Drug-Resistant TB: A Genetic Analysis Using Online Bioinformatic Tools

Contributor
Jessica M. Taylor, Rebecca M. Davidson, Michael Strong
Type Category
Instructional Materials
Types
Article , Lesson/Lesson Plan
Note
This resource, vetted by NSTA curators, is provided to teachers along with suggested modifications to make it more in line with the vision of the NGSS. While not considered to be “fully aligned,” the resources and expert recommendations provide teachers with concrete examples and expert guidance using the EQuIP rubric to adapted existing resources. Read more here.

Reviews

Description

This article describes a 90-minute real-world lesson in which students use online bioinformatics tools to compare gene sequences between one wild-type and one type of eight hypothetical mutant Mycobacterium tuberculosis (Mtb) strains. Using bioinformatics online tools, students identify single-nucleotide polymorphisms (SNP)at http://www.genome.jp/tools/clustalw, translate each gene sequence to an amino acid sequence at http://exon.gatech.edu/genemarks.cgi, and determine if the SNP in the variant sequence will affect structure and function of the protein (antibiotic resistance or susceptibility). The activity ends with students writing a scientific explanation and providing evidence and reasoning to support their claim of antibiotic resistance or susceptibility. The article provides two appendixes: student learning objectives and student instruction and questions. A rubric for the assessment of student’s scientific explanation and an answer key for the eight strains are included. The article includes a link for downloading all background information, student direction, and DNA sequences for this lesson. http://www.stronglab.org/taylor. This activity was piloted in four traditional high school biology classes (9th and 10th grades) in an urban high school. Over seventy percent of participating students said that the lesson increased their understanding of the molecular consequences of mutations.

Intended Audience

Educator and learner
Educational Level
  • Grade 12
  • Grade 11
  • Grade 10
  • Grade 9
Language
English
Access Restrictions

Free access with user action - The right to view and/or download material without financial barriers but users are required to register or experience some other low-barrier to use.

Performance Expectations

HS-LS3-2 Make and defend a claim based on evidence that inheritable genetic variations may result from: (1) new genetic combinations through meiosis, (2) viable errors occurring during replication, and/or (3) mutations caused by environmental factors.

Clarification Statement: Emphasis is on using data to support arguments for the way variation occurs.] [Assessment Boundary: Assessment does not include the phases of meiosis or the biochemical mechanism of specific steps in the process.

Assessment Boundary: Assessment does not include the phases of meiosis or the biochemical mechanism of specific steps in the process.

This resource is explicitly designed to build towards this performance expectation.

Comments about Including the Performance Expectation
Many teachers use a variety of translation activities but this lesson extends the lessons by engaging students with bioinformatics tools used by real biologists. Prior to using this lesson, teachers can engage students by discussing the history of tuberculosis or using a PBS Evolution video on drug-resistant tuberculosis (http://www.pbs.org/wgbh/evolution/educators/lessons/lesson6/teach). HHMI Biointeractive (http://www.hhmi.org/biointeractive/browse?&field_bio_biointeractive_topics[0]=23463) has a video that provides a live demonstration of how an antibiotic-resistant strain of tuberculosis managed to spread through the passengers on an airplane. Teachers need to provide access to computers.

Science and Engineering Practices

This resource appears to be designed to build towards this science and engineering practice, though the resource developer has not explicitly stated so.

Comments about Including the Science and Engineering Practice
Teachers need to model the claims evidence-reasoning approach (Part D) for students not familiar with the process. Argument-Driven Inquiry in Biology (NSTA Publication) provides a step-by-step model for using the argumentative approach in the classroom.

Disciplinary Core Ideas

This resource is explicitly designed to build towards this disciplinary core idea.

Comments about Including the Disciplinary Core Idea
In this lesson, students use online bioinformatics tools to detect mutations in Mycobacterium tuberculosis (Mtb) gene. The lesson is divided into four different activities. Part A asks students to compare single-nucleotide polymorphisms in wild-type and a hypothetical variant Mtb strain. Part B asks students to use an online translation tool. Part C asks students to determine if their Mtb proteins contain a mutation. Part D asks students make a claim supporting antibiotic resistance or susceptibility. Students will need a conceptual understanding of DNA, genes, and how mutations create change in the DNA sequences prior to completing the activity. Teachers will need to provide instructional activities on how to transcribe and translate a DNA sequence into RNA and then into amino acids.

Crosscutting Concepts

This resource appears to be designed to build towards this crosscutting concept, though the resource developer has not explicitly stated so.

Comments about Including the Crosscutting Concept
This lesson supports the Crosscutting Concept by asking students to use prior knowledge of translation in completing some of the activities. To successfully complete the lesson, students need to understand that the order of amino acids in a protein determines its shape, and consequently, the protein’s structure and function. The Crosscutting Concept is also supported when students determine if the SNP in their variant DNA sequences will affect the structure and function of the protein. Teachers not on block schedule can complete Parts A and B on Day 1 and Parts C and D on Day 2 or the final writing activity can be assigned as homework. To provide closure and engage students in critical thinking, teachers lead a whole-class reflective discussion and allow students to demonstrate what they learned in their investigation.

Resource Quality

  • Alignment to the Dimensions of the NGSS: This lesson provides real-world experiences as students use online bioinformatics tools similar to what biologists used in their jobs. These tools allow students to collect and analyze data. They use the data to make a claim and provide written evidence to support their claim and this aligns explicitly with the practice of engaging in argument from evidence. The three dimensions work well together to support students as they make sense of phenomena.

  • Instructional Supports: This lesson provides students with an essential question: “Does your assigned variant rpoB gene sequence result in resistance to the antibiotic rifampin?” To answer the question, students use online bioinformatics tools to collect data, hypothesize whether a SNP will likely cause antibiotic resistance, and write a scientific explanation justifying a claim with evidence and reasoning. This real-world lesson supports students in understanding the emerging problem associated with antibiotic resistance drugs. Bioinformatics is a fairly new field. The article provides extensive background materials on bioinformatics for teachers not familiar with the contents and in the student pages. The article provides a link for downloading student activity pages. There is a distinct difference in level of difficulty among the eight (A – H) Mtb variants. Teachers can differentiate the lesson by assigning low-performing students Mtb variants A or B and grade-level or advanced students Mtb variants (C – H). The activity was piloted in four sections of 9th and 10th grade students at a traditional urban high school. Samples of students’ performance and survey data are included in the article.

  • Monitoring Student Progress: The downloadable student pages contain questions to complete as the students complete each part of the activity. A rubric for the assessment of students’ scientific explanations is included in Table 2 of the article. Depending on the academic levels of the students, teachers need to develop additional checklists for monitoring students’ understanding of concepts.

  • Quality of Technological Interactivity: This lesson actively engages students with technology that help them develop a conceptual understanding of the transcription and translation and the role mutations play on the processes. Students need to follow the directions carefully, as using the online tools is not intuitive.