p.2
Steps in Experimental Design
How should the research problem be stated?
Concise, specific, and measurable.
p.6
Formulating Hypotheses
What defines a hypothesis in research?
It is highly specific and testable, often quantifiable.
p.15
Conclusions and Extrapolation of Results
How might you test new hypotheses generated from conclusions?
By designing new experiments based on those hypotheses.
p.5
Background Research and Literature Review
What background research was conducted regarding Zyxmyxin?
Zyxmyxin targets cell walls via a novel method, and Y. pestis is somewhat resistant to other cell wall inhibitors.
p.8
Steps in Experimental Design
What should be considered when developing a protocol and technique?
It should be highly experiment specific.
p.9
Variables and Controls in Experiments
What controls are necessary for this experiment?
Control groups without Zyxmyxin and with known antibiotics.
p.8
Steps in Experimental Design
What is required for novel protocols?
Additional testing, troubleshooting, and verification.
p.7
Variables and Controls in Experiments
What is the purpose of controls in an experiment?
To account for unintended variables.
p.14
Data Analysis and Interpretation
What can be inferred from the optical density measurements over time?
The growth response of Y. pestis to different treatments.
p.18
Importance of Experimental Design
What does good experimental design help us understand?
The scope of the conclusions we draw.
p.12
Formulating Hypotheses
What is the example hypothesis in the experimental design?
Y. pestis will be susceptible to Zyxmyxin.
p.12
Troubleshooting Experimental Failures
What should you do if the positive control exhibits unexpected outcomes?
Go back to literature to verify expectations and check experimental conditions against published data.
p.8
Steps in Experimental Design
What is important to verify about the intended protocol?
It should generate the desired information.
p.8
Steps in Experimental Design
What types of protocols can be used in experiments?
Published protocols, kits, and novel protocols.
p.7
Background Research and Literature Review
Why is additional background research often required in experimental design?
To gather necessary information before testing the hypothesis.
p.3
Formulating Hypotheses
What must be determined about Y. pestis in relation to the drug target?
Does Y. pestis have the drug target? What is known about its inhibition?
p.2
Steps in Experimental Design
What should be identified after recognizing a problem in experimental design?
The subject for investigation.
p.2
Steps in Experimental Design
What is an example of a specific and measurable research problem?
The effect of Zyxmyxin on Y. pestis survival is unknown.
p.6
Formulating Hypotheses
What role does a hypothesis serve in relation to a problem?
It serves as a possible or partial explanation of the problem.
p.16
Conclusions and Extrapolation of Results
What was NOT able to be concluded from the experiment?
Minimum effective concentration of zyxmyxin, physiological relevance of drug, why zyxmyxin works, etc.
p.17
Identifying Research Problems
What was the previous method of growing G. thermoglucosidans?
On complex media with unknown chemical composition.
p.11
Troubleshooting Experimental Failures
What are some common reasons for experimental failure?
Poor design, contamination/bad technique, unexpected variable, equipment malfunction.
p.9
Steps in Experimental Design
What biological system will be used in the experiment?
Bacteria, specifically Y. pestis.
p.8
Importance of Experimental Design
What safety and ethical concerns should be addressed in experimental design?
Laboratory PPE, biosafety levels, human and animal subjects, and research ethics.
p.10
Formulating Hypotheses
What is the example hypothesis mentioned?
Y. pestis will be susceptible to Zyxmyxin.
How is Y. pestis inoculated in the experiment?
Into growth media and observed spectrophotometrically.
p.14
Variables and Controls in Experiments
What treatments were tested on Y. pestis in the experiment?
No treatment, 0.1mM penicillin, and 0.25mM zyxmyxin.
p.15
Conclusions and Extrapolation of Results
What should you be careful about when concluding from data?
Not to over-reach based on data.
p.13
Steps in Experimental Design
What should you do after the procedure is working?
Perform the experiment and collect results.
p.11
Troubleshooting Experimental Failures
What should you consider when an experiment fails?
Failure does not always indicate that you should reject the hypothesis.
p.11
Troubleshooting Experimental Failures
What is essential for troubleshooting experiments?
