Association for Biology Laboratory Education

ABLE 2017 Poster Session

“Designing from Scratch”: A Dynamic Interdisciplinary Approach to Engage Upper Level Students in Plant Science Courses

Valeria Avanzato and John Hauptfleisch

Plant Science is quite often not the first choice in upper level courses for the undergraduate population. Laboratory sessions are restricted to taxonomical identification, the study of physiological processes, as well as microscopy to recognize plant cells and tissues. However, in upper level classes those activities should transcend the pre-digested information and pre-set up experiments with expected outcomes. A mixture of basics and “design from scratch” laboratories would challenge the students to approach plant sciences from a whole different perspective. At Coker College, plant science has joined forces with chemistry to provide students with a full semester research activity. This activity introduces students to the notion of plants as potential antimicrobial agents to treat and control human pathogens. Students are responsible for the planning and execution of their experiment. Activities include: 1) guided literature search, 2) collection of plant material, 3) experimental design (type of culture media, number of replicates, controls, incubation time and temperature, bacterial and fungal strains to be tested), 4) extraction of plant material using solvent-solvent extraction, 5) biological testing, 6) data collection, 7) analysis of results and conclusions, 8) future directions.  The benefits of the “design from scratch” type of experimentation definitely exceed the perceived downsides of the process (time, additional extracurricular work for professors, use of additional research supplies, negative results after testing, seasonal availability of plant material, etc.) while providing a unique research experience in which ownership of the research by students is successfully achieved.


Development and Implementation of a Water Quality Testing Module Across the Curriculum: Science, Liberal Arts, and Art/Design Majors

Marcus Banks

With the build out of multi-use science labs, we had the opportunity to develop a Water Quality lab unit for a new audience. We intentionally targeted the first-year core curriculum for BFA design students and developed a modular lesson plan that is scalable in terms of depth of knowledge and range of technique and is simple, relevant, and flexible enough for students with expansive interests. To date we have offered this lab module to approximately 600 students per year, spanning the first-year Parsons School of Design Sustainable Systems course, a Eugene Lang College of Liberal Arts upper-level science Water Quality Lab course, and a New School university-wide required course Liquid Cities. The Water Quality module is designed to teach the epistemology of science using bacterial coliform detection systems and highlights civic relevance by explaining how this protocol has been implemented by government agencies and citizen scientists to monitor human influences on public water systems. The module uses a simple chromogenic assay (~$1/student) to aid students in the understanding of a central pedagogical theme: both genetics and environment determine metabolic phenotype. Additionally, students gain knowledge of sterile technique. Through the lens of sustainability as a form of social justice, we are able to explore: water as a limited resource; disease communicability; and the role of infrastructure design in mitigating downstream effects of climate change. We are also able to scale this module for different courses by incorporating additional selective tests with fluorometric media and confirmatory biochemical reactions.


The SAGES Program: SoTL Advancing Graduate Education in STEM

Isabelle Barrette-Ng, Eliana El Khoury, and Leslie Reid

Each year, graduate students shoulder many hours of instructional time with undergraduate students and some have more contact hours with students than academic staff in large introductory undergraduate courses. Unfortunately, many are given minimal opportunities to develop a reflective, evidence-based teaching practice. To support graduate student teaching development, we designed and implemented the SAGES Program (SoTL Advancing Graduate Education in STEM). This program provides graduate students with the opportunity to learn about the SoTL through a semester-long course, followed by a semester-long practicum. The practicum offers graduate students an opportunity to apply what they have learned in a classroom setting, working in collaboration with a faculty partner. In this poster presentation, we will describe how the SAGES Program created a collaborative learning environment and network of practice that engaged graduate students and faculty partners. We will also invite conference attendees to conceptualize how such a program could be designed for their own institutions.


Does lecture attendance matter: Using clicker data to assess the role of lecture attendance on student performance

Michael Berger

A common mantra from university level instructors focuses around the concept that lecture attendance is necessary and results in greater student performance. I address whether attendance had an impact on student success by analyzing the relationship between percent lecture attendance and final course grade. Clickers are shown to improve student performance through active learning, but also act as mechanism to collect useful data. Attendance data was collected using clickers in an introductory environmental science course, a general biology course for non-majors, and an introductory biology course for majors. The relationship between percent lecture attendance and final course grade was analyzed. Preliminary results suggest that attendance levels below 70 percent results in a reduction in performance by one letter grade. I will examine the effect of degree program (i.e., declared major) on the relationship between attendance and student success. The outcome of this work can be used to show students the importance of attending lecture and an easy mechanism to improve student success.


