Touchdown PCR Research Articles

A novel eurythermic and thermostale lipase LipM from Pseudomonas moraviensis M9 and its application in the partial hydrolysis of algal oil.

BackgroundLipases are regularly used in biotechnology to catalyse the hydrolysis of triglycerides and the synthesis of esters. Microbial lipases in particular have been widely used in a variety of industrial applications. However, the current commercial microbial lipases cannot meet industrial demand due to rapid inactivation under harsh conditions. Therefore, in order to identify more stable enzymes, we isolated novel eurythermic and thermostable lipase(s) from Pseudomonas moraviensis M9.MethodsCloning of lipM was based on Touchdown PCR and genome walking, and then recombinant LipM was purified by guanidine hydrochloride and the nickel-nitrilotriacetic acid resins affinity chromatography. Finally, the hydrolysis of algal oil by LipM was analyzed by gas chromatograph-mass spectrometer, thin layer chromatography and gas chromatograph.ResultsThe lipM gene was first cloned from Pseudomonas moraviensis M9 via Touchdown PCR and genome walking. Sequence analysis reveals that LipM is a member of subfamily I.3 of lipases, and the predicted amino acid sequences of LipM has 82 % identity to lipase LipT from Pseudomonas mandelii JR-1, and 54 % identity to lipase PML from Pseudomonas sp. MIS38 and lipase Lip I.3 from Pseudomonas sp. CR-611. LipM was expressed in Escherichia coli, purified from inclusion bodies, and further biochemically characterized. Purified LipM differed significantly from previously reported subfamily I.3 lipases, and was eurythermic between 10 °C–95 °C. LipM activity was enhanced by Ca2+, Sr2+, Mn2+, and Ba2+, but sharply inhibited by Cu2+, Zn2+, Co2+, Ni2+, and EDTA. Compared with other lipases, LipM exhibited medium tolerance to methanol, ethanol, and isopropanol. When applied for hydrolysis of algal oil, LipM could enrich 65.88 % polyunsaturated fatty acids, which include 1.25 % eicosapentaenoic acid, 17.61 % docosapentaenoic acid, and 47.02 % docosahexaenoic acid with derivative glycerides containing 32.46 % diacylglycerols.ConclusionsA novel eurythermic I.3 subfamily lipase with high tolerance and stability was identified from Pseudomonas moraviensis and biochemically characterized. It will not only improve our understanding of subfamily I.3 lipases, but also provides an ideal biocatalyst for the enrichment of polyunsaturated fatty acids. Pseudomonas moraviensis have been investigated as a potential resource of lipases.

Phylogenic diversity analysis of rumen acetogens in adult sheep fed on conventional roughage diet

The study was conducted to screen the Indian sheep for the presence as well as diversity of rumen acetogens. Rumen liquor samples from 3 adult female sheep (Mandya x Rambouillet) was collected through stomach tube. Genomic DNA was isolated and amplified using touchdown PCR protocol for partial formyltetrahydrofolate synthetase (fhs) gene sequence. Bioinformatic analysis of obtained sequences was done to construct phylogenic tree for molecular characterization and diversity analysis. PCR based amplification and further agarose gel electrophoresis revealed the presence of fhs functional gene in sheep rumen confirming the occurrence of acetogens in adult sheep fed on conventional roughage diet. However, we could not amplify the gene acs conserved with acetogens described by Australian workers. From the phylogenic tree it is clear that act1 group is distant from all other clones (act2 - act10) obtained in this study and represent a distinct uncultured acetogens genera. The act3 and act5 clones are also present in different clusters and are distant to act2, act10, act4 and act6 are closer to each other in the phylogenic tree but distant from act1. From the phylogeny tree it is clear that majority of the acetogens in these sheep are different from those acetogens reported elsewhere in the world. Thus, there is an urgent need to screen our livestock for the acetogens species/strains and to culture them for exploring the prospects of their use as alternate H2 sink for methane mitigation from ruminants.

