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Homework Problems - Literature Learning Module: Lipids 1 KEY - Biology

Homework Problems - Literature Learning Module:  Lipids 1 KEY - Biology



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Research Paper: Sphingomyelinase Activity Causes Transbilayer Lipid Translocation in Model and Cell Membranes. Goñi (2003) The Journal of Biological Chemistry 278, 37169-37174 (doi: 10.1074/jbc.M303206200).


Sphingomyelin (SM) is a phospholipid localized mainly at the outer leaflet in microdomains or rafts of cell membranes. It can be cleaved by the protein enzyme sphingomyelinase, a phosphdiesterase, resulting in the generation of ceramide in the membrane. This enzyme cleaves SM in bilayer membranes.

1. This reaction is a hydrolysis, catalyzed by the enzyme. Draw a mechanism showing the hydrolysis (in the absence of the enzyme, which would alter the mechanism) that would give ceramide. Draw the Lewis structure of the other product as well. Finally draw a cartoon of the enyzme with reactant in the active site.

Ans: O on H2O attacks the P in SM, forming ceramide and phosphocholine.

cartoon:


Sphingomyelinase (SMase) can be activated when an external signal, such as Vitamin D3 binds to a membrane receptor, initiating a signal transduction activation of the cell. One signal in the pathway would be alteration in the SM raft, leading to changes in membrane protein arrangement and activity. The study below was designed to address how SM hydrolysis alters lipid organization in bilayers.

2. LUVs were made with a lipid ratio of SM:PE:Cholesterol (2:1:1 molar ratio) and in the presence of a water soluble protein, neuraminidase (MW 70,000). Note that these are artificial liposomes not biological membranes. As such, the SM would be expected to be equally distributed between the two leaflets. Devise a method to remove free, unencapsulated neuraminidase from the LUVs.

Ans: Make liposomes using detergent dialysis method or by extrusion through membranes. Either way, neuraminidase would be found both encapsulated and outside of the membrane. Small MW molecules on the outside of the vesicles could be removed by dialysis since the vesicles in the dialysis bag would be too big to pass through pores in the bag. The easiest way would be to use gel fitration (size exclusion) chromatography, which could easily separate the relative huge liposomes (which would elute first) from the relatively small protein (which elutes later).

  • animation of Gel Filtration Chromatography from Voet2


To study the properties of the LUVs, they were treated with GM3 ganglioside in methanol (in a volume 5% of the LUV preparation). A ganglioside is a glycolipid (contains a nonpolar lipid and polar sugar head group) usually found in membranes. The sugar head group of GM3 consists of neuraminic acid, galactose, and glucose, as shown in the structure below. Note that the encapsulated neuraminidase cleaves the terminal glycoyl-neuraminic acid from GM3. The most common types of gangliosides are glycosphingolipids. Since the final solution was 5% MeOH, an amount insufficient to alter liposome structure significantly, LUVs remained intact. Circle the polar head group.

3. Draw a cartoon diagram showing both layers of the LUV before and after addition of GM3. Use simple geometric representations for the lipid and the protein neuramindiase. Don't use Lewis structures as cartoon representations for the lipids.


4. The water soluble enzyme sphingomyelinase(SMase) was added to a suspension of these vesicles. The extent of hydrolysis of as a function of time (from 0 to 60 minutes) and the effect on hydrolysis of excess amounts of the nonionic detergent Triton X-100 with time (60-90 minutes) are shown below in Figure 1A. Previous experiments hadshown that this Triton X-100 concentration did not inhibit sphingomyelinase or neuraminidase.

Figure 1A. Sphingomyelin hydrolysis by sphingomyelinase. Average values ± S.E. (n = 4). (n = 5).

Explain using a cartoon and words the changes in the LUV on addition of SMase and of TX-100.

Ans: Addition of sphingomyelinase(1.6 units/ml) to a suspension of these vesicles induced SM hydrolysis, which reached equilibrium after 20 min, when 40%of SM had been hydrolyzed (Figure 1A). Addition of Triton X-100after 60 min caused membrane disruption, but SM hydrolysis didnot go beyond 50% at 30 min after detergent addition. Suggest that SMase must be membrane bound to cleave SM. The 50% saturation level suggest that only SM in the outer leaftlet was cleaved, and not SM in the inner leaflet.


