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