Good controls to locate issues.
p.8
Steps in Experimental Design
What type of information should you seek in an experiment?
The kind of information you are seeking should be clearly defined.
p.4
Variables and Controls in Experiments
What is an independent variable?
The variable manipulated by the researcher.
p.7
Steps in Experimental Design
What is a biological system in the context of experimental design?
The specific system used for testing the hypothesis.
p.7
Variables and Controls in Experiments
What are variables in an experiment?
Conditions that are actively changed to determine the outcome.
p.7
Variables and Controls in Experiments
What is a blank in experimental design?
A specialized control to eliminate background readings.
p.14
Data Analysis and Interpretation
What does the timepoint data represent in the experiment?
The optical density (OD) of Y. pestis under different treatments over time.
p.18
Importance of Experimental Design
How does good experimental design contribute to research?
It ensures that results are reproducible.
p.6
Identifying Research Problems
What is a key characteristic of a research problem?
It is often broader and may require multiple hypotheses to solve.
p.1
Importance of Experimental Design
What is the rationale behind experimental design?
Scientific progress requires logical experimental design to answer problems.
p.17
Steps in Experimental Design
What did researchers do to determine necessary nutrients for G. thermoglucosidans?
They systematically altered growth media.
p.4
Steps in Experimental Design
What should you do after designing a hypothesis?
Predict a solution to the problem.
p.3
Background Research and Literature Review
What does the current state of knowledge refer to in experimental design?
The existing understanding of the topic being studied.
p.3
Identifying Research Problems
What is an example of a research question mentioned?
The effect of Zyxmyxin on Y. pestis survival is unknown.
p.9
Troubleshooting Experimental Failures
What ethical or safety concerns should be considered?
Handling Y. pestis due to its potential to cause plague.
p.7
Variables and Controls in Experiments
What is a positive control?
A control that produces a known or predictable result relative to the hypothesis.
p.10
Variables and Controls in Experiments
What variable is being manipulated in the experiment?
Concentration of Zyxmyxin.
p.14
Steps in Experimental Design
What does optical density measurement indicate in the experiment?
It measures how many bacteria are in the sample.
p.18
Importance of Experimental Design
What is one reason to prioritize good experimental design?
To obtain valid results from which we can draw conclusions.
p.6
Identifying Research Problems
How are the outcomes of a problem described?
They are measurable but not necessarily quantifiable.
p.16
Formulating Hypotheses
What is the example hypothesis mentioned in the experimental design?
Y. pestis will be susceptible to Zyxmyxin.
p.5
Formulating Hypotheses
What is an example of a hypothesis related to Zyxmyxin?
Y. pestis will be susceptible to Zyxmyxin.
p.12
Troubleshooting Experimental Failures
What should you check if bacteria fail to grow?
Check growth conditions and validate stocks.
p.4
Variables and Controls in Experiments
What should be considered regarding variables in an experiment?
Think about independent and dependent variables.
What protocol or technique will be used to measure bacterial growth?
Growing bacteria in media and measuring growth with a spectrophotometer.
p.10
Troubleshooting Experimental Failures
What ethical concern is mentioned regarding the experiment?
Potential to release resistant organisms into the environment.
p.14
Data Analysis and Interpretation
What is a key consideration when analyzing data?
Is statistical analysis possible here?
p.15
Conclusions and Extrapolation of Results
What is the first step in concluding an experiment?
Based on your interpretations, the previous literature, and your hypothesis.
p.15
Conclusions and Extrapolation of Results
What does it mean to extrapolate in the context of experimental design?
To generate new hypotheses from the conclusion.
p.1
Formulating Hypotheses
What is a key process in experimental design regarding hypotheses?
Define, evaluate, and redefine hypotheses.
What aspect of carbon utilization was studied in G. thermoglucosidans?
Which sugars the organism ferments best and which produce the most ethanol.
p.17
Conclusions and Extrapolation of Results
How has metabolic profiling of G. thermoglucosidans improved?
