Polymerase Chain Reaction Southern Blot Research Articles

Successful production of human epidermal growth factor in tobacco chloroplasts in a biologically active conformation

Human epidermal growth factor (hEGF) is an important therapeutic compound with multiple applications particularly in pharmaceutical industry. Human EGF has already been expressed in different expression systems, however, the production of hEGF with bioactivity in chloroplasts has not been successful so far. In this study, we expressed a 6 × His-tagged hEGF in tobacco chloroplasts in its native conformation for the potential of large-scale production of hEGF for industrial applications. Several transplastomic plant lines were obtained, which were screened by PCR (polymerase chain reaction) using primers specific to selectable gene aadA, hEGF- and GFP-coding sequences that were included in the chloroplast expression vector. The selected lines were confirmed to be homoplasmic by PCR verification and Southern blot analysis. Immunoblotting assays of homoplasmic lines using antibodies raised against hEGF confirmed the accumulation of hEGF in transplastomic plants and the ELISA results demonstrated the expression levels of hEGF were between 0.124% and 0.165% of the total soluble proteins (TSP), namely, 23.16–25.77 ng/g of the fresh weight. In terms of activity, the data from cell proliferation and elongation assays showed that the tobacco-derived recombinant hEGF was as bioactive as its commercial counterpart. To our knowledge, this is the first report of recombinant production of hEGF with native bioactivity form in the chloroplast stroma. Overall, our results demonstrate the potential of higher plant chloroplasts for the production of a human therapeutic, hEGF, in an active conformation.

Analysis of DAZ gene expression in a partial AZFc deletion of the human Y chromosome

The azoospermia factor c (AZFc) region of the Y chromosome consists of repetitive amplicons and is therefore highly susceptible to structural rearrangements, such as deletions and duplications. The b2/b3 deletion is a partial AZFc deletion that is conventionally determined by the selective absence of sY1191 in sequence-tagged site polymerase chain reaction (PCR) and is generally believed to retain two of the four deleted in azoospermia (DAZ) genes on the Y chromosome. In the present study we determined the copy number and expression of DAZ genes in sY1191-negative individuals. Using a DAZ dosage PCR assay and Southern blot analysis we evaluated the expression of four DAZ genes in five of six sY1191-negative individuals. Furthermore, cloning and immunoblot analyses revealed that three or more DAZ genes are expressed in sY1191-negative testes with germ cells. The results indicate that the selective absence of sY1191 not only means b2/b3 deletion with two DAZ genes, but also includes another AZFc configuration with four DAZ genes. These results exemplify the prevalence of variations in the AZFc region of the human Y chromosome.

Phlebotomine Vector Ecology in the Domestic Transmission of American Cutaneous Leishmaniasis in Chaparral, Colombia

Phlebotomine vector ecology was studied in the largest recorded outbreak of American cutaneous leishmaniasis in Colombia in 2004. In two rural townships that had experienced contrasting patterns of case incidence, this study evaluated phlebotomine species composition, seasonal abundance, nocturnal activity, blood source, prevalence of Leishmania infection, and species identification. CDC miniature light traps were used to trap the phlebotomines. Traps were set indoors, peridomestically, and in woodlands. Natural infection was determined in pools by polymerase chain reaction-Southern blot, and blood sources and species identification were determined by sequencing. Large differences were observed in population abundance between the two townships evaluated. Lutzomyia longiflocosa was the most abundant species (83.1%). Abundance was higher during months with lower precipitation. Nocturnal activity was associated with human domestic activity. Blood sources identified were mainly human (85%). A high prevalence of infection was found in L. longiflocosa indoors (2.7%) and the peridomestic setting (2.5%). L. longiflocosa was responsible for domestic transmission in Chaparral.