5. The same experiment was repeated (addition of SMase to the LUVs) but instead of monitoring SM hydrolysis, glycoyl-neuraminic acid cleavage from the added GM3 was studied. Aliquots of the vesicle suspension were removed at fixed timesafter the addition of sphingomyelinase and analyzed for theGM3 product of neuraminidase activity. The results are shown in Figure 1B below.

Figure 1B. GM3 ganglioside hydrolysis by entrapped neuraminidase. (n = 5).

Describe the main difference in the results shown in graph 1b compared to 1A. Explain using a cartoon and words the changes in the LUV on addition of SMase and of TX-100.

Ans: GM3 washydrolyzed almost in parallel with SM, except that no saturationwas observed (Figure 1B). After the addition of Triton X-100,virtually all GM3 was cleaved by neuraminidase, a water soluble enzyme that doesn't need an intact bilayer to cleave GM3. One interpretationof these data is that, as a consequence of sphingomyelinaseactivity, GM3 was flipping to the inner leaflet, thus becomingaccessible to neuraminidase.


6. How was added GM3, which is found in the outer leaflet, cleaved by neuramidase, which is encapsulated? One explanation was that some encapsulated neuramidase leaked from the inside to the outside and the GM3 cleaved in the above experiment was in the outer leaftlet. To determine if neuraminidase was present on the outside of the LUVs, its activity against SMase treated vesicles as describe above was determined. The LUVs were filtered through membrane with small pores, allowing free neuramidase to pass through but not encapsulated LUV. They assayed the neuramidase using a soluble substrate of the enzyme, N-acetylneuraminyl-Gal-Glu. The results are shown in Figure 2A.

Figure 2A. Fraction of released neuraminidase in the time course of sphingomyelinase action. Free neuraminidase was separated from the vesicles by filtration. (n = 3).

Does the constant presence of neuramindase present from 1-60 minutes suggest constant leakage from the LUVs or an leakage arising from the filtration method? (Note that the value at 0 minutes (the moment of SMase addition) is the same at later times. Explain. Are the results consistent with the cleavage of GM3 shown in figure 1B from leaked neuramindase?

Ans: It was necessary to rule out the possibility of neuraminidasecoming out from the vesicles as a result of sphingomyelinaseactivity. To clarify this aspect, neuraminidase activity outside the sphingomyelinase-treated vesicles was assayed with the water-soluble substrate N-acetylneuraminyl-lactose. Even in the absence of sphingomyelinase activity(time zero), 18% of the total enzyme activity was recoveredin the filtrates. This is probably because of vesicle breakdowndue to shear stress during the filtration procedure used to isolate any "leaked" neuramidase from the encapsulated form.

7. Vesiclescontaining GM3 but not sphingomyelinase or internal neuraminidasewere treated with neuraminidase at the concentration found inthe filtrates above.

Figure 2B. ▲, hydrolyzed GM3 ganglioside when LUVs not containing neuraminidase were treated with the same amount of neuraminidase that was released in the experiment in 2A. Average values of two closely similar experiments; O, data of Figure 1B (SMase added to LUVs with encapsulated neuraminidase) replotted for comparison.

Compare the times course of GM3 hydrolysisis totally different from the one depending on sphingomyelinaseactivity. Suggest a hypothesis to account for the enhanced hydrolysis of GM3 in the presence of SMase. Draw a cartoon diagram in your explanation.

Ans: Vesiclescontaining GM3 but not sphingomyelinase or internal neuraminidasewere treated with neuraminidase at the concentration found inthe filtrates. Neuraminidase was added to the vesicle suspensionfrom the outside to ensure enzyme-substrate interaction. Inthis case (as seen in Figure 2B), the time course of GM3 hydrolysisis totally different from the one depending on sphingomyelinaseactivity. Thus, the results in Figure 1B cannot be explained onthe basis of neuraminidase efflux from the vesicles.