Abstract POSTER-BIOL-1348: No association between PARK2 and BRCA1-associated gynecologic cancers

Abstract Purpose of study: We sought to identify genomic modifiers of gynecologic cancer penetrance in BRCA1 185delAG mutation carriers. In a pilot study using the Illumina 610K Quad chip to perform a whole genome analysis of 592,532 single nucleotide polymorphisms (SNP), we found significant SNP genotype differences in the PARK2 gene between BRCA1 185delAG mutation carriers who developed gynecologic cancer (cases) compared to those who did not (controls). These SNPS created a haplotype structure that was present at four-times higher frequency in cases than controls (37% vs. 9%, p=0.0009). We hypothesized that PARK2, which has been shown to be mutated in other cancers and to have a tumor suppressive function, plays a role in the biology of BRCA1-associated gynecologic cancer development. Experimental Procedures: To validate a PARK2 risk haplotype in an independent dataset, we isolated germline DNA from 85 BRCA1 185delAG mutation carriers and used TaqMan SNP Genotyping to genotype seven SNPs in PARK2. To determine whether a correlation exits between the PARK2 risk haplotype and PARK2 expression levels in tissue, we quantified PARK2 expression in normal ovaries and ovarian cancer tissue using quantitative real-time PCR (qPCR). To determine the rate of PARK2 mutations in 17 BRCA1-associated ovarian cancers, we used a touchdown PCR protocol to amplify and sequence each PARK2 exon. To identify exon deletions and duplications in the PARK2 gene, we utilized the multiplex ligation-dependent probe amplification (MLPA) technique. Summary of Data: In an independent dataset of 85 BRCA1 185delAG mutation carriers, we found the PARK2 risk haplotype to be present in 35 (17%) of cases. The risk haplotype was present in a higher proportion of cancer cases than benign controls (6/12 or 50% vs. 29/73 or 8%), but this was not significant (p=0.54). We did not find a difference in PARK2 ovarian tissue expression levels in patients with and without the PARK2 risk haplotype. We sequenced the PARK2 gene and performed MPLA analysis from tumor DNA of 17 ovarian cancers from BRCA1 185delAG mutation carriers, but did not identify any deleterious PARK2 mutations or exon deletions and duplications. Conclusions: We did not validate a PARK2 risk haplotype as a modifier of gynecologic cancer penetrance in BRCA1 185delAG mutation carriers. We did not find evidence for PARK2 inactivation in BRCA1-associated gynecologic tumors. Citation Format: Christine Walsh, Hoorig Nassanian, Hasmik Agadjanian, Carl Miller, Sandra Orsulic, Beth Karlan. No association between PARK2 and BRCA1-associated gynecologic cancers [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-BIOL-1348.

Characterizing LipR from Pseudomonas sp. R0-14 and Applying in Enrichment of Polyunsaturated Fatty Acids from Algal Oil.

In this study, Pseudomonas R0-14, which was isolated from Arctic soil samples, showed a clear halo when grown on M9 medium agarose plates containing olive oil-rhodamine B as substrate, suggesting that it expressed putative lipase(s). A putative lipase gene, lipR, was cloned from R0-14 by genome walking and Touchdown PCR. lipR encodes a 562-amino-acid polypeptide showing a typical α/β hydrolase structure with a catalytic triad consisting of Ser153-Asp202-His260 and one α-helical lid (residues 103-113). A phylogenetic analysis revealed that LipR belongs to the lipase subfamily I.3. LipR was successfully expressed in Escherichia coli, purified, and biochemically characterized. Recombinant LipR exhibited its maximum activity towards p-nitrophenyl butyrate at pH 8.5 and 60°C with a Km of 0.37 mM and a kcat of 6.42 s(-1). It retained over 90% of its original activity after incubation at 50°C for 12 h. In addition, LipR was activated by Ca(2+), Mg(2+), Ba(2+), and Sr(2+), while strongly inhibited by Cu(2+), Zn(2+), Mn(2+), and ethylenediaminetetraacetic acid. Moreover, it showed a certain tolerance to organic solvents, including acetonitrile, isopropanol, acetone, methanol, and tert-butanol. When algal oil was hydrolyzed by LipR for 24 h, there was an enrichment of n-3 long-chain polyunsaturated fatty acids, including eicosapentaenoic acid (1.22%, 1.65-fold), docosapentaenoic acid (21.24%, 2.04-fold), and docosahexaenoic acid (36.98%, 1.33-fold), and even a certain amount of diacylglycerols was also produced. As a result, LipR has great prospect in industrial applications, especially in food and/or cosmetics applications.