Leishmania (Viannia) Infection in the Domestic Dog in Chaparral, Colombia

Peridomestic transmission of American cutaneous leishmaniasis is increasingly reported and dogs may be a reservoir of Leishmania (Viannia) in this setting. We investigated the prevalence of infection in dogs in Chaparral County, Colombia, the focus of an epidemic of human cutaneous leishmaniasis caused by Leishmania (Viannia) guyanensis. Two (0.72%) of 279 dogs had lesions typical of cutaneous leishmaniasis that were biopsy positive by kinetoplast DNA polymerase chain reaction-Southern blotting. Seroprevalence was 2.2% (6 of 279) by enzyme-linked immunosorbent assay. Buffy coat and ear skin biopsy specimens were positive by polymerase chain reaction-Southern blotting in 7.3% (10 of 137) and 11.4% (12 of 105) of dogs, respectively. Overall 20% of dogs (21 of 105) showed positive results for one or more tests. Amplification and sequencing of the Leishmania 7SL RNA gene identified L. guyanensis in one dog and L. braziliensis in two dogs. No association was identified between the risk factors evaluated and canine infection. Dogs may contribute to transmission but their role in this focus appears to be limited.

Analysis of theCYP21A2Gene with Intergenic Recombination and Multiple Gene Deletions in the RCCX Module

The most frequent bimodular RCCX module of the RP1-C4A-CYP21A1P-TNXA-RP2-C4B-CYP21A2-TNXB gene sequence is located on chromosome 6p21.3. To determine RCCX alterations, we used the polymerase chain reaction (PCR) product containing the tenascin B (TNXB) and CYP21A2 genes with TaqI digestion and Southern blot analysis with AseI and NdeI endonuclease digestion of genomic DNA from congenital adrenal hyperplasia patients with common mutations resulting from an intergenic conversion of CYP21A1P, such as an I2 splice, I172N, V281L, F306-L307insT, Q318X, and R356W, and dual mutations of I236N/V237E in the CYP21A2 gene. The results showed that a 3.7-kb fragment of the CYP21A2 gene was detected in each case, and 21.6- and 11.3-kb DNA fragments were found in the RCCX region by a Southern blot analysis with these corresponding mutations. However, the IVS2-12A/C- > G (I2 splice) haplotype in combination with the 707-714delGAGACTAC (without the P30L mutation) mutation produced a 3.2-kb TaqI fragment in the PCR product analysis and a specific 9.3-kb fragment by the Southern blot method. Therefore, we concluded that the rearrangement in the RCCX region resulting from processing of either an intergenic recombination or multiple gene deletions can be identified by the PCR analysis and Southern blot method based on a fragment-distinguishing configuration without a family study.

Direct adventitious shoot regeneration system of Euonymus fortunei var. radicans and its genetic transformation mediated by Agrobacterium tumefaciens

AbstractUsing hypocotyls as explants, the adventitious shoots of Euonymus fortunei var. radicans were differentiated directly from basal Murashige and Skoog (MS) medium supplemented with different plant growth regulators. The highest regeneration frequency was obtained with MS medium containing 0.5 mg/l 6-benzylaminopurine (BAP) and 0.01 mg/l α-naphthalene acetic acid (NAA). A regeneration frequency of 92% and 4.2 shoots per explant were obtained after 30 days of culture. The binary vector pBCGm, containing Galanthus nivalis agglutinin (GNA) gene, was introduced into Agrobacterium tumefaciens LBA4404. Hypocotyl segments of E. fortunei var. radicans were infected through A. tumefaciens-mediated transformation. Polymerase chain reaction (PCR) and PCR–Southern blot analysis results confirmed that the GNA gene was integrated into the genome of transgenic plants. The highest transformation frequency was obtained with un-precultured explants infected for 30 min with OD600=0.6 Agrobacterium tumefaciens, and co-cultivated for 3 days.

Gonadotropin-releasing hormone agonist and danazol normalize aromatase cytochrome P450 expression in eutopic endometrium from women with endometriosis, adenomyosis, or leiomyomas

Objective To investigate whether GnRH agonists or danazol therapy normalizes estrogen metabolism in the eutopic endometrium of women with endometriosis, adenomyosis, or leiomyomas. Design Prospective clinical study. Setting University hospital. Patient(s) Fifty-three women with endometriosis, adenomyosis, or leiomyomas. Intervention(s) Patients received GnRH agonist or danazol. Biopsy samples of the endometrium were obtained before and after endocrine therapy. Nontreated endometrial explants were cultured in the presence of either drug. Main outcome measure(s) Reverse transcription polymerase chain reaction-Southern blot and immunohistochemical analyses of the endometrial expression of aromatase cytochrome P450, estrogen receptor, progesterone receptor, and Ki-67. Nontreated endometrial explants were cultured in the presence of either drug. Result(s) Messenger RNA and protein of aromatase cytochrome P450 were greatly reduced in the eutopic endometrium of patients treated with GnRH agonist for 2 months or more or with danazol for 1 month or more. Culture of endometrial explants with GnRH agonist (10 −9–10 −7 M) did not change the amount of aromatase cytochrome P450, whereas danazol (10 −7–10 −6 M) efficiently reduced aromatase cytochrome P450 expression. Conclusion(s) Therapy with GnRH agonist or danazol decreases expression of aromatase cytochrome P450 in diseased eutopic endometrium. Endocrine therapy normalized in part the impaired hormonal expression of the eutopic endometrium. GnRH agonist reduced aromatase cytochrome P450 expression mainly by promoting a hypoestrogenic state, whereas danazol reduced aromatase cytochrome P450 in part by direct action on the eutopic endometrium.