8. In another experiment, antibody that binds and neutralizes the activity of neuraminidase was added to preformed LUVs and experiment 1 repeated. The graphs below the two cases

Figure 2C. GM3 ganglioside hydrolysis by LUVs with encapsulated neuraminidase, with and without antineuraminidase antibody added to the LUV suspension. The paper did not define the symbols, but one is in the absence of added antibody and the other in the presence of added antibody. The curves differ little.

Using the data presented in Graphs 1-2, draw a cartoon and explain the sequence of events in the cleavage of GM3 by neuraminidase.

Ans: No significant differenceswere found between the fractions of hydrolyzed GM3 in the presenceand absence of antibody. We concluded that GM3 hydrolysis was catalyzed by neuraminidase inside the vesicles; thus, sphingomyelinaseactivity had caused GM3 to flip to the inside lipid monolayer


9. LUVs identical to those made above but with the added fluorophore, NBD-PE, were prepared. The structure of NBD-PE is shown below.

After the LUVs were made, the liposomes were treated with the membrane-impermeant sodium dithionite, which reduces NBD fluorescence.

Excess dithionitewas removed immediately by gel filtration. Note: any remaining flourescence is from inner leaflet NBD-PE. LUVs were then treated withsphingomyelinase. Enzyme activity was the same as describedin Figure 1A. Aliquots were removed from the reaction mixtureat regular intervals and mixed with an impermeant nonspecific antibody, IgG, labeled with another fluorophore, rhodamine. When NBD is excited with UV light, it fluorescence emission wavelength overlaps the excitation wavelength of rhodamine. If the two fluorphores are close enough, excitation of NBD can lead to rhodamine fluorescence emission, in a process called fluorescence resonance energy transfer.

Figure: Excitation (---)/Emission (___)Spectra of NBD (green) and rhodamine (blue).

Results are shown in the Figure 3 below. Control experiments, also shown in the figure,indicated that in the absence of sphingomyelinase, NBD-PE fluorescenceremained invariant with time.

Figure 3. Sphingomyelin hydrolysis as in Figure 1A. •, time course of NBD-PE fluorescence intensity; O, time course of Rho-IgG fluorescence intensity; triangles are the respective controls in the absence of sphingomyelinase.

Compare the relative changes see in the presence of SMase, with the relative lack of change in its absence. Are these results consistent with the results from the other experiments above?

Ans: As the sphingomyelinase reaction proceeded, NBD-PE flopped toward theouter monolayer, and energy transfer to Rho-IgG could take place. Consequently, when the fluorescence of NBD-PE was excited, its emission intensity decreased with time, and the emission intensityof Rho-IgG increased accordingly. The corresponding data areshown in Figure 3. Control experiments, also shown in the figure,indicated that in the absence of sphingomyelinase, NBD-PE fluorescenceremained invariant with time. Thus, fluorescence energy transfermeasurements confirm that sphingomyelinase activity inducesthe transmembrane movement of lipids, in this case, the movement of NBD-PE from the inner to outer leaftle.


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1. COVID DELAY Project: Living in the Anthropocene (Interdisciplinary Honors Program) Prof. Anne McNeil Develop course curriculum, design assignments, and identify reading materials.

2. Project: Chem 210 (Organic I Lecture) Prof. Alison Narayan Teaching Materials for GSIs in Introductory Organic Chemistry

3. Project: Chem 303 (Inorganic I Lecture) Prof. Vince Pecoraro Teaching Materials for CHEM 303 and 402: Integrating Brainscape tools

4. COVID DELAY Project: Chem 130 (General Chemistry) Prof. Charles C. L. McCrory, New Discussion Section Peer-Learning Activities for Chem 130 (Winter 2020)

5. COVID DELAY Project: Chem 130 (General Chemistry) Prof. Charles C. L. McCrory, New Course-Specific GSI training for Chem 130 (Fall 2019)

6. Project: CHEM 230 (Quiz/Homework Combo) Amy Gottfried To create a one-stop, integrated homework and quiz system for CHEM 230

7. Project: CHEM 230 (Pre-course refresher) Amy Gottfried To compile (using free on-line resources) a “refresher” for students who have not had general chemistry in multiple years.