It can now be conducted more readily, allowing efficient production of desired products.
p.3
Formulating Hypotheses
What should be investigated about Y. pestis in relation to drugs?
How does Y. pestis respond to similar drugs?
p.7
Variables and Controls in Experiments
What is a negative control?
A control that should produce no change relative to the hypothesized result, often a placebo.
p.10
Variables and Controls in Experiments
What is the blank control used in this experiment?
Uninoculated growth media.
p.18
Importance of Experimental Design
Why is efficient resource utilization important in experimental design?
To utilize resources efficiently and ethically.
p.13
Steps in Experimental Design
How should data be organized after collection?
Organize and tabulate data.
p.19
Troubleshooting Experimental Failures
What should students do if they have questions or are unsure about something?
Email the instructor or come to office hours as soon as possible.
p.1
Importance of Experimental Design
How will experimental design principles be utilized?
They will be used throughout the semester.
p.9
Variables and Controls in Experiments
What is the independent variable in the experiment?
The presence of Zyxmyxin.
p.9
Steps in Experimental Design
What should be included in the experiment drawing?
Detailed layout of the experimental setup, including controls and measurement techniques.
p.7
Variables and Controls in Experiments
Why might other specific controls be necessary in an experiment?
To address unique aspects of the experimental setup.
p.10
Variables and Controls in Experiments
What is a positive control in this experiment?
Concentrations of other cell wall inhibitors with known effect.
p.14
Formulating Hypotheses
What is the example hypothesis mentioned?
Y. pestis will be susceptible to Zyxmyxin.
p.13
Data Analysis and Interpretation
What is the purpose of analyzing data in experimental design?
To interpret the observations and data within the context of the hypothesis and known information.
p.19
Importance of Experimental Design
Why is it important to keep the principles of experimental design in mind during the course?
They will be important for many activities and exams.
p.1
Identifying Research Problems
What does experimental design help define?
Focus on a specific problem.
p.16
Conclusions and Extrapolation of Results
What does extrapolation involve in the context of experimental results?
Testing new hypotheses based on the results obtained.
p.1
Background Research and Literature Review
How does experimental design relate to previous research?
It expands upon previous research and knowledge.
p.11
Troubleshooting Experimental Failures
What approach should be taken to troubleshoot effectively?
Understanding the theory behind the technique and using persistence and repetition.
p.9
Variables and Controls in Experiments
What is the dependent variable in the experiment?
The growth of Y. pestis measured by a spectrophotometer.
p.3
Formulating Hypotheses
What questions should be considered regarding Zyxmyxin?
What kind of drug is Zyxmyxin? Are there other drugs in the same family?
p.10
Troubleshooting Experimental Failures
What safety concern is associated with Y. pestis?
It is a BSL3 organism (plague).
p.16
Conclusions and Extrapolation of Results
What was the conclusion of the experiment regarding Y. pestis and zyxmyxin?
Y. pestis is susceptible to zyxmyxin at 0.25mM concentration.
p.13
Data Analysis and Interpretation
When is statistical analysis necessary in experimental design?
If necessary, during the data analysis phase.
p.19
Steps in Experimental Design
What should students do to stay prepared for each class?
Keep up with the readings on the syllabus ahead of each class.
p.17
Importance of Experimental Design
What is the industrial importance of Geobacillus thermoglucosidans?
It is a bioethanol producer.
p.9
Formulating Hypotheses
What is the working hypothesis for the experiment?
Y. pestis will be susceptible to Zyxmyxin.
p.11
Troubleshooting Experimental Failures
What method can be used to eliminate issues in experiments?
Trial and error (methodically eliminate issues).
p.4
Variables and Controls in Experiments
What is a dependent variable?
The measurable outcome of the experiment.
p.8
Steps in Experimental Design
Why is repetition important in experiments?
It allows for the possibility of statistical significance and unambiguous outcomes.
p.3
Background Research and Literature Review
What general knowledge should be gathered about Y. pestis?
What is known about Y. pestis survival in general?
p.14
Data Analysis and Interpretation
What should be done after analyzing the data?
Interpret the observations and data.