Fecal detection of enterotoxigenic Bacteroides fragilis.

Bacteroides fragilis is a common colonic symbiote of which one subtype, enterotoxigenic Bacteroides fragilis (ETBF), causes inflammatory diarrhea. However, asymptomatic ETBF colonization is common. Through its primary virulence factor, B. fragilis toxin (BFT), ETBF causes asymptomatic, chronic colitis in C57BL/6 mice and increased colon tumorigenesis in multiple intestinal neoplasia mice. Human studies suggest an association between ETBF infection, inflammatory bowel disease, and colon cancer. Additional studies on ETBF epidemiology are, therefore, crucial. The goal of this study is to develop a reliable fecal diagnostic for ETBF. To develop a sensitive assay for ETBF, we tested multiple protocols on mouse stools spiked with serially diluted ETBF. Each assay was based on either touchdown or quantitative polymerase chain reaction (qPCR) and used primers targeted to bft to detect ETBF. Using touchdown PCR or qPCR, the mean ETBF detection limit was 1.55 × 10(6) colony-forming units (CFU)/g stool and 1.33 × 10(4) CFU/g stool, respectively. Augmentation of Bacteroides spp. growth in fecal samples using PYGB (Peptone Yeast Glucose with Bile) broth enhanced ETBF detection to 2.93 × 10(2) CFU/g stool using the touchdown PCR method and 2.63 × 10(2) CFU/g stool using the qPCR method. Fecal testing using combined culture-based amplification and bft touchdown PCR is a sensitive assay for the detection of ETBF colonization and should be useful in studying the role of ETBF colonization in intestinal diseases, such as inflammatory bowel disease and colon cancer. We conclude that touchdown PCR with culture-based amplification may be the optimal ETBF detection strategy, as it performs as well as qPCR with culture-based amplification, but is a less expensive technique.

Detection of Mycobacterium ulcerans subsp. shinshuense DNA from a water channel in familial Buruli ulcer cases in Japan.

To determine if Mycobacterium ulcerans subsp. shinshuense is present in the common living environment in a case of familial concurrent occurrence of Buruli ulcer in Japan. Environmental samples were collected primarily from a water channel in the patient's residence. A combination of whole-genome amplification, touchdown PCR and DNA sequencing was used to detect M. ulcerans subsp. shinshuense DNA. M. ulcerans subsp. shinshuense DNA was detected in a crayfish sampled in July, but not in other samples including a crayfish sampled in October. These findings support an association between contaminated aquatic environments and Buruli ulcer in Japan. The data also suggest dynamic seasonal appearance of the pathogen in the environment may contribute to the seasonal variation of Buruli ulcer occurrence in Japan.

Molecular cloning and characterization of CD3ε in Chinese domestic goose (Anser cygnoides)

CD3 is one of the most important cell surface markers of T lymphocytes which play an important role in signal transmission of antigen recognition. In this study, goose CD3ε gene was cloned by touchdown PCR with the template of goose thymus cDNA. The complete open reading frame of goose CD3ε encoded 178 amino acid residues with a 21 signal peptide. Sequence alignments showed that goose CD3ε had an amino acid sequence similarity to duck (80.3%) and chicken (66.3%). The extracellular domain of goose CD3ε was efficiently expressed as fusion protein in Escherichia coli, purified by a Ni-NTA agarose column, and the purified recombinant protein was used to produce anti-GoCD3εex polyclonal antibodies. The characteristics of PAb were identified by Western blot, cellular ELISA, IFA, FCM, and LSCM analysis. These results may be useful for a better understanding of goose CD3ε and have a foundation for the study of T cell mediated immune mechanism in waterfowl.