8. Project: Chem 214 (Organic II Seminar for students in the Comprehensive Studies Program) Dr. Nicole Tuttle: Teaching Materials for New CSP seminar that accompanies CHEM 215

9. COVID DELAY Project: CHEM 260, 461, 463 (Physical Chemistry) Prof. Eitan Geva Development of interactive computer demos for undergraduate physical chemistry courses

10. COVID DELAY Project: SMART Center outreach Prof. Nils Walter Developing outreach tools for the Single Molecule Analysis in Real-Time (SMART) Center.

11. COVID DELAY Project: CHEM 125/126 (General Laboratory) Dr. A. Poniatowski General instructional development of new instructional materials for CHEM 125/126.

12. COVID DELAY Project: CHEM 125/126 (General Laboratory) Prof. Kerri Pratt Incorporating Snow Chemistry Research into CHEM 125/126.

13. Project: CHEM 246/247 (Bioanalytical Chemistry) Prof. Brandon Ruotolo Introducing Native Mass Spectrometry to Undergraduates in a CHEM 246/247

14. Project on Academic Integrity Dr. Amy Gottfried Promoting a culture of academic integrity.

15. Project: Chem 262 (Mathematical Methods) Prof. Roseanne Sension Introducing symbolic & numerical “computer math” in chemistry

16. Project: Chem 242 (Analytical Chemistry) Prof. Kicki Hakansson Lab on a chip: Incorporating Microfluidics in Undergraduate Lab

17. COVID DELAY Project: Chem 454 (Biophysical Chemistry) Prof. Julie Biteen. Topic: Learning through the literature

18. Project: Chem 646 (Chemical Separations)Prof. Brandon Ruotolo. Group Projects on Challenging Separations.

19. Project: Digital Learning Objects for Pre-college Learners Dr. Yulia Sevryugina Prof. Nicolai Lehnert. Creating digital content for Detroit-area students.

The following projects are not currently actively soliciting help, but if students are interested, please contact the faculty director for more information:

I. Project: Sustainable Polymers (MMSS Program) Prof. Anne McNeil Revise curriculum, develop and test new experiments for pre-college science program.

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VII. Project: CHEM 463 (Advanced Laboratory) Prof. Paul Zimmerman Sustainability Projects

