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Agarose Gel Electrophoresis (agarose + gel_electrophoresis)
Selected AbstractsSensitive and simultaneous analysis of five transgenic maizes using multiplex polymerase chain reaction, capillary gel electrophoresis, and laser-induced fluorescenceELECTROPHORESIS, Issue 14 2004Virginia García-Cańas Abstract The benefits of using multiplex polymerase chain reaction (PCR) followed by capillary gel electrophoresis with laser-induced fluorescence (CGE-LIF) for the simultaneous detection of five transgenic maizes (Bt11, T25, MON810, GA21, and Bt176) are demonstrated. The method uses a hexaplex PCR protocol to amplify the five mentioned transgenic amplicons plus the zein gene used as reference, followed by a CGE-LIF method to analyze the six DNA fragments. CGE-LIF was demonstrated very useful and informative for optimizing multiplex PCR parameters such as time extension, PCR buffer concentration and primers concentration. The method developed is highly sensitive and allows the simultaneous detection in a single run of percentages of transgenic maize as low as 0.054% of Bt11, 0.057% of T25, 0.036% of MON810, 0.064% of GA21, and 0.018% of Bt176 in flour obtaining signals still far from the detection limit (namely, the signal/noise ratios for the corresponding DNA peaks were 41, 124, 98, 250, 252, and 473, respectively). These percentages are well below the minimum threshold marked by the European Regulation for transgenic food labeling (i.e., 0.5,0.9%). A study on the reproducibility of the multiplex PCR-CGE-LIF procedure was also performed. Thus, values of RSD lower than 0.67 and 6.80% were obtained for migration times and corrected peak areas, respectively, for the same sample and three different days (n = 12). On the other hand, the reproducibility of the whole procedure, including four different multiplex PCR amplifications, was determined to be better than 0.66 and 23.3% for migration times and corrected peak areas, respectively. Agarose gel electrophoresis (AGE) and CGE-LIF were compared in terms of resolution and sensitivity for detecting PCR products, demonstrating that CGE-LIF can solve false positives induced by artifacts from the multiplex PCR reaction that could not be addressed by AGE. Moreover, CGE-LIF provides better resolution and sensitivity. To our knowledge, these results demonstrate for the first time that multiplex PCR-CGE-LIF is a solid alternative to determine multiple genetically modified organisms in maize flours in a single run. [source] Ferrocene-bridging dinuclear cyclen copper(II) complexes as high efficient artificial nucleases: design, synthesis and interaction with DNAAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 5 2008Kun Li Abstract Two novel cyclen copper(II) complexes bridged by ferrocene were designed and synthesized. Both of these complexes exhibited excellent cleavage ability towards plasmid DNA via an oxidative pathway without the presence of any additives. Cyclic voltammetry was used to investigate the electrochemistry characters of the interaction between the complexes and DNA. Agarose gel electrophoresis was carried out to study the DNA restriction ability of these complexes, and the results indicated that the complexes showed higher cleavage efficiency via an oxidative pathway without the presence of any additives. The mechanism of DNA cleavage catalyzed by these complexes was examined by the addition of various scavengers, and the results showed that singlet oxygen and hydroxyl radical might be responsible for the cleavage process. Copyright © 2008 John Wiley & Sons, Ltd. [source] Interleukin-1 receptor antagonist and tumour necrosis factor-alpha gene polymorphisms in Turkish patients with allergic contact dermatitisCONTACT DERMATITIS, Issue 2 2009Ilgen Ertam Background: It has been shown that the family of interleukin-1 receptor antagonist (IL-1 RA) and tumour necrosis factor-alpha (TNF,) genes are polymorphic and related to some inflammatory diseases. Allergic contact dermatitis is the classic presentation of delayed-type hypersensitivity responses to exogenous agents. A number of genes playing role in inflammatory response may be associated with allergic contact dermatitis. Objectives: To investigate whether there is an association between IL-1RA and TNF, gene polymorphisms and allergic contact dermatitis in Turkish patients with allergic contact dermatitis. Methods: This study was performed by the collaboration of Departments of Dermatology and Medical Genetics, Ege University, Faculty of Medicine. A total of 50 patients (31 females and 19 males) with allergic contact dermatitis, and 100 age- and sex-matched controls (58 females and 42 males) were included in the study. IL-1RA Variable Number of Tandem Repeats (VNTR) polymorphism in intron 2 and TNF,-308G-A polymorphism were genotyped by using polymerase chain reaction and agarose gel electrophoresis. Results: The frequency of IL-1RA 1/2 (48%) genotype was significantly higher (P = 0.002) in patient group than that is found in control group (22%). The frequency of TNF, (TNF G-308A) G/G genotype was significantly higher in patient group (68%) than that is found in control group (31%) (P = 0.008). Conclusions: Our findings suggest that TNF, (G/G) gene polymorphism may play role in susceptibility to allergic contact dermatitis in Turkish patients. [source] "In-gel patch electrophoresis:" A,new method for environmental DNA purificationELECTROPHORESIS, Issue 16 2005Changhyun Roh Abstract Most of the microorganism species are largely untapped and could represent an interesting reservoir of genes useful for biotechnological applications. Unfortunately, a major difficulty associated with the methods used to isolate environmental DNA is