Detection of Coxiella burnetii and sequencing the IS1111 gene fragment in bulk tank milk of dairy herds

Coxiella burnetii is the etiologic agent of Q fever in human. This study is aimed to determine the contamination rate of C. burnetii in bulk tank milk samples. In this study, a total number of 100 bulk milk samples collected from dairy farms in northeast of Iran and were examined for C. burnetii using touchdown PCR assay. The primers were designed to amplify a 687-bp fragment of the IS1111 gene of C. burnetii. Five samples (5%) of bovine milk were found positive for C. burnetii. Sequence analysis of PCR products revealed 100% identity with published sequences of C. burnetii in genBank. Results of this study indicate that bovine milk is an important source of C. burnetii infection in Iran.

Multiplex touchdown PCR for rapid typing of the opportunistic pathogen Propionibacterium acnes.

The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA1, IA2, and IC), sodA (types IA2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA1 (n=145), IA2 (n=20), IB (n=65), IC (n=7), II (n=45), and III (n=30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.

Allele-specific real-time polymerase chain reaction as a tool for urate transporter 1 mutation detection.

Allele-specific polymerase chain reaction (ASPCR) method has long been applied for the detection of nucleotide variations and genotyping, which are detected by the presence or absence of DNA amplification PCR products. Recently, Real-Time PCR genotyping has fast developed and offered a rapid method of detecting mutations without the need of gel electrophoresis as with ASPCR. Here, we describe an easy and rapid touchdown real-time PCR method for the detection of nucleotide variations. Using our method we successfully detect two main mutations in human urate transporter 1 (SLC22A12), W258X and R90H, and validate the results. The method can potentially be applied to genotype of various other nucleotide variations.

Polymorphism in variable number of tandem repeats of dopamine d4 gene is a genetic risk factor in attention deficit hyperactive egyptian children: pilot study.

INTRODUCTIONThe variable number of tandem repeats (VNTR) of the dopamine receptor D4 (DRD4) gene among humans may elucidate individual differences in susceptibility to neuropsychiatric diseases. Dopamine dysfunction may be involved with Attention Deficit Hyperactivity Disorder (ADHD) symptoms. In this study, we report the association between the phenotype of ADHD, a condition characterized by inattentiveness, hyperactivity, and impulsiveness, and a 48-base pair VNTR in exon 3 of the DRD4 polymorphism.SUBJECTS AND METHODSWe used a case control approach conducted on 29 ADHD and 31 ethnically matched control Egyptian children (ages 6–12 years). Cases were assessed by a psychiatric semi-structured interview and the Conners’ Parent Rating Scale. VNTR polymorphisms of the DRD4 gene were done by touchdown PCR program using exon 3-specific primers followed by agarose gel electrophoresis.RESULTSWe observed a significant association between the existence of D4.4 allele of DRD4 and ADHD (P, 0.002); 6.9% of cases showed a single D4.4 and 10.3% showed a double D4.4 as compared to controls in whom D4.4 has never been detected.CONCLUSIONChildren with smaller number of repeat alleles (two to four repeats) of the DRD4 gene have higher possibility to develop ADHD in Egyptian children.

Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain)

Environmental surveillance of Legionella pneumophila is a key component of the control measures established in urban settlements to ensure water safety and quality, with the aim of minimizing and limiting opportunistic infections in humans. In this work, we present results on the detection and genetic characterization of these bacteria in the outbreak-recurrent region of Alcoy (Comunidad Valenciana, Spain) using water and biofilm samples. We were particularly interested in studying the presence and distribution of L. pneumophila in the absence of outbreak or sporadic cases of legionellosis and in comparing the efficacy of culturing from water samples with a biofilm-based detection procedure using molecular amplification. To this end, water samples were taken from 120 sites distributed all around the city and its surroundings, as well as 60 biofilm swabs from half of the sampling sites. L. pneumophila could be isolated from water in just 4 of the locations. Touchdown PCR was applied to DNA extracted from water and also biofilm swabs, as a rapid method for both routine and outbreak investigations. L. pneumophila was detected by this method in 14 of the sites in which both water and biofilms were taken, although 13 of them tested positive using only the biofilm samples. These results show a ten-fold increase in the success rate of Legionella detection over water samples. The application of this method to study the presence of L. pneumophila in the water-supply system and risk facilities of Alcoy revealed different strains distributed in different areas of the city. Sequence Type ST578, endemic in the area and responsible for most clinical cases, was detected in one of the sampling sites. The number of positive samples correlated with water temperature but not with chlorine levels. The direct analysis of biofilm swabs improves the detection rate and genetic characterization of L. pneumophila and can complement analyses based on bacterial culture.

Cloning of expansin genes in ramie (Boehmeria nivea L.) based on universal fast walking

Gene cloning is the first step to study the expression profiles and functions of a particular gene; considerable cloning methods have been developed. Expansin, thought to involve in the cell-wall modification events, was not cloned in ramie (Boehmeria nivea L.), which is one of the most important bast fiber crops with little conducted molecular research, especially on its fiber development. Studying the expansin gene family will uncover its possible relationship with ramie fiber development and other growth events. As a result, five expansin genes were cloned with full-length and their sequence information was investigated. Additionally, the phylogenetic analysis was conducted, which suggested that the cloned genes belong to the α-subfamily, and these genes expressed differently during ramie fiber developmental process. In this study, we aimed to apply a strategy for cloning novel full-length genes from genomic DNA of ramie, based on using degenerate primers, touchdown polymerase chain reaction and universal fast walking protocols. By cloning five full-length expansin genes, we believe the polymerase chain reaction-based gene cloning strategy could be applied to general gene studies in ramie and other crops.

P47 * THE IDENTIFICATION OF NOVEL APTAMERS TO GLIOMA

INTRODUCTION: Glioma represent less than 2% of all cancer cases in the UK, however, 80% of these tumours are glioblastoma (GBM). GBM is a highly aggressive tumour with poor patient survival rates, despite treatment involving surgery and radiotherapy with adjuvant chemotherapy. Delivery systems that have the ability to distinguish neoplasms from non-cancerous tissues, such as aptamers, may improve patient outcome. Aptamers have previously been shown to selectively target glioma cell lines. Aptamers can also be raised to known biomarkers that are crucial for cell survival, and once bound may inhibit glioma growth. The aim of this study was to produce novel aptamers to known glioma targets and to optimise the systematic evolution of ligands by exponential enrichment (SELEX) procedure with a view to produce Aptamers against patient tissue biopsies which ultimately have low cell numbers. METHOD: Cell lines SVGp12 and U87MG were utilised to determine the lowest number of cells which returned detectable DNA aptamers. Each iterative round of SELEX was optimised by determining the optimal number of touchdown PCR cycles. Furthermore, aptamers were selected against biomarkers related to gliomagenesis via counter SELEX. RESULTS: Optimisation of cell SELEX showed 100 cells and 15-17 cycles of TD-PCR were sufficient for selection. After 6 rounds of counter SELEX, aptamers selected towards a biomarker indicative of glioma were sequenced. CONCLUSION: Aptamers were selected using minimal amounts of sample, and the optimised procedure will now be used to identify aptamers which target primary tissues. Specificity of sequenced aptamers to the known biomarker and potential inhibition of glioma growth will be confirmed in future studies.

In vivo HIV-1 hypermutation and viral loads among antiretroviral-naive Brazilian patients.