Bioinformatics of the Green Fluorescent Proteins

Alma E. Rodriguez Estrada

Transformation of Escherichia coli with the Green Fluorescent Protein (GFP) is a laboratory activity that has become increasingly popular at diverse levels of education ranging from middle school to undergraduate courses. There are several mutant GFP genes that encode proteins with small differences in their amino acid sequence. This bioinformatics activity was designed for a molecular biology course. Through this bioinformatics activity, students learn how to use the Basic Local Alignment Search Tool (BLAST) and the Protein Data Bank to analyze the gene and amino acid sequences of different GFP variants while reviewing general concepts of gene and protein structure.


The Use of DNA Barcoding to Teach Students the Importance of Classifying Biodiversity

Antonia Florio

Students can develop an awareness and concern for biodiversity loss by learning to identify the organisms around their neighborhoods or campuses. In response to this, we have implemented DNA barcoding curriculum at St. Francis College (SFC) to identify species in New York City (NYC). Classifying species based on morphology can prove challenging for students because they often become frustrated by species descriptions and taxonomic keys. The use of DNA barcoding has been championed as a way to overcome this, while also providing an inquiry-based approach for student-driven research.  Using the DNA barcoding method, students propose projects, collect samples, extract whole genomic DNA, and use PCR to amplify the appropriate gene for their taxonomic group (plants: chloroplast genes rbcL and matk; animals: mitochondrial COI; fungi: nuclear ITS; and bacteria: 16S rRNA). Successful PCRs (confirmed by gel electrophoresis) can then either be sequenced in-house or sent away to a company for Sanger sequencing. Students clean their data using any sequence editing program, and perform BLAST searches through Genbank to identify their samples. Students can also learn how to resolve evolutionary relationships by generating multiple sequence alignments and phylogenetic trees.  This poster will summarize how we have used DNA barcoding at SFC to introduce high school and undergraduate students to classifying NYC biodiversity. The pros and cons of the method are presented, and a framework for implementing the project over a semester is proposed.


Enhancing Ecological Education through Civic Engagement

Jessica Goldstein and Sarah Salm

We wanted to improve the way that we taught about human impact on the environment to our non-science students in a laboratory class. In the past, as part of one lab activity, we asked each student to calculate his or her own carbon and ecological footprint, but we found that many students had a hard time with these abstract concepts. To increase their engagement and understanding, we combined the data-heavy footprint calculations with a tangible community-based civic engagement project. We asked students to volunteer at an organization in their community that would have a positive impact on their environment. During the experience, they had to collect data and present what they learned in either a poster session or Powerpoint presentation. Students chose to work on varied projects ranging from community park clean-ups to composting workshops, to salvaging and restoring bicycles for urban youth. These projects got students interested, engaged, and excited about learning ecological concepts. It also enhanced student’s communication skills by asking them to present their experiences to their classmates. This poster will describe how to implement this project as well as discuss what students learned from their experiences.


Establishing a Tissue and Bacterial Cell Culture Lab in Appalachia to Research Tick Borne Lyme Disease

Lucy Hritzo

Lyme Disease (LD) is caused by the spirochete Borrelia burgdorferi (B.b.), transmitted by Ixodes species ticks and has become the most common vector-borne illness in the United States, Europe, and the Northern Hemisphere.1,5 Newly revised estimates from the Center for Disease Control (CDC) suggest that there are likely to be over 300,000 new cases per year in the United States, but the actual number is much higher with many cases underreported and undiagnosed.1,2,3,4,5 As LD is so prevalent, especially in Appalachia with few studying it, it is important to investigate Tick-Borne LD. To study LD at Wheeling Jesuit University(WJU), a small university in Appalachia, it is crucial to have the proper equipment and sterile space.

