PTC) arise from intrachromosomal inversions fusing the tyrosine kinase domain of RET with either the H4 (RET/PTC1) or the ELE1/RFG genes (RET/PTC3). PTEN codes for a dual-specificity phosphatase and maps to chromosome 10q22-23. Germline mutations confer susceptibility to Cowden syndrome whereas somatic mutations or deletions are common in several sporadic human tumors. Decreased PTEN expression has been implicated in thyroid cancer development. We report the characterization of a new chromosome 10 rearrangement involving H4 and PTEN. The initial H4/PTEN rearrangement was discovered as a non-specific product of RT-PCR for RET/PTC1 in irradiated thyroid cell lines. Sequencing revealed a transcript consisting of exon 1 and 2 of H4 fused with exons 3-6 of PTEN. Nested RT-PCR with specific primers bracketing the breakpoints confirmed the H4/PTEN rearrangements in irradiated KAT-1 and KAT-50 cells. Additional H4/PTEN variants, generated by recombination of either exon 1 or exon 2 of H4 with exon 6 of PTEN, were found in non-irradiated KAK-1, KAT-50, ARO and NPA cells. Their origin through chromosomal recombination was confirmed by detection of the reciprocal PTEN/H4 product. H4/PTEN recombination was not a clonal event in any of the cell lines, as Southern blots with appropriate probes failed to demonstrate aberrant bands, and multicolor FISH of KAK1 cells with BAC probes for H4 and PTEN did not show a signal overlap in all cells. Based on PCR of serially diluted samples, the minimal frequency of spontaneous recombination between these loci was estimated to be approximately 1/10(6) cells. H4/PTEN products were found by nested RT-PCR in 4/14 normal thyroid tissues (28%) and 14/18 PTC (78%) (P<0.01). H4/PTEN is another example of recombination involving the H4 locus, and points to the high susceptibility of thyroid cells to intrachromosomal gene rearrangements. As this also represents a plausible mechanism for loss-of-function of PTEN, other thyroid neoplastic phenotypes and eventually other cancer types need to be screened for clonal H4/PTEN rearrangements.

Chromosome Mapping↗

PubMed1998

Detection of gonadotrophin releasing hormone and its receptor mRNA in human placental trophoblasts using in-situ reverse transcription-polymerase chain reaction.

Neuropeptides such as gonadotrophin releasing hormone (GnRH) are presumed to play an important role in the regulation of the function and growth of human placenta. Knowledge about the placental site of GnRH expression and the eventual co-localization of its peptide with the GnRH receptor (GnRH-R) is crucial for a better understanding of possible autocrine/paracrine mechanisms. We therefore investigated these questions by use of in-situ reverse transcription-polymerase chain reaction (RT-PCR) alone or in combination with immunocytochemistry in human first and third trimester placentae. Paraffin-embedded placental sections (7 microm thick), or single trophoblasts in monolayer cultures for up to 3 days, were treated with proteinase K. Following RT with GnRH or GnRH-R specific oligoprimers, PCR was performed employing primers with exon-exon overlaps to exclude non-specific DNA amplification. Detection of the amplicons was accomplished by nested PCR which was performed with digoxigenin-labelled dUTP and nitroblue tetrazolium/5-bromo-4-chloro-3-indoyl-phosphate (NBT/BCIP) for substrate visualization. The GnRH peptide was detected using a sandwich-antibody assay. GnRH and GnRH-R gene expression was found in all first and third trimester placentae, with abundant signals for the GnRH and GnRH-R message both in the cyto- and syncytiotrophoblasts. Single trophoblasts of different gestational ages in culture also displayed GnRH expression in individual cytotrophoblasts and in syncytiotrophoblast-like fusionates. Additional immunostaining revealed GnRH peptide to be co-localized with GnRH-R message in trophoblast layers. Since messages for GnRH and GnRH-R were found in virtually all trophoblasts, we infer that GnRH and GnRH-R are co-expressed in identical cells. These data strongly suggest that the trophoblasts are the source of GnRH, and that there is autocrine/ paracrine regulation by GnRH in human placenta.

Female↗

PubMed1993

Cloning of the 5' mRNA for the 230-kD bullous pemphigoid antigen by rapid amplification of cDNA ends.

The 230-kD bullous pemphigoid antigen (BPAG1), defined by autoantibodies in patient sera, is a hemidesmosomal plaque protein in the same gene family as the intracellular proteins desmoplakin I/II and plectin. We had previously isolated, from a lambda gt11 library, overlapping cDNA clones with 6921 bp of mRNA sequence for BPAG1. The coding sequence encoded by these clones included the 3' stop codon but not the 5' coding and non-coding region of the mRNA. To obtain these sequences we used the polymerase chain reaction (PCR) method called rapid amplification of cDNA ends (RACE). The PCR products were cloned into plasmids and sequenced. With five PCR primers we were able to obtain overlapping clones containing the 5' region of the mRNA. An upstream stop codon in frame with the rest of the coding sequence demonstrates that the full 5' coding sequence is obtained. Four different PCR products from two separate reactions had the same 5' end, suggesting that this 5' end is near, or at, the transcription start site. No alternatively spliced clones were found and no transmembrane site was predicted, confirming that BPAG1 is an intracellular hemidesmosomal plaque protein.

Amino Acid Sequence↗