Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic - Essay Example

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Running head: Description of the 16SrDNA analysis and how it is interpreted with respected bacterial phylogenic Institution of Affiliation: Date: The 16SrDNA analysis It was shown in laboratories of Woese amongst others that phylogenetic relationship pertaining and, indeed, the entire forms of life could be determined via comparing a stable portion of the genetic code…
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Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic
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Running head: of the 16SrDNA analysis and how it is interpreted with respected bacterial phylogenic Institution of Affiliation: Date: The 16SrDNA analysis It was shown in laboratories of Woese amongst others that phylogenetic relationship pertaining and, indeed, the entire forms of life could be determined via comparing a stable portion of the genetic code. The portion of the DNA today used on most occasions for taxonomic reasons for bacteria is referred to as the 16SrRNA gene. This gene is also designated as 16SrDNA, where the two terms have been used interchangeably but now the ASM policy currently stipulates that 16SrRNA gene takes priority (Jill, 2004). The 16SrRNA gene has the ability to be compared not just among the entire bacteria but also can be compared with archeobacteria’s 16SrRNA and eucayotes’ 18SrRNA gene. With this understanding we can now delve into 16SrRNA gene sequence analysis. A commercial system (such as ABI; PrepMan DNA extraction reagent) or a standard method is used in extracting bacteria genomic DNA from whole cells. For the PCR the DNA is applies as a template to amplify a segment ranging about 500 or 1,500 bp relating to 16SrRNA gene sequence. Wide based or conventional primers complementary to preserved areas are utilized so that the area can be amplified from a given bacteria. The products of the PCR are purified to get rid of excess nucleotides and primers; a number of good commercial kits are present (e.g., Microcon-100 i.e. Microconncentrator columns [Millipore] and QiaQick PCR kit of purification [Qiagen]) (Jill, 2004). The following step is known as cycle sequencing. It is identical to PCR as it uses DNA (The first PCR cycle’s purified products) as the template. The two, reserve and forward sequences apply as templates in different reactions in which just the reverse or forward primer is used. A difference exist between PCR and Cycle sequencing as no new template is formed in the latter and the product involves a mixture of various lengths of DNA. This is attained by adding particularly labeled bases known as dye terminator, which, when incorporated randomly in this second cycle, they terminate the sequence (Janda & Abbott, 2007). Therefore, fragments of each magnitude are generated. Because every one of the four extra labeled terminator bases has dissimilar fluorescent dye, every of them absorbs at a dissimilar wavelength, the terminal base relating to every fragment can be determined via a fluorometer. Products are purified to get rid of unincorporated dye terminators, and using capillary electrophoresis or gel electrophoresis we determine the length of each product. Because we then understand the length as well as terminal base relating to every fragment, the bases’ sequences can be determined. The DNA’s two strands are sequenced dissimilarly, generating both reverse and forward (complementary) sequences (Janda & Abbott, 2007). The electropherogram, used for tracing detection of the fragments separated as they elute out of the column in which every base is represented via a dissimilar color, can be automatically or manually edited. It is probable to have fragments of several lengths thus well separated which each base of a 500-bp series can be determined. Electropherogram’s visual reediting can be used to resolve most of the ambiguities when they occur. How the 16SrDNA analysis is interpreted with respected bacterial phylogenic It is important that the quality of sequences is examined prior to using them. For instance, in a study that of strains of Actinomyces, sequences from Public database (GenBank-EMBL), a commercial database and the researcher’s internally generated databases were compared (Lang, Darling, & Eisen, 2013). The kind Actinomyces turicensis strain in the GenBank database as well as the 12 clinical strains which were sequenced indicated minimal (not any to two) dissimilarities as well as no ambiguous bases, showing that all were sequences of good quality. The sequence of the kind A. Meyeri’s strain from MicroSeq was of high quality also. Nonetheless, the kind A. gravaenitzii strain in the GenBank database came out of poorer quality, with sequenced (5%) 25 N’s in 500 bp. Therefore, it originally seemed that the phenotypically identical strains of A. gravaenitzii were genetically extra heterogeneous than the strains of A. turicensis, even though this might not be true. Even though most ambiguities have the ability of resolving a reediting of the initial electropherogram if present, there can also be circumstances in which it is impossible to decide a matchless base to a given position (Lang, Darling, & Eisen, 2013). Always this is due to some technical difficulty, e.g., the initial specimen was an impure culture, the labeled product yield was too low, or there was malfunctioning of the column. In the case of reference, there are always a number of unreadable bases and the entire sequencing procedure should be repeated. At the same time, there is a possibility that intracellular polymorphisms may result into problems in getting an effortlessly interpretable sequence; i.e., because there are 16SrRNA gene multiple copies within a single-cell genome, a possibility of existing numerous dissimilar sequences and therefore there could be two dissimilar base pairs at a particular location (Thomas, Gilbert, & Meyer, 2012). The presence of gene alleles of variant 16SrRNA in a single genome can be seen successfully demonstrated in several reports. In a nutshell for better interpretation of the 16SrRNA analysis one must understand the difficulties that may come up and how to resolve them. In so doing the results of the study in question becomes both valid and reliable for the scientific application intended. References Janda, J. M., & Abbott, L. S. (2007). 16SrRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls. Journal of Clinical Microbiology, 2761-2764. Jill, E. C. (2004). Impact of 16SrRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clinical Microbiology Review, 840-862. Lang, M. J., Darling, E. A., & Eisen, A. J. (2013). Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS ONE, 1371-1380. Thomas, T., Gilbert, J., & Meyer, F. (2012). Metagenomics - a guide from sampling to data analysis. Microbial Informatics and Experimentation , 2042-5783-2-3. Read More
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