To research LD, an updated, sterilized cell-culture environment was needed and there was no tissue/bacterial cell-culture lab up and running at WJU. I proposed to take a decommissioned space and assemble a sterile fully functioning bacterial cell lab, allowing for/focusing on microbiological/bacterial studies. This project was multi-step: we acquired various approvals for a working area; secured, cleaned, and sterilized the space; and facilitated regulatory consensus with the university administration.  We located the keystone of a bacterial cell-culture lab, by applying for various grants, as well as contacting other universities/businesses, finally procuring a Bio-Safety Level II, Bio-Safety Cabinet(BSLII BSC). This BSC is crucial to the success of a bacterial cell culture lab, as it protects the person using the hood, and also protects the pathogen and cells from contamination. Without a BSLII BSC, LD cannot be studied at WJU. We wrote and submitted various grants, as well as contacted other universities/businesses, and have procured a BSLII BSC.  To study LD at WJU in Appalachia, it is critical to conclude/verify that B.b. can be grown successfully in this new sterile environment in the BSLII BSC and lab, conducive to culturing bacteria.


Investigating Critical Periods in Bean Beetle Development : Incorporating Guided Inquiry Research into a Developmental Biology Laboratory Course

Kathryn Lipson

Integrating research into undergraduate courses allows students to fully experience the scientific process. To this end, a guided inquiry of the teratogenic effects of ethanol on developing organisms was incorporated into the Developmental Biology Laboratory course at WNEU. Introductory lessons about the bean beetle model system and culturing, principles of teratology, and effects of ethanol on early development are presented. Students are then posed the question. “ Is ethanol teratogenic to bean beetles? If so, is there a critical period during bean beetle development when ethanol exposure is particularly detrimental?” During this semester-long research project, students work in pairs to design and perform experiments to answer these questions. As a class, students discuss data collection, and identify the different potential variables, including concentration of ethanol , volume of ethanol, and duration of exposure . Each student pair typically designs a different experiment so that as a class, we can address as many variables as possible. Students submit detailed research plans to be edited by the instructor before beginning the experiments. The projects require time outside of class meetings, and reinforce the importance of proper experimental planning and routine. At the end of the semester, students write formal research reports detailing their findings, and give a Powerpoint presentation to the class. This format is useful for instructors wishing to incorporate multiple semi-independent research projects into undergraduate laboratory curricula.


Application of a Proposed Test for Alzheimer’s Disease to Investigate Olfaction in the Human A&P Laboratory

Karen McMahon

Stamps et al. (2013) described a simple olfactory test to identify patients in the early stages of Alzheimer’s Disease. Previous studies have shown that the olfactory cortex, especially in the left hemisphere, is impaired early in the onset of Alzheimer’s Disease resulting in the inability to identify familiar odors with the left nostril. This report inspired a lab exercise for the Human Anatomy Laboratory. Students hypothesized that olfactory detection distance would be symmetrical for both nostrils and male students would have a shorter olfactory detection distance than female students. The test subject was seated with eyes closed and asked to close one nostril with a wad of cotton. A 30 cm ruler was placed with the 0 end near the nostril tested. Peanut butter was the olfactant. A heaping teaspoon of peanut butter (~ 14 g) was placed in a paper cup (4cm diameter; 3cm depth) at the 36 cm end of the ruler. The cup was slowly moved along the ruler toward the nostril until the subject indicated that the odor of peanut butter was detected. The olfactory detection distance was recorded. Each nostril was tested separately with a 90 second delay between tests. The peanut butter cup was covered during the delay. Most subjects showed no significant difference in olfactory detection distance between the nostrils (males right = 9.02 cm, left = 9.74 cm; females right = 12.72 cm, left=13.08 cm). A few individuals showed strong asymmetry between the right and left nostrils with one female subject unable to detect the odor of peanut butter at all with the left nostril. The mean olfactory distance for male students was 9.38 cm which is slightly lower than that of female students at 12.90cm. This exercise has been used successfully at S.T. E. M. and other biology classes.


The Battle of the Water Filters

Kathleen A. Nolan and Alison Dell

As part of our general biology course that includes a lab, students are required to partake in a group research project that results in a lab report and a poster. An intriguing and successful project was to have a “contest” to see which water filters worked the best. The students learned about Rita Colwell’s experiment of decreasing cholera infection rates in Bangladesh by using sari cloth to filter the local drinking water. (She recorded a decrease of cholera by 48% in those who used the sari cloth.) Our students tested cotton cloth (T-shirt), denin, and a LifeStraw to filter water from the East River in the Brooklyn Bridge Park in New York City. They used nutrient and McConkey agar plates for their tests. The LifeStraw filter reduced bacteria ten-fold whereas there was no reduction in bacteria with the two types of cloth. This project could be used as an inquiry-based exercise with a focus on environmental justice in which students can simulate experiments that they might conduct while living in an area where the water supply might be compromised.