related to the contamination of the extracted material with humic substances. These polyphenolic compounds inhibit the DNA processing reactions and severely impede cloning procedures. In this work, we describe a rapid, simple, and efficient method for the purification of genomic DNA from environmental samples: we added a chromatography step directly embedded into an agarose gel electrophoresis. This strategy enabled the DNA extraction from various environmental samples and it appeared that the purity grade was compatible with digestion by restriction enzymes and polymerase chain reaction (PCR) amplifications. [source] Vertical agarose gel electrophoresis and electroblotting of high-molecular-weight proteinsELECTROPHORESIS, Issue 11 2003Chad M. Warren Abstract The electrophoretic separation of high-molecular-weight proteins (>,500 kDa) using polyacrylamide is difficult because gels with a large enough pore size for adequate protein mobility are mechanically unstable. A 1% vertical sodium dodecyl sulfate (SDS)-agarose gel electrophoresis (VAGE) system has been developed that allows titin (a protein with the largest known SDS subunit size of 3000,4000 kDa) to migrate over 10 cm in a ,13 cm resolving gel. Such migration gives clear and reproducible separation of titin isoforms. Proteins ranging in size from myosin heavy chain (,,220 kDa) up to titin can be resolved on this gel system. Electroblotting of these very large proteins was nearly 100% efficient. This VAGE system has revealed two titin size variants in rabbit psoas muscle, two N2BA bands in rabbit cardiac muscle, and species differences between titins from rat and rabbit muscle. Agarose electrophoresis should be the method of choice for separation and blotting of proteins with very large subunit sizes. [source] The prothrombin gene is expressed in the rat kidneyFEBS JOURNAL, Issue 1 2000Implications for urolithiasis research There is considerable interest in determining the role of prothrombin fragments, especially urinary prothrombin fragment 1 (UPTF1), in the pathogenesis of calcium oxalate (CaOx) urinary calculi. This fragment is present in abundance in the matrix of CaOx crystals generated in human urine in vitro and has also been detected in human urinary stones containing calcium. More recently, prothrombin gene expression has been reported in the human kidney. However, studies examining the renal biosynthesis of prothrombin or perhaps only its fragments during experimental lithogenesis, and in consequence, the role of UPTF1 in stone formation, cannot be carried out in humans. The aim of this investigation therefore was to determine whether prothrombin gene expression is present in the rat kidney. Total RNA was isolated from the kidneys and livers of 12 rats. Using reverse transcriptase PCR, mRNAs corresponding to the thrombin and fragment 1 + 2 (F1+2) regions of prothrombin were analysed by agarose gel electrophoresis. The expression of glyceraldehyde 3-phosphate dehydrogenase was also examined to determine whether the quality of the tissue mRNAs was adequate for analyses. The amplified products were identified by sequence analysis. All kidneys displayed evidence of expression of the thrombin and F1+2 domains of the prothrombin gene. Furthermore, the sequences of these PCR-derived products from kidney were identical to those from liver. This suggests that the prothrombins secreted by these two organs are identical. The fact that prothrombin biosynthesis occurs in both the human and rat kidney presents an opportunity for using established rat models of stone disease to evaluate the influence of lithogenic conditions on prothrombin gene expression, and the potential role of UPTF1 in vivo. [source] Isolation of DNA from genetically modified oils by fast protein liquid chromatographyINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 7 2010Li Huang Summary In this study, a novel method of fast protein liquid chromatography (FPLC) anion exchange chromatography was developed for isolation of DNA from processed genetically modified (GM) oils. Four kinds of different GM edible oil had been chosen as model sample. Salmon DNA was used as the control sample to determine the pH values and NaCl in mobile phase buffer. Applying pH 8 and NaCl gradient 0.5,2 m were chosen for the DNA isolation. The quality and purity of isolated DNA were tested with agarose gel electrophoresis, scanned with UV absorbance spectra and amplified by polymerase chain reaction (PCR). The result indicated that the quantity of DNA isolated by FPLC was suitable for further PCR analyses. Furthermore, it is more effective and less time-consuming in comparison with cetyltrimethylammonium bromide method and High Pure GMO Sample Preparation Kit method. [source] Anti-Fenton reaction activity of three taxa of water yam (Dioscorea alata L.)INTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 9 2007Tsu-Shing Wang Summary In the present study, we compared the anti-Fenton reaction activity of three taxa of water yam (Dioscorea alata L.): DS2, TN2 and PSY [D. alata L. var. purpurea (Roxb.) M. Pouch]. Anti-Fenton reaction activity was evaluated by measuring the damage inflicted on calf thymus DNA by copper ions combined with hydrogen peroxide with the use of an ethidium bromide binding assay and agarose gel electrophoresis. We found that extracts of tuber pulp from all three taxa of yam had significant anti-Fenton reaction activity. The protection pattern of the three tuber pulp extracts was similar to that of EDTA, a typical divalent metal ion chelator, which displayed a significant protection lag-phase. With the use of thin-layer chromatography, we found that a common, major ansialdehyde-sulphuric acid stained spot (possibly a polysaccharide mucilage) with