Fibroblast growth factor receptor (FGFR) 4 correlated with the malignancy of human astrocytomas

Fibroblast growth factor receptor (FGFR) 4 possesses high affinity to acidic and basic fibroblast growth factors (FGFs). The authors focused on FGFR 4 expression in astrocytoma because the FGF expression increases as the tumor malignancy progresses. Forty-one astrocytoma specimens were examined by immunohistochemistry and polymerase chain reaction-Southern blot. FGFR 4 was negative in all seven Grade II astrocytomas by immunohistochemistry, while positive in four among 15 Grade III and in 13 among 19 Grade IV astrocytomas. The median survival time of Grade III astrocytoma patients was 22.3 months in FGFR 4 negative group and 14.5 months in positive group (p < 0.05). Those of Grade IV patients were 14.2 months in FGFR 4 negative group and 11.9 months in positive group (p > 0.05, not significant). However, FGFR 4 mRNA was detected in all specimens suggesting activated translation system of FGFR 4 in progression of the tumor malignancy. Histologically diagnosed Grade III astrocytoma patients can be divided into two groups; one with median survival time close to those with Grade II astrocytoma patients, and the other similar to that of glioblastoma patients. The authors concluded that FGFR 4 must be an important factor which predicts short survival Grade III astrocytoma patients, who require strict adjuvant therapy in accordance with glioblastoma. [Neurol Res 2002; 24: 244-248]

Assessment of the PCR-Southern blot technique for the analysis of viremia in patients with acute hepatitis A

Assessment of viremia in hepatitis A virus (HAV) infection is not frequently performed with conventional methods because the techniques used are laborious, have low sensitivity are usually performed in feces. The aims of this study were to develop a polymerase chain reaction (PCR) and Southern blot technique to detect HAV-RNA in the serum of patients with acute HAV infection and to determine the relationship between HAV-RNA and anti-HAV IgM and alanine aminotransferase (ALT) levels. The presence of HAV-RNA was studied in 26 serum samples from 21 patients with acute hepatitis A. We also studied 11 samples from patients with acute hepatitis B and 15 samples from patients with non-A, non-E hepatitis. HAV-RNA was detected in 10 (38%) of the 26 serum samples from patients with acute hepatitis A. Simple PCR was positive in 5 samples and PRC-Southern blot was positive in 10. All the serum samples obtained during the first week of onset were HAV-RNA positive and 50% of those obtained during the second week were positive. None of the serum samples obtained after the second week of onset were HAV-RNA positive. None of the serum samples from the 11 patients with acute hepatitis B or from the 15 patients with non-A, non-E acute hepatitis were positive for HAV-RNA. No significant relationship was detected between HAV-RNA detection and an IgM anti-HAV or ALT positive result. In conclusion, the presence of HAV-RNA in acute hepatitis A is frequent but the PCR Southern blot technique is required for detection, which is transitory during the first weeks after onset.

Incidence of human papillomavirus 16 and 18 infection and p53 mutation in patients with oral squamous cell carcinoma in Japan

The purpose of this study was to investigate the prevalence of human papillomaviruses (HPVs) 16 and 18 infection, and p53 mutation in oral squamous cell carcinomas (SCCs) in Japanese patients. Our results showed a higher incidence of HPV16 and 18 infections than previous studies because we combined the findings of a consensus polymerase chain reaction (PCR), restriction fragment length polymorphism by using the restriction enzyme digestion of the PCR products and Southern blot hybridization. Each HPV16 and 18 E6/E7 DNA was detected in 9 (20%) and 25 (54%) of 46 samples. The p53 mutation in the exons from 5 to 8 were detected in 20 out of 46 samples (43%) by a PCR-single strand conformation polymorphism analysis. There was a significant relationship between HPV16 and the p53 mutation (P =0.02) suggesting that HPV16 infection has a mutagenic effect in oral SCC. However, neither HPV infection nor p53 mutation influenced survival.