From Temperate to Tropical Islands: Learning Biology through the Partners in the Parks program

Kathleen Nolan and William Glider

This year we organized and/or participated in two excursions with students sponsored by a unique partnership between the National Collegiate Honors Council and the National Parks Service called the Partners in the Parks. This partnership, eight years strong, was founded by Joan Digby, Honors Director at LIU Post. This program is interdisciplinary in nature, and weaves the history of place with knowledge about biological ecosystems of the areas. The two excursions we led were to the Boston Harbor Islands National Recreation Area and Boston National Historic Park and the U.S. Virgin Islands National Park. Activities included camping or staying in rustic cabins, cooking meals, learning about the ecology and geology of the areas, and the history of Boston and the U.S. Virgin Islands. Biology became especially relevant in the history of the U.S. Virgin islands when pointing out that the decline of slavery and indentured servants was directly proportional to the decline of soil quality due to sugar cane growth on plantations. In Boston, students learned how the harbor became cleaner after an installation of a sewage treatment plant and how Spectacle Island was transformed from a dumpsite to a beautifully landscaped island complete with hiking trails after landfill restoration. Students also cleared invasive species from Peddocks Island under the direction of park rangers. On St. John in the U.S. Virgin Islands, students snorkeled and learned about coral reef, mangrove, and sea grass bed ecology, and about tropical plants indigenous to the area while hiking. The two experiential learning excursions were an effective way to infuse the curriculum with hands-on learning about biological concepts.


Media-Enhanced Feedback – An Easily Effective and Affective Option for Learning

Alp Oran

For the student, high quality and timely feedback from the course assessment tools has an important impact on student engagement and can affect their ability to learn (Crook, Mauchline, Maw, Lawson, Drinkwater, Lundqvist, Orsmond, Gomez, & Park, 2012). Unfortunately, despite a broad awareness by educators of its effects on and for learning, less effective assessment practices persist to the detriment of the learning environment. A digital audio/video approach to feedback and assessment, also referred to as media-enhanced (ME), offers the educator the option of sharing constructive criticism in an emotionally supportive framework, a difference that may be difficult or too time-consuming to communicate in traditional text-based formats. This affective component to assessment may be the difference between engagement and disengagement from the course curriculum. I decided to introduce a media-enhanced assessment component in three different undergraduate science courses offered during the 2015-16 and 2016-17 school years at the University of Ottawa. After the semesters were completed, I engaged in a collective case study analysis (with elements based on Grounded Theory) that addressed the following research question: “What are the perceived advantages and disadvantages with ME assessment?” The study used a social constructivist interpretative framework in which I co-created with the help of my student interviewees a plausible 3-phase model that described what transpired when students experienced ME feedback and how it compared to their historical feedback experiences. Conference attendees will learn how undergraduate science students respond to assessment as well as learn how ME-feedback positions itself within this framework, offering convenient and arguably more appropriate opportunities (of assessment) for learning than other traditional forms of assessment.


Introduction of Inquiry Based Labs for Non-Science Major Biology Students At the University of North Georgia

Linda Purvis and Swapna Bhat

Previously, our non-majors introductory biology course laboratory material was very passive for student learning. This is a popular course yet also a basic core requirement that students must take. However, most came into the course with the predisposition that it will be boring and have no application for their career or life. Materials used were almost two decades old and did not reflect a lot of the recent advances made in biology. The overall goal was to introduce guided inquiry based labs that are up-to-date and relevant to everyday life. We developed inquiry based creative lab experiences for non-science focused students while initiating engaging lab modules that will replace our previous passive learning set up. We believe that a successful biology course for non-majors will encourage students to develop a child-like curiosity about the wonders of the living world around them. As informed citizens they will be able to evaluate, question and discriminate information provided to them via different media.


