Free

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

Comments (0) Cite this document
Summary
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…
Download full paperFile format: .doc, available for editing
GRAB THE BEST PAPER94% of users find it useful
Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic
Read TextPreview

Extract of sample "Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic"

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
Cite this document
  • APA
  • MLA
  • CHICAGO
(“Describe the 16SrDNA analysis and how it is interpreted with respected Essay”, n.d.)
Describe the 16SrDNA analysis and how it is interpreted with respected Essay. Retrieved from https://studentshare.org/biology/1498503-describe-the
(Describe the 16SrDNA Analysis and How It Is Interpreted With Respected Essay)
Describe the 16SrDNA Analysis and How It Is Interpreted With Respected Essay. https://studentshare.org/biology/1498503-describe-the.
“Describe the 16SrDNA Analysis and How It Is Interpreted With Respected Essay”, n.d. https://studentshare.org/biology/1498503-describe-the.
  • Cited: 0 times
Comments (0)
Click to create a comment or rate a document

CHECK THESE SAMPLES OF Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic

Bacterial transmission

...0. INTRODUCTION Bacterial transmission has been aided by contact with living organisms as well as by non-living. This is with respect to the ability of infectious organisms to flourish on inert surfaces (Ellis, 2006). According to Shrutz (2003) the microbes also thrive in the air below the 500 feet altitude including spores of Bacillus and Clostridium, algae, Micrococcus, Corynebacterium among others. Respiratory bacteria are mainly dispersed in the air through droplets of saliva and mucous produced when one coughs, sneezes, talks or laughs (Shrutz, 2003). According to Rutala et al. (2006), the microbes, which are freely present in the the air, can in most cases be evident on computer keyboards. In this...
11 Pages(2750 words)Thesis

Bacterial Meningitis - Pediatric

..., and obtaining daily weight to determine possible fluid retention and prevent cerebral edema. As shock is also possible to occur, the nurse continuously monitors vital signs, blood pressure, capillary refill, and level of consciousness in order to prevent the complication or quickly respond once it occurs. Seizures may be present in bacterial meningitis, thereby it is important to put the side rails up and place the bed in the lowest position possible to prevent falls. The family should also be educated on how to position the patient before, during, and after seizure episodes. Administering drugs on schedule according to the doctor’s order is important to eradicate the causative agent and diminish...
4 Pages(1000 words)Research Paper

Bacterial cells Quantification

...?The Effect of Lysozyme Solution on Micrococcus lysodeikticus Cell Counts Introduction Bacterial cell quantification is useful in many areas of biology, in that it allows us to know the number of cells, or the viable cell count. This information can be used in antibiotic sensitivity testing, or infection severity, for example. Bacterial cell quantification can be done in several ways, but this experiment will be using a spectrophotometer to measure the relationship between the bacterial cell concentration and the absorbance of light. Results using known concentrations are often used to find the cell count of an unknown solution, and this is what will be achieved here. Additionally, the...
4 Pages(1000 words)Lab Report

How should the second amendment be interpreted

...Amendment and how it should be interpreted Second Amendment was not included in the United States Constitution out of whim but rather as a product of their vision and prevailing circumstance during that time. The self-defense nature of the Second Amendment was borne out of the influences of classical liberal thinking among the Founders of the United States that citizens must be prepared to defend their society against any criminal usurpation or tyrannical ministers or the pillaging of any entity (Weighley 45). We have to note here that Founders of the US Constitution did not put the stewardship of society solely to government and its police powers but also to its citizenry to effectively guard and defend...
7 Pages(1750 words)Research Paper

