James C. Clements: Week 2

Assignment Prompt - Preparation for Journal Club 1

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.
2. Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
   • What is the main result presented in this paper?
   • What is the importance or significance of this work?
   • What were the limitations in previous studies that led them to perform this work?
   • What were the methods used in the study?
   • Briefly state the result shown in each of the figures.
     • What do the X and Y axes represent?
     • How were the measurements made?
     • What trends are shown by the plots and what conclusions can you draw from the data?
   • What is the overall conclusion of the study and what are some future directions for research?

Response

Vocab

• Acetaldehyde - a colourless, flammable liquid used in the manufacture of acetic acid, perfumes, and flavors. It is also an intermediate in the metabolism of alcohol. [1]
• Acetate - a salt or ester of acetic acid [2]
• Amino acid starvation - lengthy and continuous deprivation of amino acids [3]
• Biosynthetic gene - A gene related to the building up of a chemical Compound in the physiologic processes of a living organism [4]
• Gram-negative bacteria - bacteria which lose crystal violet stain but are stained pink when treated by grams method [5]
• Northern Analysis (blot) - An electroblotting method in which rNA is transferred to a filter and detected by hybridisation to (32)P labelled RNA or dNA. [6]
• Oligonucleotide - linear sequence of up to 20 nucleotides joined by phosphodiester bonds [7]
• Proline - One of the 20 amino acids directly coded for in proteins [8]
• Reductoisomerase - an enzyme that catalyzes a reduction reaction and catalyzes its substrate to an isomeric form [9] [10]
• Standard Error of Mean - The standard deviation of a data set or of the population divided by the square root of the sample size [11]

Shared Journal Questions and Answers

1. What was the purpose of this assignment? - To become familiar with the article which will soon be discussed; to learn any unknown terms that it uses and to gain exposure to the methodology. (Perhaps so that we can eventually model this system?)
2. What aspect of this assignment came most easily to you? - finding definitions for the the vocabulary; mind you, not all of the terms were readily available.
3. What aspect of this assignment was the most challenging for you? - outlining the article: I understand the format that was used was devised to split things up into categories, but it made certain aspects of the paper difficult to keep track of.
4. What (yet) do you not understand? - Why was this published in the Journal of Bacteriology? This doesn't seem like a very suitable place for an article about eukaryotic acquisition of nitrogen.