Sarah Carratt: Week 2

Instructions

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?
3. Each group of students will be assigned one section of the paper. The group will be responsible for explaining the section, including any tables/figures in detail to the class. Groups will be assigned on 1/20/11 in class. Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.
   • Physiological parameters section, Figure 1: James, Nick
   • Northern analysis section, Figure 2: Carmen, Alondra
   • Enzyme activities section, Figure 3: Sarah

Online Sources

• Article: The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae
• Biology Dictionary
• Gene Ontology
• NCI Dictionary of Cancer Terms

Student Response

Terms and Definitions

1. ammonia assimilation: The utilization of ammonia (or ammonium ions) in the net synthesis of nitrogen-containing molecules; e.g., glutamine synthetase. [1]
2. residual: Remaining or left behind. [2]
3. proline: One of the 20 amino acids directly coded for in proteins. [3]
4. biosynthetic: Relating to or produced by biosynthesis, which is the creation of more complex molecules from simpler molecules, such as the conversion of glucose to starch. [4]
5. gram-negative bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by grams method. [5]
6. gram-positive bacteria: Bacteria that retain the stain or that are resistant to decolourisation by alcohol during grams method of staining. [6]
7. flux: The total amount of a quantity passing through a given surface per unit time. Typical quantities include (magnetic) field lines, particles, heat, energy, mass of fluid, etc. [7]
8. biomass:The total mass of all living material in a specific area, habitat, or region. [8]
9. parameter: A variable whose measure is indicative of a quantity or function that cannot itself be precisely determined by direct methods, for example, blood pressure and pulse rate are parameters of cardiovascular function and the level of glucose in blood and urine is a parameter of carbohydrate metabolism. [9]
10. quantification:The expression of a numerical amount. [10]

Article Outline

Abstract

• "Saccharomyces cerevisiae" was grown in cultures with various amounts of ammonia.
• While the uptake of ammonia proved to be constant, there was a difference in net output when the culture was given more ammonia.
• Increases in ammonia resulted in:
  • Higher concentrations of intracellular glutamate and glutamine
  • Increases in levels of NAD-dependent glutamate dehydrogenase activity and its mRNA (gene GDH2)
  • Decreases in levels of NADPH-dependent glutamate dehydrogenase activity and its mRNA (gene GDH1)
  • Decreases in the levels of mRNA for the amino acid permease-encoding genes GAP1 and PUT4
• Nitrogen metabolism is likely to be based on the abundance of ammonia and the ability to consume the ammonia longer because of its excess.
• Nitrogen metabolism is NOT likely to be based on a change in the rate of consumption because of excess ammonia.

Introduction

• Background:
  • Saccharomyces cerevisia get nitrogen from ammonia.
  • Ammonia allows for better growth when compared to proline or urea.
• Other Research:
  • Ammonia concentration is the thing to focus on.
• Important Variables to Consider:
  • External ammonia concentration
  • Rate of ammonia assimilation (i.e., the ammonia flux)

Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.

Results

Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.

Discussion

States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.

References

List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

Questions

1. In this experiment, the scientists grew budding yeast in ammonia and tested the effects of nitrogen limitation, nitrogen excess and glucose limitation on the yeast. The results were that