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Answer questions 18-19 using the following prompt. You are working in a research lab that is studying the role of Helicobacter pylori in the formation of stomach ulcers.  You conduct an experiment that compares a wild type H. pylori strain that produces urease (87-3887) to a mutant strain of H. pylori strain that does NOT produce urease (26ul).  You infect piglets with one of the two strains and record the number that are infected and the number that develop stomach ulcers (gastritis) in the table below.

Answer two of Hanage’s questions listed below.  Provide support for your answer. Do the results presented in Figure 5 detect differences that matter? Do the results presented in Figure 5 show correlation or causation?  

[a] is a common microbe (that we discussed in class) that is associated with vaginal dysbiosis and is part of the bar colored [b] in Figure 2.b.  For full credit, Include the genus and species name in the first blank and use the provided figure key to name the color in the second blank.

Answer questions 13-15 based on the figure below. This is a heat map that compares the transcriptome of individuals with a general Mycoplasma pneumoniae infection of the lungs (GMPP) and those with a complex Mycoplasma pneumoniae infection of the lungs (CMPP).  Each column represents data from a single patient and each row represents a single gene.  The gradation of color represents the value of log2 FC (FC = fold change).

Name one microbe that is part of the RED complex commonly associated with periodontitis.  You must write the full genus and species name for full credit.

The research also found a(n) ___ in the 4-ethylphenyl sulfate  in the mice displaying autistic-like behavior.

This systems biology technique is advantageous because it…

Which of the following is/are factor(s) that affect(s) the oral microbiota?  Choose all that apply.

Choose one of the following figures from the exam (Exam Figure 1, Wu (2019) Figure 6, Barnard (2016) Figure 2 or Exam Figure 4).  For the figure you chose answer the following prompts: Identify which figure you chose. Hanage’s question: Is the experiment detecting differences that matter?  Explain. Hange’s question: Does the experiment show causation or just correlation?  Explain. Hanage’s question: Can anything else explain these results? Explain.

 In Figure 2 from Barnard (2016) Each column represents a(n) [e] and each row represents a(n) [f].