Hypermutation alludes to an excessive number of specific guanine-to-adenine (G- >A) substitutions in proviral DNA and this phenomenon is attributed to the catalytic activity of cellular APOBECs. Population studies relating hypermutation and the progression of infection by human immunodeficiency virus type 1 (HIV-1) have been performed to elucidate the effect of hypermutation on the natural course of HIV-1 infection. However, the many different approaches employed to assess hypermutation in nucleotide sequences render the comparison of results difficult. This study selected 157 treatment-naive patients and sought to correlate the hypermutation level of the proviral sequences in clinical samples with demographic variables, HIV-1 RNA viral load, and the level of CD4(+) T cells. Nested touchdown polymerase chain reaction (PCR) was performed with specific primers to detect hypermutation in the region of HIV-1 integrase, and the amplified sequences were run in agarose gels with HA-Yellow. The analysis of gel migration patterns using the k-means clustering method was validated by its agreement with the results obtained with the software Hypermut. Hypermutation was found in 31.2% of the investigated samples, and a correlation was observed between higher hypermutation levels and higher viral load levels. These findings suggest a high frequency of hypermutation detection in a Brazilian cohort, which can reflect a particular characteristic of this population, but also can result from the method approach by aiming at hypermutation-sensitive sites. Furthermore, we found that hypermutation events are pervasive during HIV-1 infection as a consequence of high viral replication, reflecting its role during disease progression.

Touchdown polymerase chain reaction detection of polycystic kidney disease and laboratory findings in different cat populations.

Autosomal-dominant polycystic kidney disease (ADPKD) is the most prevalent inherited genetic disease of cats, predominantly affecting Persian and Persian-related cats. A point mutation (C→A transversion) in exon 29 of the PKD1 gene causes ADPKD, and is the specific molecular target for genetic diagnosis in cats. The current study describes a newly developed touchdown polymerase chain reaction (PCR) to detect this single point mutation, using 2 primers specific for the mutant allele, adapted from an existing multiplex amplification refractory mutation system (ARMS PCR). Furthermore, correlations between the clinical outcomes of tested animals and the results of the genetic test were investigated. A total of 334 cats were tested, 188 from the Veterinary Hospital of Small Animals at the University of Brasilia, and 146 from an anti-rabies vaccine campaign of the Federal District. A total prevalence of 9% was evident among the samples, with 33% of the Persian cats testing positive, and 7% of the Brazilian long- and shorthaired cats testing positive. Prevalence was not correlated with gender or hemogram. Positive animals exhibited hyperglobulinemia ( P = 0.02). This research demonstrated that the mutation does not only occur in Persian and Persian-related cats, and that a touchdown PCR can be used to diagnose ADPKD.

IDENTIFICATION OF COXIELLA BURNETII BY TOUCH-DOWN PCR ASSAY IN UNPASTEURIZED MILK AND DAIRY PRODUCTS IN NORTH - EAST OF IRAN

Coxiella burnetii is the causative agent of the zoonotic disease Q fever, and ruminants being considered as the main source for human infection. Although the main route of infection in human is inhalation of contaminated aerosols, oral transmission by contaminated raw milk or unpasteurized dairy products is also a possible route of infection. Raw milk or dairy products produced from unpasteurized milk may contain virulent C. burnetii. OBJECTIVES: This study aimed to determine the contamination rate of milk and unpasteurized dairy products with C. burnetii. METHODS: Touch-down PCR was used to examine the presence of C. burnetii on 147 dairy product samples collected from local traditional and commercial markets in Mashhad-Khorasan Razavi province- Iran. RESULTS: 2 of 28 (7.14%) cheese samples, 2 of 26 (7.69%) yoghurt samples, 8 of 23 (34.78%) sheep milk samples, and 2 of 60 (3.33%) cow milk samples were found to be positive for C. burnetii DNA. However, 10 goat milk samples were found to be negative. CONCLUSIONS: The results of this study indicate that the clinically healthy dairy livestock and their dairy products are important sources of C. burnetii infection.