  1. Project: The Anthropocene (Interdisciplinary Honors Course) Prof. Anne McNeil Identify reading materials and develop reading prompts/learning objectives for each class and discussion. This interdisciplinary honors course focuses on human-induced changes to our planet. It was first taught in W19 and is scheduled for W20 and W21. The students read papers and book chapters covering a wide range of topics, from geology to climate change to politics to economics to the Clean Water Act. This FFGSI project is aimed at helping prune some duplicate readings and identify new readings as well as develop new reading prompts/quizzes for each class and discussion.
  2. Project: Chem 210 (Organic I Lecture) Prof. Alison Narayan Topic: Teaching Materials for GSIs in Introductory Organic Chemistry The primary focus of this FFGSI position is to develop teaching materials for the GSIs teaching discussion sections that can be used to provide a more consistent experience for the students across each discussion section. With GSI training and the right teaching tools, we can provide a more consistent and excellent teaching experience from one GSI to the next, which will serve our students all the better, regardless of which discussion section they choose. I also want to develop worksheets that can be given to the students, that help them build the confidence needed as they learn material throughout the course. I believe that if we can help the students feel confident about their knowledge and apply it on intermediate level problems, they will be more able and willing to work out the difficult, exam-style problems of the coursepack, which is their best bet at succeeding in the course. By providing some structure for GSIs and a conceptual stepping stone to those difficult coursepack problems, I think the students will get more out of their discussion sections and be much more willing to keep going. A second goal of this position is to foster communication among the cohort of 210 GSIs to share teaching strategies and clarify concepts.
  3. Project: Chem 303 (Organic I Lecture) Prof. Vince Pecoraro Teaching Materials for CHEM 303 & 402: Integrating Brainscape. My thought for this project is to provide a Brainscape approach to learning some of the material in 303/402. I would use Brainscape exercises to build vocabulary for the subject and exercises to help then master some of the concepts. I would try to then give graded quizzes in the discussion section to evaluate their learning. The idea is for students to get feedback more rapidly on their understanding.
  4. Project: Chem 130 (General Chemistry) Prof. Charles C. L. McCrory, New Discussion Section Peer-Learning Activities for Chem 130 (Winter 2021) The purpose of this FFGSI is to develop a set of new peer-learning activities for Chem 130 discussion sections to better facilitate conceptual knowledge development among students. These activities will build upon and adapt the current active-learning activities used in the course, but incorporate new variety into the curriculum. The FFGSI will help develop 12 discussion topic-specific discussion activities adapted from published peer-learning exercises that have already been shown to increase conceptual knowledge among students.
  5. Project: Chem 130 (General Chemistry) Prof. Charles C. L. McCrory, New Course-Specific GSI training for Chem 130 (Winter 2021) The purpose of this FFGSI is to develop a training program specifically tailored for Chem 130 GSIs loosely modeled on the “Teaching Academy” for new faculty at the University of Michigan. The FFGSI will help develop a one-day intensive training session focusing on the interconnection of content knowledge and pedagogical content knowledge for specific Chem 130 course concepts. In addition, the FFGSI will help to develop a series of short interactive training modules for eventual incorporation into weekly Chem 130 staff meetings on various topics related to instruction such as “facilitating peer learning,” “creating inclusive and supportive class environments,” and “dealing with disruptive students.”
  6. Project: CHEM 230 (Quiz/Homework Combo) Amy Gottfried Now that CHEM 230 is a flipped classroom, students watch lecture content before coming to class. To check their comprehension, students take a short Canvas quiz and do a few homework problems. The quiz questions are delivered through Canvas and the homework problems come through Sapling. The goal of this project is to streamline the process and get all questions into a single format/system: minimizing the questions and maximizing the results.
  7. Project: CHEM 230 (Pre-course refresher) Amy Gottfried Students arrive in CHEM 230 with different general chemistry backgrounds (high chemistry + high placement exam score AP or IB Chemistry CHEM 125, 126, and 130.) To goal of this project is to compile (using free on-line resources) a “refresher” for students who have not had general chemistry in multiple years.
  8. Project: Chem 214 (Organic II Seminar for students in the Comprehensive Studies Program) Dr. Nicole Tuttle – Topic: Teaching Materials for New CSP seminar that accompanies CHEM 215. CHEM 214 is a new 1-credit course for students in the Comprehensive Studies Program that will run in Winter 2021 as a co-enrollment with CHEM 215. The primary focus of this FFGSI position is to develop teaching materials for the group and individual assignments in this new course. In particular, I’d like to identify key topics, concepts, and misconceptions that affect students’ learning in CHEM 215 and use those to develop structured group assignments. In addition, I’d like to extend the reflective/metacognitive assignments that I’ve developed for CHEM 209 into a productive direction for students who have a semester of organic chemistry learning already. I’d like to co-develop these materials with an FFGSI, and this project has the flexibility to be informed by the FFGSI’s interests.