an Rf of 0.09 may be the most likely contributor to the anti-Fenton reaction activities of the yam tuber extracts investigated. The present study identifies the mechanism of the health benefit of the Dioscorea family. The copper-chelating and absorbing capability of yam tuber pulp extracts may be useful in functional screening. [source] Distribution of type III secretion systems in Vibrio parahaemolyticus from the northern Gulf of MexicoJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2010N.F. Noriea III Abstract Aims:, Two well-characterized Vibrio parahaemolyticus pathogenicity factors , thermostable direct haemolysin (TDH) and TDH - related haemolysin , are produced by strains containing the tdh and trh genes, respectively. Most strains of V. parahaemolyticus contain two nonredundant type III secretion systems (T3SS), T3SS1 and T3SS2, both of which contribute to pathogenicity. Furthermore, a recent study has revealed two distinct lineages of the V. parahaemolyticus T3SS2: T3SS2, and T3SS2,. The aim of this study was to determine the incidence of these pathogenicity factors in environmental isolates of V. parahaemolyticus. Methods and Results:, We collected 130 V. parahaemolyticus isolates (TCBS agar) containing tdh and/or trh (determined by colony hybridization) from sediment, oyster and water in the northern Gulf of Mexico and screened them and 12 clinical isolates (PCR and agarose gel electrophoresis) for pathogenicity factors tdh, trh, T3SS1, T3SS2, and T3SS2,. The majority of potential pathogens were detected in the sediment, including all tdh,/trh+ isolates. T3SS2, components were detected in all tdh+/trh, isolates and zero of 109 trh+ isolates. One T3SS2, gene, vopB2, was found in all tdh+/trh, clinical strains but not in any of the 130 environmental strains. Fluorescence in situ hybridization adapted for individual gene recognition (RING-FISH) was used to confirm the presence/absence of vopB2. T3SS2, was found in all tdh,/trh+ isolates and in no tdh+/trh, isolates. Conclusions:, The combination of haemolysins found in each isolate consistently corresponded to the presence and type of T3SS detected. The vopB2 gene may represent a novel marker for identifying increased virulence among strains. Significance and Impact of the Study:, This is the first study to confirm the presence of T3SS2, genes in V. parahaemolyticus strains isolated from the Gulf of Mexico and one of the few that examines the distribution and co-existence of tdh, trh, T3SS1, T3SS2, and T3SS2, in a large collection of environmental strains. [source] The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLPJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004C. Whitby Abstract Aims:, To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. Methods and Results:, Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. Conclusions:, Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1,16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. Significance and Impact of the Study:, This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment. [source] Aging Increases the Interleukin-1,,Induced INOS Gene Expression and Nitric Oxide (NO) Production in Vascular Smooth Muscle CellsJOURNAL OF CARDIAC SURGERY, Issue 6 2002Gabriel HH Chan Objectives: Inducible form of nitric oxide synthase (iNOS) is induced by cytokines (e.g. interleukin-1, (IL-1,)) during pathological conditions, such as sepsis. Excessive NO synthesis in blood vessels during sepsis can result in massive vasodilation and life-threatening hypotension. In addition, chronic expression of iNOS contributes to onset of diabetes, autoimmune diseases, arthritis, renal toxicity, and neurodegenerative disorders. The purpose of the present study was to examine the effect of aging on the levels of expression of iNOS induced by a low concentration (5 ng/ml) of IL-1, in VSMCs. Methods: Gene expression of iNOS was determined by RT-PCR and analysis of the PCR products by both agarose gel electrophoresis and capillary electrophoresis with laser-induced fluorescence detector (CE-LIF). This new CE-LIF technique, just developed in our laboratory, provides greater than 1,000 fold better sensitivity compared to agarose gels. The production of nitrite, the stable metabolite of NO, was measured (by a modified Griess reaction) in the media of cultured VSMCs isolated from young and elderly rats (3-month and 20-months old, respectively) of both genders following the exposure to IL-1, (5 ng/ml). VSMCs were used in their 1st passage to avoid phenotypic changes that typically occur in cultures of VSMCs after 3-10 passages. Results: IL-1, (5 ng/ml) caused a much larger increase in iNOS mRNA in VSMCs of elderly rats as compared to young rats. Furthermore, IL-1, (5 ng/ml) had no significant effect on nitrite levels in VSMCs of young, but significantly increased nitrite levels by 7.9 fold in VSMCs from elderly male rats and by 2.6 fold in VSMCs from elderly female rats, as compared to young rats. A report had previously shown that the neuropeptide CGRP could synergistically enhance the expression of iNOS caused by IL-1, in later passages (10-15 passages) of rat aortic VSMCs (i.e. phenotypically modulated VSMCs). We found that IL-1, and CGRP together did not act synergistically to increase production of nitrite in our phenotypically normal (1st passage) VSMCs. Conclusion: IL-1,, at a low concentration (5 ng/ml), preferentially induces iNOS expression and increases production of NO in VSMCs of elderly rats as compared to young rats. The data suggest that aging enhances the responsiveness of VSMCs to the iNOS-inducing actions of the cytokine IL-1,. This may be a contributing factor in the increased risk of developing severe hypotension in elderly patients with sepsis. (Supported