BIOL 1210 Antibiotic Resistance Bioinformatics Activity Case Study.docx

BIOL 1210 Antibiotic Resistance Bioinformatics Activity Case Study.docx

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BIOL 1210_001 Antibiotic Resistance Bioinformatics Assignment 15 points+ up to 5 bonus for Part 2 You may work as teams, yet each upload your own document with results and answers. This activity is computer based using online tools. The objectives for these activities are for you to: Identify and characterize the difference between antibiotic resistant bacteria and non-antibiotic resistant (susceptible) bacteria. Become familiar with NCBI (National Center of Biotechnology Information) https://www.ncbi.nlm.nih.gov databases and tools that provides access to virtually all published biomedical and genomic information Become familiar with a bioinformatics tool B asic L ocal A lignment S earch T ool that is commonly used to identify regions of sequence similarity between a query sequence and a designated database. Conduct a BLAST searches to assess prevalence of antibiotic resistance genes in sequenced bacteria. Use the NCBI Primer-BLAST tool to Identify PCR primer sequences that may be useful to identify one of the antibiotic resistance genes in clinical samples. Use BLAST analyses to identify the source of resistance in a sample from a from an infected individual that is not responding to antibiotics. (adapted from a case study http://sciencecases.lib.buffalo.edu/cs/collection/detail.asp?case_id=711&id=711 yet you do NOT need to access this material) Part 1 Kristen and Brent are two fictional college students. Brent discovered a small abscess on his right elbow that did not heal after a few days as expected. He went to his doctor to investigate. Kristen is another student, and she had knee surgery due to a sports injury. The surgery went well, yet a week later, the incision became hot, red and swollen, and she felt and had a fever. Both Brent and Kristen were given the antibiotic drug oxacillin, which is commonly given for skin infections. Within a few days, Brent’s lesion was gone, yet Kristen did not improve. 1. What might be the source of Brent and Kristen’s infections? 2. Why might the antibiotic have failed to alleviate Kristen’s infection?
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David, the staff microbiologist, obtained from both Brent and Kristen’s wounds. He carried out standard microbiology analyses and determined that both students were infected with the same bacteria, We will focus on the DNA analyses that were applied to try to understand why Brent responded to the antibiotic, yet Kristen did not although both were infected with the same species of bacteria. First, DNA was isolated from each bacterial strain—the sample from Brent and the sample from Kristen. Second, the staff microbiologist had a suspicion as to the source of Kristen’s resistance, so he wanted to investigate. He carried out PCR on their samples, thus creating > a million copies of a unique segment of the DNA that had been associated with this type of resistance. The PCR reaction on Brent’s sample did NOT produce an amplified segment (called a PCR product). However, he did obtain a PCR product from Kristin’s sample.
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