This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces the idea of computers as tools to help understand aspects of biology.

primary literature discussion of Bt corn effects

Incorporating authentic research experiences into undergraduate labs, while shown to be particularly effective at engaging and retaining students in STEM majors, can be difficult to accomplish within the constraints of resource availability or cost, and time limitations. One area that is particularly amenable to adaptation for undergraduate lab classes is the discovery and validation of targets of microRNAs (miRs). The human genome encodes several hundred, possibly several thousand miRs, each of which is a 22 nucleotide long RNA molecule capable of regulating the expression of multiple target genes. miRs have been shown to be critical during development, for human health and disease, and are currently being investigated as both therapeutic agents, as well as possible drug targets. A lack in understanding the mechanisms by which miRs recognize their targets makes computer-based predictions of miR targets quite inaccurate, necessitating experimental verification of such predictions. In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research. Students use a variety of databases to identify likely candidate genes whose expression may be altered by a given miR, and then experimentally test their predictions in human cells. This inquiry-based module gives students a taste of real scientific research and excites them about the possibility that, even as a student, they have the potential to contribute to this cutting edge research.

Students often memorize the definition of a transcriptional promoter but fail to fully understand the critical role promoters play in gene expression. This laboratory lesson allows students to conduct original research by identifying and characterizing promoters found in prokaryotes. Students start with primary literature, design and clone a short promoter, and test how well their promoter works. This laboratory lesson is an easy way for faculty with limited time and budgets to give their students access to real research in the context of traditional teaching labs that meet once a week for under three hours. The pClone Red Introductory Biology lesson uses synthetic biology methods and makes cloning so simple that we have 100% success rates with first year students. Students use a database to archive their promoter sequences and the performance of the promoter under standard conditions. The database permits synthetic biology researchers around the world to find a promoter that suits their needs and compare relative levels of transcription. The core methodology in this lesson is identical to the core methodology in the companion Genetics Lesson by Eckdahl and Campbell. The methods are reproduced in both lessons for the benefit of readers. The two CourseSource lessons provide the detailed information needed to reproduce the pedagogical research results published in CBE - Life Sciences Education by Campbell et al., 2014.

Students often memorize the definition of a transcriptional promoter but fail to fully understand the critical role promoters play in gene expression.  This laboratory lesson allows students to conduct original research by characterizing functional regions within known prokaryotic promoters.  Students begin the lesson by learning the properties of transcriptional promoter DNA sequences.  They design mutations for a constitutive promoter and discuss their designs as a class to choose which mutations to clone and characterize.  This lesson provides an easy way for faculty with limited time and budgets to give their students access to real research in the context of traditional teaching labs that meet once a week for under three hours.  The pClone Red Genetics lesson uses synthetic biology methods and makes cloning so simple that we have 100% success rates with sophomores taking Genetics.  Students archive promoter sequences and their performances under standard conditions.  The database permits synthetic biology researchers around the world to find a promoter that suits their needs and compare relative levels of transcription.  The core methodology in this lesson is identical to the core methodology in the companion Introductory Biology Lesson by Campbell and Eckdahl. The methods are reproduced in both lessons for the benefit of readers.  The two CourseSource lessons provide the detailed information needed to reproduce the pedagogical research results published in CBE – Life Sciences Education by Campbell et al., 2014.

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An understanding of protein structure, function, and interaction is central to biochemistry. One angle into this topic is to engage students in considering protein domains as modules that develop form and execute function semi-independently. Here, I describe a modular guided inquiry Lesson for students with an introductory background in molecular biology and biochemistry. The Lesson enables students to further explore how we define and investigate the structure and function of protein domains in a research context. Activities focus on bioinformatic approaches and interpretation and design of experiments to investigate protein interactions. Possible extensions into wet-lab and/or research projects are also highlighted. Students from various science majors enrolled in an intermediate-level biochemistry course reported that this Lesson strengthened their ability to analyze protein sequence and structure and to understand approaches to determining protein interactions.