Clonally accumulating T cells in the anterior chamber of Behçet disease

PURPOSE: To clarify the nature of infiltrating T cells into the anterior chamber of a patient with Behçet disease. METHODS: Aqueous humor was obtained from a patient with ocular Behçet disease by paracentesis. RNA isolated from the cells in aqueous humor was reverse transcribed into complementary DNA. Complementary DNA encoding the variable (V) diversity (D) joining (J) (junctional) region of T-cell receptor β chain V domain (TCR BV) chain was amplified by T-cell receptor BV family polymerase chain reaction. RESULTS: Polymerase chain reaction Southern blot analysis showed that T-cell receptor BV3, BV5, and BV7 were dominantly expressed on ocular T cells of this patient. In addition, DNA sequencing revealed that monoclonal or oligoclonal T-cell accumulation was found in T-cell receptor BV3 +, BV5 +, and BV7 + T cells. CONCLUSION: These findings suggest that some T cells infiltrating into the anterior chamber of a patient with ocular Behçet disease expand by antigen-driven stimulation, indicating the pivotal role of T cells in the pathogenesis of ocular Behçet disease.

PCR based detection of mycobacteria in paraffin wax embedded material routinely processed for morphological examination.

BACKGROUND: The incidence of mycobacterial infections has increased during the past five years. A prompt diagnosis is indispensable for initiating appropriate treatment. Because culturing of mycobacteria takes three to six...

Characterization of Candida krusei strains from spontaneously fermented maize dough by profiles of assimilation, chromosome profile, polymerase chain reaction and restriction endonuclease analysis.

Several isolates of Candida krusei from indigenous spontaneously fermented maize dough have been characterized for the purpose of selecting appropriate starter cultures and methods for their subspecifies typing. The present work describes the occurrence of C. krusei in Ghanaian fermented maize dough. For detailed pheno- and genotyping, 48 representative isolates were selected and comparison was made with clinical isolates of C. krusei and reference cultures. The techniques applied included the assimilation of carbon compounds by the API ID 32 C kit, determination of chromosome profile by pulse field gel electrophoresis, polymerase chain reaction (PCR) profiles, restriction endonuclease analysis (REA) and Southern blot hybridization. For the 48 isolates tested, 82% had the same assimilation profiles, being able to assimilate N-acetyl-glucosamine, DL-lactate, glycerol and to ferment glucose. Chromosome and PCR profiles, REA and Southern blot hybridization techniques all had a high discriminatory power and revealed DNA polymorphism, which allowed for discrimination among the strains and hence subspecific typing. On the basis of PCR and REA profiles, isolates were grouped into clusters. Southern blot hybridization appeared to be the most sensitive with respect to strain specificity. Our results demonstrated that the three methods, PCR, REA and Southern blot hybridization, were suitable tools, easy to analyse, fast (with regard to PCR) and reliable methods for the typing of C. krusei isolates to species and below species level. Based on the use of these techniques, we demonstrated that several strains of C. krusei were involved in the fermentation of maize dough from the onset and remain dominant throughout the fermentation.

Ipriflavone down-regulates endothelin receptor levels during differentiation of rat calvarial osteoblast-like cells.

Ipriflavone (7-isopropoxy-3-phenyl-4H-1-benzopyran-4-one) is a synthetic flavonoid that has been shown to stimulate the activity of osteoblasts. We show here that ipriflavone also promotes the deposition of calcium and the formation of mineralized nodules by newborn rat calvarial osteoblast-like (ROB) cells as well as the activity of alkaline phosphatase. We reported previously that endothelin-1 inhibits the differentiation of ROB cells [Y. Hiruma et al. (1998) J. Cardiovasc. Pharmacol. 31, S521-S523]. Therefore, we examined the effects of ipriflavone on the expression of endothelin receptors in ROB cells by polymerase chain reaction-Southern blot analysis and in binding assays with 125I-labeled endothelin-1. Ipriflavone reduced levels of endothelin ETA receptors (to 48% of the control level) in ROB cells around day 7 in our standard cultures, while it had no apparent effect on the expression of the mRNA for the endothelin ETA receptor. By contrast, treatment with 10(-7) M endothelin-1 on days 6 through 9 alone suppressed mineralization by ROB cells. Ipriflavone also reduced the ability of endothelin-1 to inhibit mineralization by ROB cells. These results suggest that the acceleration of osteoblastic differentiation by ipriflavone might be due, at least in part, to a time-specific down-regulation of endothelin receptors.