by a Direct Grant for Research). [source] Psychosine-induced apoptosis and cytokine activation in immune peripheral cells of Krabbe patients,JOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2007Patrizia Formichi Globoid cell leukodystrophy or Krabbe disease (KD), is a hereditary disorder caused by galactosylceramidase deficiency. Progressive accumulation of psychosine is considered to be the critical pathogenetic mechanism of cell death in the Krabbe brain. Psychosine mechanism of action has not been fully elucidated. It seems to induce apoptosis in oligodendrocytes through a mitochondrial pathway and to up-regulate inflammatory cytokines production resulting in oligodendrocyte loss. Our aim was to evaluate the role of psychosine in apoptotic cell death and inflammatory response in a group of patients affected by KD using peripheral blood lymphocytes (PBLs) and peripheral blood mononuclear cells (PBMCs) as a cellular model. PBLs from KP and healthy controls were exposed to 20 µM psychosine and analysed by flow cytometry, agarose gel electrophoresis and fluorescence microscopy. Our results showed that psychosine induces apoptosis in PBLs through a mitochondrial pathway, but the apoptotic response was quite low especially KP. The role of psychosine in the up-regulation of cytokines (TNFalpha, IL8 and MCP1) has been evaluated by ELISA in PBMCs from KP and controls after stimulation with LPS and phytohemagglutinin. Both in basal condition and after LPS stimulation, cells from KP showed a significant increase in TNF-, production, reduced MCP1 levels and no modification in IL8. These results indicate that lymphomonocytes from KP had a basal proinflammatory pattern that was amplified by psychosine. In conclusion, the reduced apoptotic response and the atypical cytokine production observed in our experiments, suggest an involvement of inflammatory pattern in immune peripheral cells of KP. J. Cell. Physiol. 212:737,743, 2007. © 2007 Wiley-Liss, Inc. [source] Rapid detection of bordetella pertussis by real-time PCR using SYBR green I and a LightCycler instrumentJOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 5 2004S. K. Poddar Abstract A polymerase chain reaction (PCR) assay in real-time for detection of B. pertussis using SYBR green I as the reporter fluorophore and LightCycler instrument (a thermocycler coupled to a fluorescence detection device) was established and evaluated. The amplified amplicon using series diluted control prototype strain (ATCC strain #9797) of B. pertussis was analyzed for the fluorescent melting profile, and melting temperature (Tm) was determined. When examined, amplicons using a representative set of clinical isolates of B. pertussis were found to have the same Tm value (86 ± 0.5°C, the specificity parameter of detection) as the control prototype strain as expected. Amplified product was also analyzed and detected by agarose gel electrophoresis. The detection limit by fluorescent profile and Tm analysis was 10-fold better than that detected by agarose gel analysis. J. Clin. Lab. Anal. 18:265,270, 2004. © 2004 Wiley-Liss, Inc. [source] Association of interleukin-1 receptor antagonist gene polymorphisms with early onset periodontitis in JapaneseJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 10 2002Hideaki Tai Abstract Background/Aims: Early onset periodontitis (EOP), newly ,aggressive periodontitis', is considered to have genetic basis, which have not been clearly defined. The interleukin-1 (IL-1) gene cluster polymorphism as one of genetic factors may influence the expression of several chronic inflammatory diseases. The aim of this study is to investigate the frequency of single nucleotide polymorphisms (SNPs) in the genes encoding IL-1,, IL-1, and a variable number of tandem repeat (VNTR) polymorphisms in the IL-1 receptor antagonist gene (IL-1RN) in 47 generalized EOP (G-EOP) patients and 97 periodontally healthy controls. Material and methods: All subjects were of Japanese descent and systemically healthy. They were identified according to established clinical criteria. SNPs in the IL-1, (+ 4845) and IL-1, (, 511, + 3954) genes were analyzed by amplifying the polymorphic region using polymerase chain reaction (PCR), followed by restriction-enzyme digestion and agarose gel electrophoresis. IL-1RN (VNTR) polymorphisms were then detected by PCR amplification and fragment size analysis. Results: There was no significant difference in the IL-, (+ 4845) and IL-1, (, 511, +,3954) genotypes and allele frequencies between G-EOP patients and healthy controls. However, the frequency of IL-1RN (VNTR) polymorphic alleles was found to be significantly increased in G-EOP patients (,2 test, P = 0.007; odds ratio = 3.40). Additionally, the carriage rate of IL-1RN (VNTR) polymorphisms was significantly higher in G-EOP patients than in healthy controls (,2 test, P = 0.005; odds ratio = 3.81). Conclusion: These findings suggest that IL-1RN (VNTR) polymorphisms are associated with G-EOP in Japanese. [source] Association of low density lipoprotein receptor related protein-associated protein (LRPAP1) gene insertion/deletion polymorphism with gallstone diseaseJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 5 2006MANJUSHA DIXIT Abstract Background and Aim:, Gallstones are byproducts of cholesterol supersaturated bile. Various studies have indicated that there might be a genetic predisposition to the disease. Receptor-associated protein (RAP) is a molecular chaperone for low density lipoprotein receptor-related protein (LRP), which plays a key role in cholesterol metabolism. Intron 5 insertion/deletion polymorphism of RAP gene (LRPAP1) has been implicated in other diseases sharing etiology with gallstone disease (GSD). Methods:, To analyze the