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The Polymerase Chain Reaction and other molecular technologies were applied to isolate the DNA fragment reflecting the Open Reading Frame II of the I-18 C gene. This research object was realized and the importance of this result has been discussed in view of the mechanisms of the regulation of gene expression.
The technology for the preparation of the template in the research aimed to isolate the DNA fragment reflecting the Open Reading Frame II of the I-18 C gene is presented i.e. the linearisation of the template by Bam H I digestion, the purification of the template and the estimation of the template concentration.
To construct a genomic library of Veillonella parvula H2, total DNA was extracted, sheared by a Hydroshear machine, and the DNA fragments ligated a into Smal-digested vector pUC18 before being transformed into E. coli DH5a. Colonies were selected on Luria-Bertani (LB) plates containing ampicillin, 5-bromo-4-chloro-3-indoyl-3-galactose (X-gal), and isopropy-β-D-thiogalactoside (IPTG) and proliferated. Recombinant plasmids were analysed for the presence of inserted DNA fragments of 3-4 kb by restriction mapping. The titre of the library was determined to be 10⁵ pfu/mL according to the formula N=ln(l-p)/(l-f). The genomic library consisted of 99% of the genome of Veillonella parvula, demonstrating a successful library construction.
The chromosomal I-18 C region of Chironomus tentans contains the I-18 C gene. Two different open reading frames (i.e. the ORF I and II) of two different transcripts (i.e. the 1.8 kb and 4.6 kb RNA) of the I-18 C gene of Chironomus tentans were isolated, at the DNA level, by the Polymerase Chain Reaction, then were cloned into the bluescript vector and finally were cloned into the pET-3a vector in order to translate them in T7 RNA polymerase / promoter system of E. coli. It was possible to obtain the ORF I overexpressed. In a case of the ORF II the low molecular weight polypeptide was detected, however it was not overexpressed, but still this polypeptide was strongly visible on the SDS-polyacrylamide gel.
The technology used for the cloning of the open reading frame (ORF) I and II reflecting DNA fragments of the I-18 C gene in regard to the preparation of the intermediate vector i.e. the bluescript for the ligation with the ORF I and II reflecting DNA fragments, is presented. The main steps include the Eco RV digestion of the bluescript plasmid, the phenol / methylene chloride extraction of the plasmid, dephosphorylation of the bluescript plasmid and finally its extraction with the phenol and ethanol precipitation.
Different mechanisms of regulation regarding the Open Reading Frames (ORFs) have been discussed to have a broader perspective that is necessary to evaluate the role of the ORFs of the I-18 C gene. This consideration includes the ORF II of the I-18 C gene which is the object of the presented research.
The technology used to amplify and isolate the DNA fragment reflecting the Open Reading Frame II of the I-18 C gene of Chironomus tentans is described i.e. the Polymerase Chain Reactioin and the agarose gel electrophoresis of this reaction product, as well as the blunting reaction of the product and its isolation.
The level of polymorphism, genetic variability and relatedness of the Antarctic hairgrass Deschampsia antarctica Desv. Populations from South Shetlands Is. (King George I., Penguin I., Livingstone I.), from vicinity of Antarctic Peninsula (Galindez I., Uruguay I.), and Falklands Is. (Jason Is., Sealion I.) were studied using the AFLP approach. Six EcoRI/MseI type selective primer pairs combinations were used for AFLP profiling and amplified scoreable DNA fragments; than AMOVA and PCA were performed. The level of molecular variability among all individuals from all the analysed populations was low and reach only 5.4 % irrespective of the distance between the localities and it was not significant at a broader geographical scale, even among the three groups of populations (South Shetlands Is., vicinity of Antarctic Peninsula, and Falklands Is.). PCA analysis shows that all populations formed uniform groups according to their locations.
The I-18 C region of the polytenic chromosome of Chironomus tentans contains the I-18 C gene. Two DNA fragments, reflecting two different open reading frames (i.e.ORF I and II) of two different transcripts (i.e. 1.8 and 4.6 kb RNA) of the I-18 C gene were isolated, then were cloned into the intermediate vector and next to the final vector in order to translate them in T7 RNA polymerase / promoter system. The translation of the ORF I and II was performed to obtain the polypeptides of these ORFs for further study. Here, the scheme of the performed experiments and the applied technology that were necessary to realize the goal of this research, are presented.
The technology applied for the cloning of the open reading frame (ORF) I and II reflecting DNA fragments of the I-18 C gene of Chironomus tentans in regard to the preparation of the inserts for ligation with the bluescript and the modification of this intermediate vector, is described. The ORF I reflecting DNA fragment prepared for ligation with the bluescript vector, had one end blunt (i.e. the 5’ end with the Nde I restriction site) and the second end was sticky (i.e. the 3’ end after the Bam HI digestion of this insert). Subsequently, the bluescript vector for this ligation had also one end blunt (i.e. the 5’ end with the Nde I restriction site) and the second end was sticky (i.e. the 3’ end after the Bam HI digestion). The ORF II reflecting DNA fragment prepared for the ligation had both ends blunt and so the vector.
The above mentioned technology in a case of the DNA fragment reflecting the Open Reading Frame II of the I-18 C gene is described i.e. the primers design, purification and phosphorylation of the oligonucleotide primers.
Phenotypic approaches based on metabolic and biological characteristics of Corynebacterium pseudotuberculosis have been limited due to insufficient discrimination between closely related isolates. In this paper we present performance and convenience of three molecular typing methods: BOX-PCR, random amplification of polymorphic DNA (RAPD) and amplification of DNA fragments surrounding rare restriction site (ADSRRS-fingerprinting) in genome analysis of these bacteria. Among examined 61 strains there were distinguished four, eight and 10 different genotypes by BOX-PCR, RAPD and ADSRRS-fingerprinting, respectively. The value of discrimination index was the lowest for BOX-PCR (D = 0.265), much bigger for RAPD (D = 0.539) and the highest for ADSRRS-fingerprinting (D = 0.604). The good discriminatory ability and reproducibility of RAPD and ADSRRS-fingerprinting indicates that those techniques may be particularly applied for epidemiological studies of C. pseudotuberculosis isolates. We found that ADSRRS-fingerprinting is a rapid method offering good discrimination power, excellent reproducibility and may be applied for epidemiological studies of intraspecific genetic relatedness of C. pseudotuberculosis strains.
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