Using Zebrafish to Explore Development in a Large Introductory Biology Laboratory Course

Jennifer Rahn

Zebrafish are well-known for their scientific utility as an animal model for studying developmental processes. In addition to being inexpensive to acquire and maintain, zebrafish are capable of consistently producing hundreds of optically transparent, rapidly developing embryos which can be harvested by simple techniques without harm to the female. At the College of William and Mary, my Introductory Biology laboratory is a two-semester course with a typical enrollment of 350-400 students operating independently from the Introduction to Biology lecture course. For the Spring 2017 semester, I developed a four-week module focusing on development using zebrafish as an animal model. In Week 1, students were given information about six different chemicals or drugs with either known or suspected teratogenic effects in humans: lithium, valproic acid, retinoic acid, ethanol, thalidomide and permethrin. While working in groups of four, students selected a chemical of interest and designed an experiment to test the effect of their chosen chemical on zebrafish development. Using a small zebrafish colony I established using 10-gallon aquaria, I was able to generate embryos for the students on a daily basis. The treated zebrafish embryos were allowed to develop to 5 days of age at which point they were fixed and stored. The following week, students examined their fixed zebrafish for developmental abnormalities and performed a staining procedure to examine cartilage formation in the exposed zebrafish. During Week 3, students worked together to compile their data, explore connections of their findings to human health, and prepare a 15 minute presentation to be given to the section during Week 4. By using zebrafish as an animal model, students were able to visualize the consequences of altering early development and make connections to human developmental abnormalities.


Teaching the Scientific Method in a Large Introductory Biology Two-Semester Lab Sequence

Linda Robinson

One of our goals in teaching Introductory Biology labs is to teach students the scientific method. After a two-semester Introductory Biology lab sequence, students should be able to formulate hypotheses, design a simple experiment, understand the concept and utility of experimental controls, analyze and interpret results, and communicate their findings. We have developed lab exercises during the first semester where we: 1) give students the experimental question and ask them to formulate a research hypothesis and a null hypothesis, 2) ask students to design positive and negative controls for an experiment given a choice of conditions, 3) teach students to construct line and bar graphs, calculate averages and standard deviations, perform t-tests and chi-square tests 4) ask students questions about their experiments that lead them toward interpretation of results, and 5) communicate findings by answering directed questions. In the second semester of the introductory biology sequence, we have developed an inquiry-based multi-week module based on metagenomic analysis of bacterial diversity using next generation sequencing technologies. In this lab module, students work on a real research question to obtain, analyze, interpret, and communicate their data using the skills that they developed during the first semester sequence. At the end of the second semester, students think about the next step that they would take to test their hypothesis or whether they would develop a new hypothesis based on their results. This two-semester sequence takes students through learning the fundamentals of experimental design and the scientific method in the first semester using a step-wise skill building learning approach, followed by tackling a real research question that requires more independent thinking and creativity in the second semester.


Laboratory Exercise: Regulation of Gene Expression using Lac Z reporter Genes: Expression of Gal4-activated Galactose Metabolism Genes with TATA/CATA Variant Elements at the Core Promoter in Saccaromyces cervisiae

Farida Safadi-Chamberlain

Regulation of gene expression regulation in eukaryotes is implemented at the levels of gene promoters and protein activators. Consensus DNA sequences that are rich in adenine and thiamine nucleotides (referred to as TATA elements) in the proximity (core promoter) of gene start sites are key DNA elements where specific TATA binding proteins (TBP) bind to facilitate transcription initiation by assembling RNA polymerase II and general transcription factors at the gene start site. The eukaryotic single cellular yeast Saccaromyces cervisiae is an ideal organism to teach students the components of gene expression. TATA elements to which TBPs bind with high affinity have been identified in yeast. Yeast TATA elements and their variants, TBPs and the transcription factors assembled at the core promoters have been studied extensively in the Stargell lab at Colorado State University. Yeast containing a construct of either TATA element or its variant CATA element at the core promoter of a GAL4 inducible Galactose regulon was used in conjunction with the prokaryotic lacZ reporter gene system to teach the regulation of gene expression to entry-level biology students. The lab exercise used these yeast constructs and galactose to induce expression of the Gal4-regulated gene expression measured by the expression of the reporter gene lac Z, and to compare gene expression in the absence of galactose induction. β-galactosidase assay was employed using the substrate ONPG and the spectrophotometric analysis of its yellow product. Students’ results consistently showed a 2 to 4-fold increased expression of lac Z in the yeast construct containing TATA-Gal4/LacZ compared to that containing the variant CATA-Gal4/LacZ when induced by galactose. Yeast containing the same gene constructs grown with glucose expressed no β-galactosidase activity. Work is in progress to introduce variants of the TATA elements that were shown in vivo to have a gradient of gene expression.