association of insertion/deletion polymorphism in GSD, 130 gallstone patients and 202 healthy subjects took part in the present study. For genotyping, polymerase chain reaction was followed by 2% agarose gel electrophoresis. Results:, The results showed that frequencies of D and I allele were 65.77% and 34.23% in patients, 76.24% and 23.76% in controls, respectively. Frequency of I allele was significantly higher in the patient group than in the control group (P = 0.003). Conclusion:, In the present study I (insertion) allele was found to be associated with GSD. [source] Effect of berberine on proliferation, cell cycle and apoptosis in HeLa and L1210 cellsJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 8 2003a Jantová Previous studies on the anticancer activity of protoberberine alkaloids against a variety of cancer cell lines were extended to human tumour HeLa and murine leukemia L1210 cell lines. An attempt was also made to investigate the relationship between the cytotoxic activity of berberine and its molecular mechanism of action. Cytotoxicity was measured in-vitro using a primary biochemical screening according to Oyama and Eagle, and the growth inhibition assay. The in-vitro cytotoxic techniques were complemented by cell cycle analysis and determination of apoptotic DNA fragmentation in L1210 cells. Berberine acted cytotoxically on both tumour cell lines. The sensitivity of leukemia L1210 cells to the berberine was higher than that of HeLa cells. The IC100 was below 100 ,g mL,1 for HeLa cells and approached a 10 , mL,1 limit for the leukemia L1210 cells. For both cell lines the IC50 was found to be less than 4 ,g mL,1, a limit put forward by the National Cancer Institute (NCI) for classification of the compound as a potential anticancer drug. In L1210 cells treated with 10,50 , mL,1 berberine, G0/G1 cell cycle arrest was observed. Futhermore, a concentration-dependent decrease of cells in S phase and increase in G2/M phase was detected. In addition, apoptosis detected as sub-G0 cell population in cell cycle measurement was proved in 25,100 ,g mL,1 berberine-treated cells by monitoring the apoptotic DNA fragmentation (DNA ladder) using agarose gel electrophoresis. [source] Identification of novel sequence variants in the neurofilament-light gene in a Japanese population: analysis of Charcot-Marie-Tooth disease patients and normal individualsJOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 4 2002Tsuyoshi Yoshihara Abstract Mutations of the neurofilament-light (NEFL/NF-L) gene were examined in 124 unrelated Japanese patients with Charcot-Marie-Tooth disease (CMT) without known gene mutations, and 248 normal Japanese individuals. A new method, which can detect basepair mismatches with RNase cleavage on agarose gel electrophoresis, coupled with DNA sequencing, identified 8 novel sequence variations in the NF-L gene. In these sequence variants, 5 variants were polymorphisms, including 3 single nucleotide polymorphisms (SNPs), and 3 other missense mutations (Pro22Thr, Asn97Ser and Ala148Val) were found in the patients with CMT phenotype. The variant alleles in the NF-L gene could influence the developing process of CMT phenotype and also might cause CMT phenotype. [source] HCV-RNA In Sural Nerve From Hcv Infected Patients With Peripheral NeuropathyJOURNAL OF THE PERIPHERAL NERVOUS SYSTEM, Issue 1 2001L De Martino Objective: Evaluation of hepatitis C virus (HCV) by reverse transcription-polymerase chain reaction (RT-PCR) in peripheral nerve tissues from HCV infected patients with peripheral neuropathy. METHODS: RT-PCR was performed on homogenates of nerve biopsies from 17 consecutive HCV-positive patients with peripheral neuropathy, with or without mixed cryoglobulinemia, hospitalised from 1996 to 2000. Sural nerve specimens were frozen in iso-pentane pre-cooled in liquid nitrogen and stored at ,80°C until use. RNA was extracted from ten 7-,m thick cryostatic sections or from a nerve trunk specimen of about 3 mm length, collected from each biopsy. Three different protocols of RNA extraction were tested (1,3). Complementary DNAs (cDNAs) were obtained without or with RNasin (Promega, Madison, WI) addition in the reaction mixture to inhibit residual RNase activity. Two sets of commercially available PCR primers for the outer and the nested reaction were used. PCR products were analysed by agarose gel electrophoresis and ethidium bromide staining. Serum samples and liver specimens from proven HCV positive patients served as positive controls, whereas sera from healthy subjects were negative controls. RESULTS: Sufficient amount of RNA could be obtained either by cryostatic sections or by in toto nerve specimens. Extraction by Trizol (Gibco-BRL) allowed the best concentration and purity of RNA as assessed by biophotometry. The presence of RNasin didn't improve the cDNA synthesis. The resulting amplification product of the nested PCR was 187 bp long. We have always observed this product in our positive controls and never in the negative. Six samples from patients either with or without cryoglobulinemia resulted positive; 7 were negative. Four samples gave variable results. CONCLUSIONS: While 40% of the nerves in our series were undoubtedly HCV positive, the cause(s) of negative and variable results in the remaining samples is likely more complex than variations in the detection protocols and deserve further investigations. REFERENCES: 1) Chomczynski P, Sacchi N (1987). Anal Biochem 162:156. 2) Marquardt O et al. (1996). Med Microbiol Lett 5:55. 