READING A SCIENTIFIC PAPER FOR FORMAT AND FOR CONTENT
DUE in class Mar 12-14, Sp 2007 20 points PLEASE type and 1.5 space your answers.
"Ribosomal DNA Sequencing for Identification of Aerobic Gram-positive Rods in the Clinical Laboratory (an 18-month evaluation)." by P.P. Bosshard, S. Abels, R. Zbinden, E.C. Bottger, and M. Altwegg; Sept 2003; J Clinical Micro Vol 41: 4134-4140.
You may need to search outside sources to answer some questions. Make a copy for yourself so you can add comments as we discuss the paper.
Abstract

  • How would you define or describe an abstract\
  • What types of information do the authors include in their abstract?

Introduction

  • How would you describe the purpose of an Introduction? Summarize the main topics that are discussed in the Intro..
  • Do the authors discuss any of their results in the Intro? Where in an Intro. is this information usually given

Materials and Methods

  • Where do the authors obtain their bacterial samples
  • Describe the difference in the cell wall between a gram-positive and a gram-negative bacterium. How does a gram stain distinguish between them
  • The authors use several common tests to identify bacteria. List them
  • What is lysozyme and what does it do? What might bve happening when the authors add NaOH and sodium dodecyl sulfate (SDS) and incubate at 95'C
  • These authors use PCR to amplify position 10-806 based on the E. coli rDNA sequence. In class we will determine the region that the different Molecular Lab sections are amplifying, but all of our PCR products are shorter. What would be the advantage of amplifying a longer segment of DNA
  • How long are the primers used by the authors? Degenerate bases are places on the DNA where more than one base (A, T, G, C) may be present. What would be the reason for including these degenerate bases in the primers?
  • PCR cycles: What happens during the initial 95'C segment? What is the reason for the final 72'C segment? What type of files are these (soak, time delay, etc.)? What is their annealing temperature
  • What primer was used for cycle sequencing? What DNA strand is copied? What type of sequencer was used?
  • Describe the process used for analyzing the sequences. How did the authors deal with undetermined nucleotides (N)?
  • The authors had strict criteria for identification. What were these?

Results

  • How are the results presented? What is the purpose of sub-topics within the results section?.
  • Tables 2-4 present a great deal of information. Is this an effective way to present their data? Why do you think so? Could you think of a better way?
  • A) KNOWNS
  • What was the purpose of including conventionally well-defined isolates?
  • In two of the 37 cases, discrepancies were found in the results. Describe what happened in these two cases.
  • In a different two out of the 37 cases, the molecular approach was not able to identify species while the traditional approach was. What were the author's criteria? What might be done to obtain a molecular species identification from these two samples?
  • B) UNKNOWNS
  • 136 gram-positive rods were investigated by both methods. A lot of data is presented in the tables and in the text. provide a summary of their main findings
  • in how many instances were conventional methods incorrect? In how many instances were conventional methods better?.
  • what was the success rate of the molecular method at the genus level in assigning a species designation to the unknowns? How does this compare to their results using conventional microbiology?

Discussion

  • How would you describe or define the Discussion section of a paper?
  • The Discussion is broken up into several sub-topics, but they are not given separate headings. What are the main areas that the authors want to discuss?
  • Figure 1 is a type of flow-chart. Why did the authors include a figure of this type?
  • Do the authors summarize their work and its main conclusions in the Discussion?
  • Do the authors speculate or extrapolate at all in the Discussion? Can you (briefly) show examples?
  • Do the authors believe that 16s rDNA sequencing is a good method for identifying bacteria? What evidence do they use?
  • What do the authors feel are the advantages to their sequencing approach?
  • Do the authors believe that conventional methods should be abandoned in favor of 16s rDNA sequencing?
  • In the last several paragraphs, the authors discuss two potential problems with identification via DNA sequence. Describe these problems. How can each one affect the results?
  • Now that you have thoroughly analyzed the paper, go back and reread just the Abstract. Does the abstract accurately represent their paper?

Find another article by the first author of this manuscript and give the reference