Beginning undergraduate students in biology need basic laboratory, data analysis, and science process skills to pursue more complex questions in course-based undergraduate research experiences (CUREs). To this end, we designed an introductory lesson that helps students learn to use common laboratory equipment such as analytical balances and micropipettes, analyze and present data in Google and Microsoft spreadsheet software, and perform simple descriptive and inferential statistics for hypothesis testing. In this lesson, students first learn to use micropipettes by pipetting specific volumes of water correctly and incorrectly. After determining the masses of the water samples pipetted, students enter the data into a shared Google spreadsheet and then use statistics to test a null hypothesis; ultimately, they determine if there is a statistically significant difference between the mass of water pipetted correctly versus incorrectly. Together, these activities introduce students to important data analysis and science process skills while also orienting them to basic laboratory equipment.

Beginning undergraduate students in biology need basic laboratory, data analysis, and science process skills to pursue more complex questions in course-based undergraduate research experiences (CUREs). To this end, we designed an introductory lesson that helps students learn to use common laboratory equipment such as analytical balances and micropipettes, analyze and present data in Google and Microsoft spreadsheet software, and perform simple descriptive and inferential statistics for hypothesis testing. In this lesson, students first learn to use micropipettes by pipetting specific volumes of water correctly and incorrectly. After determining the masses of the water samples pipetted, students enter the data into a shared Google spreadsheet and then use statistics to test a null hypothesis; ultimately, they determine if there is a statistically significant difference between the mass of water pipetted correctly versus incorrectly. Together, these activities introduce students to important data analysis and science process skills while also orienting them to basic laboratory equipment.

Reported misconceptions of enzyme-substrate interactions highlight the necessity for better, targeted instructional tools and assessments. A series of active learning activities with corresponding three-dimensional (3D) physical models were developed to target undergraduate biochemistry students’ conceptual understanding of space, electrostatic interactions, and stereochemistry in enzyme-substrate interactions. This lesson includes two activities utilizing physical models of elastase, chymotrypsin, and trypsin. These enzymes are widely taught in undergraduate biochemistry courses and are exceptional examples of a variety of enzyme paradigms. The Model Exploration activity guides students in an exploration of these models to connect conceptual and visual content. The Problem Solving activity uses two-dimensional representations of the physical models to further build student's understanding of enzyme-substrate interactions. These activities are implemented in two consecutive fifty-minute classes or alternatively combined for a seventy-five-minute class. These lessons are an inclusive, student-centered approach to teaching that enables students to confront misconceptions and promotes mastery of the material.

Primary image: Backbones and Surfaces and Substrates! Oh My! Undergraduate Biochemistry Students Working with the Serine Protease Model Set.

The central dogma of biology is a foundational concept that is traditionally included in genetics curricula at all academic levels. Despite its ubiquitous presence throughout genetics education, students persistently struggle with both the fundamental and advanced topics of the central dogma. In particular, students conflate the role of genomic variations in DNA replication, transcription, and translation. As research and healthcare increasingly utilizes genomic medicine to link genetic variants to clinical phenotypes, it is critically important for biology and health science students to understand the role of genetic variation in molecular genetics. This lesson focuses on the role of missense mutations in the central dogma using a case study of cystic fibrosis. The case study is paired with a creative activity in which students draw the molecular parts of the central dogma. This helps students to connect the abstract concepts of the central dogma to a real-world clinical example. The effectiveness of this lesson was evaluated for two semesters of a Human Genetics course using end-of-unit exam questions. The active-learning lesson is an engaging activity that reinforces the role of genetic variation in the central dogma and the effects on clinical phenotypes. This lesson is highly customizable and adaptable to courses of various sizes, levels, course lengths, and teaching modalities.

Primary image: Molecular View of the Central Dogma. This drawing was produced by a student at Bloomsburg University’s Human Genetics course for Part 1 of this lesson.

Data from a study on the amounts of low-density-lipoprotein (LDL), form of cholesterol, in blood plasma is presented. Students build, validate, and use a compartment model of the kinetic exchange of the LDL between body tissue and blood plasma.

We consider modeling of data from a clinical experiment administered as oral doses of 400 mg ibuprofen, an analgesic pain reliever. Concentrations of ibuprofen in the serum/plasma of the subjects were recorded after the initial ingestion of the drug.

pharmacokinetics modeling

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