3) Chomczynski P (1993). Bio/Techniques 15:532. [source] Comparison of three DNA extraction methods for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp. aviumLETTERS IN APPLIED MICROBIOLOGY, Issue 1 2008A. Amaro Abstract Aims:, To compare three methods for DNA extraction from Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp. avium. Methods and Results:, The DNA was extracted from mycobacterial cultures using enzymatic extraction, combined bead beating and enzymatic extraction and cetyltrimethylammonium bromide (CTAB) extraction. The yield and quality of DNA were compared by spectrophotometry, agarose gel electrophoresis, restriction endonuclease analysis and PCR. The combined bead beating and enzymatic extraction method yielded more DNA. However, that method produced some sheared DNA, visible either by agarose gel electrophoresis or by restriction endonuclease analysis. All methods were appropriate for PCR amplification of a 123 bp fragment of IS6110 in M. bovis and M. tuberculosis, and of a 1700 bp fragment of FR300 region in M. avium avium. Conclusions:, Combined bead beating and enzymatic extraction method was the most efficient and easy method for extracting DNA from bacteria of the M. tuberculosis complex. Significance and Impact of the Study:, The results reveal important differences among the DNA extraction methods for mycobacteria, which are relevant for the success of further downstream molecular analysis. [source] Novel Hyaluronan-Based Nanocarriers for Transmucosal Delivery of MacromoleculesMACROMOLECULAR BIOSCIENCE, Issue 5 2008María de la Fuente Abstract The goal of this work was to design a new nanocarrier composed of the glycosaminoglycan hyaluronan and the polysaccharide chitosan, intended for the transmucosal delivery of macromolecules. The nanoparticles were characterized for their size and superficial charge. The incorporation of hyaluronan was verified by agarose gel electrophoresis and Fourier transform infrared (FT-IR) spectroscopy. The ability of the nanosystems to encapsulate macromolecules was studied taking the hydrophilic protein bovine serum albumin (BSA) and the hydrophobic polypeptide Cyclosporine A (CyA) as models. Results showed that the experimental conditions could be conveniently adjusted in order to modulate the physicochemical properties of the carriers and their composition. Moreover, the nanoparticles provided high association efficiencies of the selected macromolecules. [source] A set of primers for amplification of mitochondrial DNA in Picea abies and other conifer speciesMOLECULAR ECOLOGY RESOURCES, Issue 4 2002S. Jeandroz Abstract Thirteen primer pairs generating intraspecific length and/or presence-absence polymorphism in Picea abies have been obtained from a P. abies mtDNA library, using different methodologies (agarose gel electrophoresis, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), single-strand conformation (SSCP). Poly-morphism tests were extended successfully to other Picea species (P. omorika, P. engelmanii and P. glauca) and species belonging to other conifer genera (Abies alba, Larix laricina and Pinus pinaster). This set of PCR-based mitochondrial markers can provide promising tools for studying phylogeography or phylogeny in P. abies and other conifer species in which the mt genome is generally the only one to be transmitted via the female gamete. [source] MUC2, MUC5AC and MUC5B in the mucus of a patient with pseudomyxoma peritonei: Biochemical and immunohistochemical studyPATHOLOGY INTERNATIONAL, Issue 8 2007Anwar S. Mall A 58-year-old man with a 1 year history of progressive abdominal distension underwent a laparotomy for pseudomyxoma peritonei. The mucin was identified and characterized in the present study. Approximately 6 L of crude mucus in the sol (highly viscous) and gel (semisolid) phases was obtained from the patient's peritoneal cavity. The sol material was briefly homogenized followed by slow stirring at dilutions of up to 1:10 with 6 mol/L guanidinium chloride and proteolytic inhibitors for periods of up to 48 h. Preparative and analytical gel filtration on Sepharose 2B showed some PAS-positive material eluting in the void volume accompanied by equal or larger amounts of protein in the void and included volumes of the columns. Sodium dodecylsulfate,polyacrylamide gel electrophoresis of purified mucin on a 4,20% gradient gel showed PAS-positive material on the top of the running gel and a distinct smaller-sized species of mucin of higher electrophoretic mobility with background material in between the large and small mucin. Western blot (confirmed by immunohistochemical analysis) after agarose gel electrophoresis showed the presence of MUC2, MUC5AC and MUC5B in the mucus. There was no MUC1, MUC1core or MUC6 in the tissue. Histopathological examination confirmed a mucinous appendicular adenocarcinoma. Histology showed the mucin to be predominantly of the sulfated and non-sulfated acidic type. Serine, threonine and proline comprised 21.6% of the total amino acid composition of the sample. The viscous nature of the material is due to the presence of three gel-forming mucins and possibly to its high content of protein. [source] Molecular characterization of sickle cell anemia in the Northern Brazilian state of ParáAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 5 2010Greice De Lemos Cardoso To assess ,+-thalassemia deletion alleles, ,-thalassemia mutations and haplotypes linked to the HBB*S cluster in a sample of 130 unrelated sickle cell anemia (SCA) patients (55% female) from Belém, Pará State, for their possible effects on the patients' survival. -,3.7, -,42, -,20.5, and ,MED ,+-thalassemia deletion alleles were investigated using multiplex gap-PCR method. Characterization of ,-thalassemia mutations was made by direct genomic sequencing of the ,-globin gene amplified through polymerase chain reaction (PCR). Haplotypes were determined by analysis of six polymorphic restriction sites [(1) XmnI-5,,G, (2) HindIII-,G, (3) HindIII-,A, (4) HincII-,,, (5) HincII-3,,,, and (6) HinfI-5,,] followed by restriction digestion and agarose gel electrophoresis. Twenty-one patients (16%) presented -,3.7 thalassemia. Sixteen of those (76%) were heterozygous (-,3.7/,,) and 5 (24%) were homozygous (-,3.7/-,3.7). -,4.2, -,20.5 and ,MED deletions were not found. Nine cases of sickle cell-, thalassemia were found and four different ,-thal mutations were identified: ,+ ,88 (C>T), 3.8%; ,+ codon 24 (T > A), 1.5%; ,+ IVSI-110 (G > A), 0.7% and , (IVSI-1 (G > A), 0.7%. No differences according to age were observed in -,3.7 deletion, ,-thalassemia and HHB*S haplotypes distribution. Our results suggest that although ,- and ,-thalassemia and ,S haplotypes may have modulating effect on clinical expression and hematological parameters of SCA, these genetic variables probably have little influence on the subjects' survival. Am. J. Hum. Biol. 22:573,577, 2010. © 2010 Wiley-Liss, Inc. [source] Antitumor activity of chloroform fraction of Scutellaria barbata and its active constituentsPHYTOTHERAPY RESEARCH, Issue 9 2007Jianqing Yu Abstract Scutellaria barbata (SB) is widely used as an antitumor agent in China, but the antitumor components of SB are still unclear. The antitumor activity of various fractions of an ethanol extract of SB was studied in six human malignant cell lines. Bio-based assays showed that non-polar and low-polar solvent fractions of SB had dose-dependent cytotoxicities on six cancer cell lines. The IC50 values of these fractions on the cancer cell lines tested ranged from 16 to 70 µg/mL after 48 h of treatment. Among them, the chloroform fraction (CE-SB) had the strongest cytotoxicity on cancer cell lines with a lower cytotoxic effect on a normal liver cell line. Bel-7402 cell apoptosis induced by CE-SB was examined using Hoechst 33258 staining, agarose gel electrophoresis and flow cytometry. CE-SB dose-dependently decreased the S phase content. Treatment with CE-SB caused cytochrome c release and activation of caspase-9. The antitumor activity of CE-SB in vivo was also evaluated. At 60 mg/kg/day, CE-SB significantly inhibited the solid tumor proliferation and increased the life span of ascites tumor bearing mice (p < 0.01). CE-SB was subjected to bioassay-guided isolation of the active compounds by chromatography on silica gel and Sephadex LH-20. Phytol, wogonin, luteolin and hispidulin were obtained as cytotoxic constituents. Copyright © 2007 John Wiley & Sons, Ltd. [source] Rotundifuran, a labdane type diterpene from Vitex rotundifolia, induces apoptosis in human myeloid leukaemia cellsPHYTOTHERAPY RESEARCH, Issue 6 2001W. G. Ko Abstract The inhibitory effect of rotundifuran, a labdane type diterpene isolated from the fruit of Vitex rotundifolia, on the proliferation of human myeloid leukaemia HL-60 cells was examined. The concentration required for 50% inhibition of the growth after 96,h was 22.5,µM. The mode of cell death induced by rotundifuran was found to be apoptosis, which was judged by the morphological alteration of the cells and by the detection of DNA fragmentation using agarose gel electrophoresis. The degree of apoptosis was quantified by a sandwich enzyme immunoassay and flowcytometric analysis. These results suggest that rotundifuran may be used as a potential chemopreventive and chemotherapeutic agent. Copyright © 2001 John Wiley & Sons, Ltd. [source] Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2002Mike Manefield An ongoing challenge within microbial ecology is the development of methodologies that attribute microbial community functions to microbial diversity. One approach, involving the incorporation of stable isotopes from labelled tracer compounds into biological signature molecules (biomarkers), may overcome this current limitation. To examine the potential of RNA as the biomarker in stable isotope probing we have generated a series of atom % 13C-enriched RNA samples through exploitation of the anabolic abilities of a phenol-degrading environmental isolate. Isotope ratio mass spectrometry was used to determine the atom % 13C of each RNA sample (ca. 1,100%). The corresponding buoyant density (1.755,1.795,g,mL,1) was determined by equilibrium density gradient centrifugation and agarose gel electrophoresis. This empirically defined relationship between the atom % 13C of RNA and its buoyant density suggests ribonucleic acids with atom % 13C enrichments greater than 10% can be isolated by equilibrium density centrifugation. The processing and analysis of isolated RNA by reverse transcription polymerase chain reaction, denaturing gradient gel electrophoresis, cloning and sequencing are discussed. The RNA-based stable isotope probing protocol presented here will find particular utility in assessing the roles of microbial community members in the biodegradation of natural and anthropogenic xenobiotic compounds. Copyright © 2002 John Wiley & Sons, Ltd. [source] Sex Identification of the Black Swan (Cygnus atratus) using the Locus-specific PCR and Implications for its ReproductionREPRODUCTION IN DOMESTIC ANIMALS, Issue 3 2005P-J He Contents Over the last 4,5 years the small captive population of black swans (Cygnus atratus) has consistently failed to reproduce at the Chengdu Research Base of Giant Panda Breeding. The probable cause was hypothesized to be an abnormal sex distribution of the population. The black swan is an example of a sexually monomorphic species. The locus-specific polymerase chain reaction (PCR) approach based on the chromo-helicase-DNA-binding 1 (CHD1) gene, was adopted for the sex determination of the black swans. For this purpose, F1, F2 and R primers were designed using the primerselect software for amplification of the CHD1 gene region. DNA agarose