Expression of P450c17 messenger ribonucleic acid in postmenopausal human ovary tissues

Objective: To investigate the expression of the P450c17 gene in postmenopausal human ovaries compared with normal cycling ovaries. Design: Prospective nonrandomized clinical research study. Setting: Servei de Medicina Reproductiva and Centre d’Investigacions en Bioquı́mica i Biologia Molecular, Hospitals Vall d’Hebron, Barcelona, Spain. Patient(s): Six premenopausal women and four postmenopausal women undergoing bilateral oophorectomy for nonovarian gynecologic disease. Intervention(s): Extraction of 10 mL of peripheral venous blood for hormone measurements. Extraction of RNA from surgically removed ovaries for Northern blot, ribonuclease protection, and reverse transcriptase polymerase chain reaction Southern blot assays. Main Outcome Measure(s): Definition of the reproductive cycle state of each patient and determination of the level of P450c17 gene expression in all samples with the use of the semiquantitative reverse transcriptase polymerase chain reaction Southern blot assay. Result(s): P450c17 messenger RNA levels in postmenopausal ovaries varied considerably between samples. Although the levels were similar to those detected in the early follicular phase, one of the samples had levels as high as those observed in the late follicular phase. Conclusion(s): Although the degree varied from one sample to another, all the postmenopausal ovaries studied expressed the P450c17 gene at the messenger RNA level. In a sample from a patient with endometrial adenocarcinoma, the level was as high as the levels observed in the late follicular phase.

Steroid Receptor mRNA Levels in Human Corpus luteum

To understand the biology of sex steroids in the human corpus luteum, the expression of estrogen receptor alpha, progesterone receptor, and androgen receptor mRNA levels was determined by semiquantitative reverse-transcription polymerase chain reaction-Southern blot analysis. Expression of all receptor mRNAs was detected in all samples analyzed. Each steroid receptor mRNA level was significantly lower (p < 0.05) during the late secretory phase than that during the early or the mid-secretory phase of the endometrium. These findings support the concept of a local role for sex steroids in modulating the function and life span of the human corpus luteum.

Up-regulation of glial fibrillary acidic protein in the retina of primate eyes with experimental glaucoma.

To identify molecular mechanisms of retinal responses to intraocular pressure elevation in primate experimental glaucoma. An experimental glaucoma model was created by repeated laser trabeculophotocoagulation. After the preparation of complementary DNAs from extracted total RNAs in the retinas, polymerase chain reaction (PCR) experiments were performed for the following screening target genes: beta-tubulin beta 2 and beta 5 and glial fibrillary acidic protein (GFAP). To investigate the amplified sequences derived from the PCR experiments, sequencing, subcloning, and Southern blot analysis of PCR products were performed. In addition, an immunohistochemical analysis was performed in an attempt to show the distribution of the target gene products in the retinas. A series of PCR experiments suggested up-regulation of gene expression for GFAP but not for beta-tubulins. Sequencing of the PCR products and results of the Southern blot analysis showed that the amplified sequences were derived mainly from the target gene, GFAP, and that increased expression of GFAP was found despite the severity of glaucoma. Immunohistochemical studies also demonstrated increased expression of GFAP proteins in Müller cells and astrocytes in the retinas of primate eyes with experimental glaucoma. Our study showed up-regulation of GFAP at gene and protein levels, which suggests that glial components in the retina may contribute to the pathologic processes induced by elevated intraocular pressure.