John Stith Pemberton, Respected Pharmacist

...John Stith Pemberton, Respected Pharmacist (School) John Stith Pemberton, Respected Pharmacist JohnStith Pemberton was the inventor of several successful patent medicines in the 19th century, but his dream was to combine a tasty drink with a health tonic. In 1886, his dream came true with the development of Coca-Cola, one of the most popular non-alcoholic drinks of all time. In addition, he contributed to the field of pharmacy by making sure the various tonics he offered were legitimately helpful, which ultimately put an end to quack medicine and raised the standards of alternative medicine practices (John Pemberton, 2006; Our Georgia History, 2006; Hayes, 1996). Background Information Most research...
3 Pages(750 words)Essay

Molecular and Genomic Analysis of Bacterial Pathogenicity

...Molecular and Genomic Analysis of Bacterial Pathogeni Introduction "Analysis," in the Oxford dictionary, is defined as "resolution into simple elements." In genetic analysis we must be clear about what we resolve and into what simpler elements. Mainly as a consequence of the development of microbial genetics, genetic analysis has increased enormously its resolving power in recent years, so much so that it now goes beyond that of physical or chemical techniques applied to biological organization (Pontecorvo, 1958). The essential process on which genetic analysis is based is recombination. Consider the analogy with microscopy, which is based instead on diffraction. The resolving power attained in microscopy depends on the quality... of the...
13 Pages(3250 words)Essay

Bacterial Meningitis

...and the health practitioner must exert a high degree of suspicion to diagnose the condition. Some of the clinical features are fever or low body temperature, seizures, decreased intake of feeds, high irritability, persistent vomiting, lethargy and shrill cry (Mace, 283). In newborns, decreased breast feeding and lethargy may be the only clinical presentation. Neck rigidity may not be typical in younger children, infants and newborns. In meningococcal meningitis rash and splenomegaly may also be present ((Jacewicz, Merck Manual). Diagnosis Diagnosis of bacterial meningitis is established based on cerebrospinal fluid or CSF analysis. Typical CSF picture in bacterial meningitis is...
4 Pages(1000 words)Research Paper

Bacterial Meningitis

...Meningococcal disease Screening Program for Creig College Increasing number of college students, especially freshman residing in dormitories are infected by the meningococcal disease. In order to create better awareness about the disease among students, the college is conducting a screening program that will provide educational information (brochure) about meningitis to students and queries related to the symptoms and nature of the disease will be clarified. Follow-up after the screening program Students who attend the screening program will be referred to a local hospital for further screening and testing procedures. For further information about the disease contact the Creig College Health Services or log on to http... disease Screening...
2 Pages(500 words)Coursework

Bacterial Transformation

... Bacterial Transformation Historical Perspective The process of transformation was initially described by Fred Griffith in1928.Evidently, he demonstrated how characteristics could be acquires by living nonpathogenic bacteria from disease causing bacteria that were dead. Consequently, these eventually transform to disease producing ones. Later on, it was discovered that this principle was evident in DNA. Further discoveries showed that shreds of naked DNA can be accepted by natural bacteria within their environment. Furthermore, the dead bacteria of different species or the same can act as parent material for fragments of DNA. To this end, transformation entails the process in which DNA fragments are taken up by bacteria. Purpose... of...
4 Pages(1000 words)Term Paper

Bacterial Meningitis

...Bacterial Meningitis of the of the Infection of the membranes that enclose the spinal cord and the brain istermed meningitis. It can arise from bacterial, fungal or viral infections. Meningitis caused by bacteria is known as bacterial meningitis. It is a serious ailment that can result in the death of the patient. In general, it transpires in people who undergo a head injury or among individuals with a weakened immune system. This disease predominates among children and youth. Certain adults are also susceptible to develop this infection. Those who abuse alcohol, indulge in prolonged and deep kissing, suffer from chronic ear and nose infection, and who have contracted pneumococcal...
5 Pages(1250 words)Research Paper
sponsored ads
We use cookies to create the best experience for you. Keep on browsing if you are OK with that, or find out how to manage cookies.

Let us find you another Essay on topic Describe the 16SrDNA analysis and how it is interpreted with respected bacterial phylogentic for FREE!

Contact Us