Optimization of PCR product of GC rich astrocyte elevated gene 1 promoter

Background and Objectives: Most housekeeping genes, tumor-suppressor genes, and approx 40% of tissue specific genes contain G+C sequences in their promoter region that are very difficult to amplify. AEG-1 plays a significant role in invasion, metastasis, angiogenesis and chemoresistance, apoptosis, angiogenesis and aging Material and Methods:In this study, we proposed an improved polymerase chain reaction (PCR) method to be used for successful amplification of the Astrocyte elevated gene -1gene promoter region that contains >70% G+C content in a sequence of 495 bp and some transcription initiation sites in hepatocellularcarcinoma patient. Results: The results showed that using of DMSO co-amplification touchdown PCR and pfu enzyme can inhibit the formation of secondary structure in DNA Sequences and increase the PCR product. Conclusion: Therefore, this method can be recommended to amplify other GC-rich genomic templates.

Direct and Rapid Diagnosis of Extra-Pulmonary Tuberculosis in Archival Tissue by Nested and Touchdown PCR

Aims: To identify and differentiate mycobacterium spp. in archival formalin-fixed, paraffinembedded tissue by PCR to supply additional differential diagnostic method for Mycobacterium infections, where tuberculosis had been tested for by histopathological methods but without culturing. Place and Duration of Study: Department of Medical Laboratory Sciences, Department of Pathology and Microbiology (Faculty of Medicine) and King Abdulla University Hospital, between January 2004 and July 2010. Methodology: Fifty-six extra-pulmonary specimens of formalin-fixed, paraffin-embedded tissue obtained from patients showing granulomatus inflammation and/or other histopathologic features. Specimens were analyzed by a hemi-nested PCR assay targeting the gene encoding for 16S ribosomal RNA, which is common to all mycobacteria spp. The PCR positive specimens were amplified by a touch-down PCR targeting a fragment in the insertion sequence IS6110 specific to Mycobacterium tuberculosis complex. Results were compared to acid fast bacilli stain and with histopathology of each specimen. Results: M. tuberculosis complex DNA was detected in 27 (48.2%) specimens, and nonOriginal Research Article Article British Microbiology Research Journal, 4(5): 530-539, 2014 531 tuberculous mycobacteria in four specimens, compared to 10 (18%) specimens that were positive by acid fast staining. The positive cases were observed more in the lymph nodes, and pleural specimens. Conclusions: This study is among few studies to use the touch-down PCR assay as a promising auxiliary tool for the diagnosis of extra-pulmonary tuberculosis in archival tissue specimens. It could be used in conjunction with routine laboratory tests (e.g., cultures, acid fast staining) and clinical criteria of the patient to increase the accurate diagnosis of such cases. It is also recommended that culture be routinely done for all tuberculosis suspected cases.

Survey of the Parasite Toxoplasma gondii in Human Consumed Ovine Meat in Tunis City

Toxoplasmosis has been recognized as parasitic zoonosis with the highest human incidence. The human infection by the parasite can lead to severe clinical manifestations in congenital toxoplasmosis and immunocompromised patients. Contamination occurs mainly by foodborne ways especially consumption of raw or undercooked meat. In contrast to other foodborne infections, toxoplasmosis is a chronic infection which would make its economic and social impact much higher than even previously anticipated. Ovine meat was advanced as a major risk factor, so we investigated its parasite survey, under natural conditions. Serological MAT technique and touchdown PCR approaches were used for prevalence determination of the parasite in slaughtered sheep intended to human consumption in Tunis City. The genotyping was carried by SNPs analysis of SAG3 marker. Anti-Toxoplasma antibodies were present in 38.2% of young sheep and in 73.6% of adult sheep. Molecular detection revealed the contamination of 50% of ewes’ tissue. Sequencing and SNPs analysis enabled unambiguous typing of meat isolates and revealed the presence of mixed strains as those previously identified from clinical samples in the same area. Our findings conclude that slaughtered sheep are highly infected, suggesting them as a major risk factor of Toxoplasma gondii transmission by meat consumption. Special aware should target consequently this factor when recommendations have to be established by the health care commanders.