Simple and rapid identification of low level hepatitis B virus DNA by the nested polymerase chain reaction

A rapid and sensitive method has been developed to detect hepatitis B virus DNA (HBV) by nested polymerase chain reaction (PCR) technique with primers specific for the surface and core regions in capillary thermal cycler within 80 min. The lower limit for detection by present PCR method is 10−5 pg of recombinant HBV DNA which is equivalent to that determined by one round of PCR amplification and Southern blot hybridization analysis. When boiled HBV positive serum was serially diluted 10-fold, HBV DNA was successfully determined in 1 μl≈10−3 μl of serum. HBV DNA was detected by present method in 69 clinical samples including HBsAg positives and negatives by enzyme-linked immunosorbent assay (ELISA). When serum samples were amplified by nested PCR using surface and core region primers, HBV DNAs were detected in 37 of 69 samples (53.6%) and 18 of 69 samples (26.1%), respectively. These results can inform the infectious state of HBsAg positive pateints. A simple and rapid nested PCR protocol by using boiled serum as DNA template has been described for the clinical utility to determine HBV DNA in human serum.

Sequence-specific, single-primer amplification and detection of PCR products for identification of hepatitis viruses.

A simple system to detect polymerase chain reaction (PCR) amplification products was developed. This detection method has the sensitivity and the specificity of nested primer PCR amplification or Southern blot hybridization of PCR product. Digoxigenin-labeled PCR products were hybridized with a biotinylated probe in liquid phase and captured on to microtiter wells coated with antidigoxigenin followed by detection with streptavidin-peroxidase. The sensitivity of this assay for the detection of hepatitis A virus, hepatitis B virus, and hepatitis C virus is equal to that of existing nucleic acid detection systems.

Analysis of Clonal Rearrangements of the Ig Heavy Chain Locus in Acute Leukemia

Clonal rearrangements of the Ig heavy chain (IGH) locus occur in nearly all cases of B-cell precursor acute leukemia (BCP-ALL). Some of these rearrangements may be detected by polymerase chain reaction (PCR) using VH gene framework III (FRIII) and JH consensus primers. However, about 20% of BCP-ALLs fail to amplify with this technique. To determine the causes of these PCR failures and to investigate any possible association with specific subgroups of disease, we analyzed 72 acute leukemias of defined immunophenotype and cytogenetics, comparing FRIII with VH-family leader-specific PCR methods and Southern blotting. Of 37 BCP-ALL cases, 6 (16.2%) failed totally to amplify with FRIII and JH primers. None of these cases amplified with VH leader primers. Additionally, all cases retained germline VH6 genes and 5 of 11 rearranged alleles amplified with a consensus DH primer, indicating that these rearrangements represented biallelic DH-JH recombinations. Among the 6 FRIII and VH leader PCR-negative BCP-ALL cases, there was no common immunophenotype or consistent cytogenetic abnormality, although all showed structural chromosomal abnormalities and 3 of 5 successfully karyotyped had abnormalities of chromosome 12p. 13 cases with t(9;22)(q34;q11) Philadelphia chromosome-positive [Ph+]) and IGH rearrangements (9 BCP-ALL and 4 biphenotypic cases) were also analyzed. Of 23 rearranged IGH alleles, 19 (82%) were positive by FRIII PCR, and all 4 remaining alleles were amplified by VH leader primers. Use of the leader primers in these Ph+ cases also detected 3 additional clonal rearrangements that were not anticipated from Southern blotting; such unexpected bands were not observed in 21 other Ph- cases. The additional bands represented "new" and unrelated VH rearrangements rather than VH-VH replacement events. We conclude that biallelic DHJH rearrangements occur in a subgroup of BCP-ALL; in these cases, the activation of the full VHDHJH recombination mechanism had not occurred. Therefore, these cases of BCP-ALL were arrested at an early stage of B-cell differentiation. In contrast, all Ph+ BCP-ALLs and biphenotypic acute leukemias, which may represent the transformation of multipotent hemopoietic stem cells, had undergone VHDHJH recombination. Of 9 Ph+ BCP-ALL cases, 3 also showed ongoing VHDHJH rearrangement, reflecting the persistent expression of the VHDHJH recombinase. Finally, sequence analysis of 33 rearranged VHDHJH genes showed that only 3 including 2 Ph+ BCP-ALL maintained an intact open-reading frame. Loss of the open-reading frame occurred not only because of out-of-frame VHDH and DHJH joining, but also because of VH gene mutation and deletion. These data show that most BCP-ALLs may represent the neoplastic transformation of BCPs destined to die in the bone marrow.