  9. Project: CHEM 260, 461, 463 (Physical Chemistry) Prof. Eitan Geva Development of interactive computer demos for undergraduate physical chemistry courses Chem260/230 Compute-to-Learn (C2L) Honors Studio. A new pedagogy, called Compute-to-Learn (C2L), is being implemented within the framework of a supplemental, peer-led weekly 2 hour session, in a studio environment, where undergraduate students enrolled in introductory Physical Chemistry courses (Chem260 and Chem230) collaborate to create interactive computer demonstrations of basic Physical Chemistry concepts, using Wolfram Mathematica (a powerful computing environment commonly used in academia, industry, and education). The C2L pedagogy emphasizes action-based learning activities designed to promote students’ integration of new idea, within a collaborative apprenticeship environment that mimics the authentic experience of how science is done in real life. Senior undergraduate students who participated in a previous iteration of the studio serve as peer leaders whose role is to guide activities and help the students stay on track towards completing the project within the 13-week semester. The FFGSIs assigned to this project will be charged with further development of the pedagogy and assessment tools of its impact on students learning and outlook, as well as training, supervising and mentoring the undergraduate peer leaders and coordinating studio activities.”
  10. Project: SMART Center outreach Prof. Nils Walter Topic: Developing outreach tools for the Single Molecule Analysis in Real-Time (SMART) Center There is an urgent need to capitalize on the recent successes of single molecule and super-resolution fluorescence microscopy, as underscored by the 2014 Nobel Prize in Chemistry to three founders of the field with ties to the U-M. Starting in 2010, the U-M invested in this leading-edge research area through support of a successful NSF Major Research Instrumentation (MRI) application that seeded the Single Molecule Analysis in Real- Time (SMART) Center, housed in Chemistry and Biophysics but open to all users across the entire U-M. Both research groups already versed in single molecule analysis and those that never before experienced them ― but appreciate their broad impact equally on the basic and applied sciences from systems biology to materials design ― using with increasing success the SMART Center’s currently five single molecule and super-resolution microscopes. To enhance outreach across campus and beyond, three types of activities need to be developed: (1) hands-on demonstrations of assays that users developed on the SMART Center microscopes, to be integrated as modules into existing undergraduate and graduate courses at the U-M such as Chem 352, Biophys 450, and Biophys 521 (2) a “Single Molecule Roadshow” to bring mobile hands-on experimentation to inner-city high schools in the Detroit school district with large underrepresented groups, Ann Arbor’s Hands-on Museum, and Detroit’s Science Center and (3) web-based information and activities to introduce the concepts of single molecule research. In combination, we expect these efforts to provide for the kind of stimulating intellectual immersion that is known to foster innovation and the ‘eureka’ effect in young minds.
  11. Project: CHEM 125/126 (General Laboratory) Dr. A. Poniatowski Topic:General instructional development of new instructional materials for CHEM 125/126. Our goal for the Chemistry 125/126 lab course is to move towards a classroom structure centered on a research context from the traditional chemical sub-disciplines that are of interest to our students. One example is a project focused on a biomedical theme: We have focused on incorporating direct application of original scientific research to the course, focusing first on the biomedical/biochemical research field. During the fall semester, we formulated 2 objectives: 1) developing experimental procedures with direct application to the biological and biomedical field and 2) creating presentation/discussion questions (denoted as team demonstration questions) for each experiment currently on the syllabus that have applications to biomedical research.
  12. Project: CHEM 125/126 (General Laboratory) Prof. Kerri Pratt Topic: Incorporating Snow Chemistry Research into CHEM 125/126. Our goal is to develop two sections of the Chemistry 125/126 lab course based on original snow chemistry research, focused on understanding implications of Arctic sea ice loss and the application of road salts in the wintertime in the mid-latitudes. Course development will include designing and implementing experiments, creating lab worksheets and other class materials. The overall goal of the course is to expose students to original research to develop critical thinking, writing, and presentation skills.
  13. Project: CHEM 246/247 (Bioanalytical Chemistry) Prof. Brandon Ruotolo Topic: Introducing Native Mass Spectrometry to Undergraduates in a CHEM 246/247 Native mass spectrometry has become an increasingly important tool in science-related fields, especially when combined with electrospray ionization (ESI). However, many undergraduate students are ill-prepared to use this type of instrumentation that is now required by pharmaceutical and biotechnology companies world-wide. In this project, two workflows for ESI-MS experiments that explore protein- protein and protein-ligand interactions in a biochemical analysis laboratory will expose undergraduate students to principles of protein systems and mass spectrometry.