A Novel Physiology Teaching Laboratory Investigating the Mechanisms of Ammonia Excretion across the Gill Epithelium of Marine Crustaceans

Kevin G-E. Scott and D. Weihrauch

With few exceptions, marine crustaceans are ammoniotelic, excreting nitrogenous wastes primarily as ammonia/ammonium (NH3/NH4+). This novel teaching lab uses modern scientific research techniques to demonstrate the mechanisms of ammonia excretion in the Dungeness crab (Metacarcinus magister). Over a two-week period, students will complete three separate experiments. First, live crabs in a closed environment are used to gain insight into physiological ammonia excretion rates. Next, using isolated crab gills, students will test the gill’s ability to actively excrete ammonia against inward directed concentration gradients (up to ten-fold). Lastly, potential mechanisms of ammonia excretion are investigated through exposing the isolated gills to various pharmacological blocking agents including ouabain (Na+/K+ ATPase), colchicine (microtubule trafficking), dintrophenol (ATP synthase uncoupler), azide (cytochrome c), and cesium ions (K+ channels). These mechanisms have been well characterized in the green shore crab (Carcinus maenas), however, they are currently unknown in Metacarcinus magister, giving the student a glimpse into active scientific research. Teaching fundamentals in the context of current research and using modern equipment, provides students with a solid background and better prepares them for today’s research environment.


Using Harvard Forest signature Datasets to Teach ‘Big-Data’ Organization, Summary, and Analysis in Undergraduate Ecology

Robert Smith

Due to initiatives such as the National Science Funded Long-Term Ecological Research program and the National Ecological Observatory Network and other long-standing research stations (e.g., Harvard Forest), long-term and spatially broad datasets are increasingly available for use in basic ecological research, assessment, and biomonitoring. A need exists to train undergraduates to understand the source and composition of large datasets as well as how to organize, summarize, and perform basic analysis of this unique type of data. I am developing a lab for an undergraduate general ecology course to use Harvard Forest’s signature datasets that requires students to generate an original hypothesis and test it through an open-ended process or data exploration and simple (often descriptive) statistical analyses. Students increase their proficiency in Microsoft Excel and learn about the scientific method. The project includes a trip to Harvard Forest to help students develop a more concrete understanding of the data. Only anecdotal educational outcomes were collected during the first two iterations of this course, but formal learning outcomes assessments are planned for future classes.


Vats of Preservative No More: Vacuum Sealing Specimens in Chordate Biology Labs

Joy Stacey

Traditionally, mid-level chordate biology labs employ large vats of preservative for storage of specimens on both short and long-term scales. Motivated by the logistics of using and disposing of large volumes of preservative in compliance with health and safety regulations, vacuum sealing was investigated as a method to maintain instructor prosections and student study specimens over varying periods of time. A readily available commercial grade vacusealer and food preparation plastic bags were used to seal specimens (perch, lamprey, shark, frog, mudpuppy, snake, mink, fetal pig, and rabbit) dipped in or sprayed with Wardsafe®, 20% isopropyl alcohol and Infutrace®. Specimens were monitored for quality from four to eighteen months. Specimen quality varied with animal and preservative used. While this method necessitates a redistribution of time and effort, the advantages in terms reduction in the amount of preservative used, time associated with specimen retrieval at the start of lab period, and end of semester cleanup make it preferable to holding specimens in large vats of preservative. The logistics needed for the successful use of this method will be illustrated and discussed.


REIL Biology: Integrating a Cyanobacterial Molecular Systematics Research Project into an Introductory Biology Laboratory

Catherine Wheeler and Jeffrey Johansen

Participation in a novel molecular systematics research project was used to teach introductory biology students concepts of DNA structure and replication, PCR, cloning, restriction analysis and molecular systematics. This poster will present the results of this project over the past two years as well as the pros and cons of incorporating research into an introductory level course.