gel electrophoresis showed that the female control displayed two bands, whereas only a single band was found in the male control. Sequence analyses of all seven unknown sex black swans demonstrated the sex-specific DNA band for female. Therefore, it was inferred that all the individuals of the black swan population are females, which has resulted in unfertilized eggs and reproduction failure. This method can be extended to the sexing of other monomorphic avian species and will assist in the design of breeding projects. [source] Age-Related Mitochondrial DNA Mutations in the Human LarynxTHE LARYNGOSCOPE, Issue 12 2000Jose M. Manaligod MD Abstract Objective To determine whether age-related mitochondrial DNA mutations occur in the human larynx. Study Design Genetic study of cadaveric larynx specimens. Methods Vocal fold mucosa, thyroarytenoid muscle, and cricoarytenoid joint tissue were harvested from 13 fresh postmortem larynges (age range, 2 d,82 y). DNA was extracted from each sample, and the polymerase chain reaction (PCR) was used to amplify a target DNA sequence resulting from the common age-associated, 4977,base-pair (bp) mitochondrial DNA deletion. PCR products were visualized by agarose gel electrophoresis. Automated sequencing determined the sequence of identified PCR products. Subjects Thirteen cadaveric larynges were obtained through the University of Kentucky Medical Center (Lexington, KY). Specimens from patients with a history of head and neck cancer, previous laryngeal trauma, or surgery were excluded. Results Strongly positive bands were identified in samples from three individuals. Weaker bands were seen in samples from four other samples. No band was noted from the two pediatric larynges. Different band patterns were seen among the three different tissue sites in the larynges with positive PCR products, but no consistent pattern was seen. Sequencing of the identified PCR products from selected samples confirmed that they were products of the age-associated, 4977-bp mitochondrial DNA deletion. Conclusions An age-associated mitochondrial DNA deletion was detected in several postmortem human larynges. Its presence seemed to increase in appearance with age. In the larynges in which the deletion occurred, there were individual regional differences in the occurrence of the deletion, but no consistent pattern was noted across all individuals who carried the deletion. [source] Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genesTHE PLANT JOURNAL, Issue 2 2002Gabino Ríos Summary To assist in the analysis of plant gene functions we have generated a new Arabidopsis insertion mutant collection of 90 000 lines that carry the T-DNA of Agrobacterium gene fusion vector pPCV6NFHyg. Segregation analysis indicates that the average frequency of insertion sites is 1.29 per line, predicting about 116 100 independent tagged loci in the collection. The average T-DNA copy number estimated by Southern DNA hybridization is 2.4, as over 50% of the insertion loci contain tandem T-DNA copies. The collection is pooled in two arrays providing 40 PCR templates, each containing DNA from either 4000 or 5000 individual plants. A rapid and sensitive PCR technique using high-quality template DNA accelerates the identification of T-DNA tagged genes without DNA hybridization. The PCR screening is performed by agarose gel electrophoresis followed by isolation and direct sequencing of DNA fragments of amplified T-DNA insert junctions. To estimate the mutation recovery rate, 39 700 lines have been screened for T-DNA tags in 154 genes yielding 87 confirmed mutations in 73 target genes. Screening the whole collection with both T-DNA border primers requires 170 PCR reactions that are expected to detect a mutation in a gene with at least twofold redundancy and an estimated probability of 77%. Using this technique, an M2 family segregating a characterized gene mutation can be identified within 4 weeks. [source] Homo- and heteropolynuclear copper(II) complexes containing a new diimine,dioxime ligand and 1,10-phenanthroline: synthesis, characterization, solvent-extraction studies, catalase-like functions and DNA cleavage abilitiesAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 12 2009Bülent Dede Abstract A series of homo-, heterodinuclear and homotrinuclear copper(II) complexes containing a new Schiff base ligand and 1,10-phenanthroline were synthesized. Based on results of elemental analyses, FTIR, 1H- and 13C-NMR spectra, conductivity measurements and magnetic susceptibility measurements, the complexes had general compositions {[Cu(L)(H2O)M(phen)2](ClO4)2 [M = Cu(II), Mn(II), Co(II)]} and {[Cu3(L)2(H2O)2](ClO4)2}. The metal:L:phen ratio is 2:1:2 for the dinuclear copper(II) complexes and the metal:L ratio was 3:2 for the trinuclear copper(II) complex. The liquid,liquid extraction of various transition metal cations [Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Pb(II), Cd(II), Hg(II)] from the aqueous phase to the organic phase was carried out using the diimine,dioxime ligand. It was concluded that the ligand can effectively be used in solvent extraction of copper(II) from the aqueous phase to the organic phase. Furthermore, catalytic activitiy of the complexes for the disproportionation of hydrogen peroxide was also investigated in the presence of imidazole. Dinuclear copper(II),manganese(II) complex has some similarity to manganese catalase in structure and activity. The interaction between these complexes and DNA has also been investigated by agarose gel electrophoresis; we found that the homo- and heterodinuclear copper complexes can cleave supercoiled pBR322 DNA to nicked and linear forms in the presence of H2O2. Copyright © 2009 John Wiley & Sons, Ltd. [source] | |||||||||||||||||||