  14. Project on Academic Integrity Dr. Amy Gottfried Topic: Promoting a culture of academic integrity. Allegations of cheating on a (chemistry) final exam were made against a student whose “wandering eyes” were captured on a cell phone video. The judicial process and appeal shed light on many valuable lessons. The goal of this project would be to explore student, faculty, and GSI rights and responsibilities in promoting and maintaining academic integrity to gather data on how exams are proctored across campus to open a dialogue about proctoring to evaluate any benefits in making the process more uniform and to formulate an educational campaign for GSIs and faculty on these findings.
  15. Project: Chem 262 (Mathematical Methods) Prof. Roseanne Sension Topic: Introducing symbolic & numerical “computer math” in chemistry This project will use the Matlab (Mathworks) interface to develop 6-12 exercises for Chem 262. The course has 12 weekly homework assignments and the goal will be to add one computer based exercise to each assignment. These exercises will integrate into homework problems and allow the students to dig deeper. The number of exercises developed for Winter ’16 will depend on the amount of time required to develop and test each exercise. A minimum effort of 10 hours per exercise is anticipated to design and implement productive exercises based on Prof. Sension’s experience designing and implementing the MathCad curriculum for Chem 462.
  16. Project: Chem 242 (Analytical Chemistry) Prof. Kicki Hakansson Topic: Lab on a chip: Incorporating Microfluidics in Undergraduate Lab Polydimethlysiloxane (PDMS) is a common material used to fabricate microfluidic channels and chips, using soft lithography techniques. The three main steps in this process include rapid prototyping, replica molding and sealing. Depending on the number of chips required, this process could be very time consuming and tedious. With 3-D printing, the fabrication time is greatly reduced as a single machine does the process. Additionally, use of a 3-D printer is more reproducible as the device fabrication is done by single engineering drawing software. We previously described a novel experiment, which uses an Agar-based microfluidic device (manuscript in preparation) to quantify salicylate concentration. Here, we propose to use 3-D printed microfluidic devices, an approach which will potentially improve data quality by removing artificial defects that arise from the Agar-based workflow. Using the 3- D printed microfluidic device, we will explore fundamentals of laminar vs. turbulent flows by altering chip geometries (i.e. Y-channel and zigzag geometries) and fluid viscosities (methanol vs. water) to promote mixing. Once mixing is achieved, the reaction of iron (III) and salicylate will be observed in order to construct a calibration curve for the determination of salicylate concentration. When iron (III) and salicylate reacts, they form a purple solution. The degree of purple will be probed using image analysis software. Finally, the image analysis will be compared to spectrophotometric determination from a previous experiment.
  17. Project: Chem 454 (Biophysical Chemistry) Prof. Julie Biteen. Topic: Learning through the literature. In Chemistry 454, students learn about the modern techniques that are used to characterize the structure and dynamics of biological molecules. In order to deepen the students’ understanding of these approaches in the context of real-world applications, we will develop a set of readings from the current literature. The FFGSI will need to select recent, high-impact publications, which are exciting while understandable to a junior-level undergraduate. Furthermore, the selection will need to span the topics covered in the course. The FFGSI will also create a rubric for evaluating student comprehension of the literature. Finally, the FFGSI will develop and implement methods to encourage meaningful scientific discourse about the papers whether the conversations are in-person or online.
  18. Project: Chem 646 (Chemical Separations) Prof. Brandon Ruotolo. Group Projects on Challenging Separations. The purpose of the FFGSI position will be to design and implement group projects for students in 646. There are many examples of “real-world” analytes that are difficult to separate such as glycans, lipids, and chemical pollutants, among others. These group projects will require students to research a set of these analytes and the current approaches for separating them. Groups will then present across multiple class days on different facets of their analytes including their relevance, why they are difficult to separate, and current state of the art approaches for separating and analyzing them. The role of the FFGSI will be finding suitable analytes for the project topics and then developing a unique set of probing questions/requirements for each topic. The FFGSI will also create rubrics for the projects, and pre- and post-surveys related to the group projects and course overall.
  19. Digital Learning Objects for Pre-college Learners The Chemistry Librarian, Dr. Yulia Sevryugina and Prof. Nicolai Lehnert propose to develop and implement a series of digital learning objects (DLOs) on information literacy for teaching pre-college and entry level college students with interests in science, technology, engineering and math (STEM). Specifically, we focus on pre-college learners from historically underrepresented and underserved populations who participate in the 7-weeks summer internship program D-RISE (Detroit Research Internship Summer Experience).i We believe that by providing access to our proposed digital content to high school students, we can introduce them to valuable university-level education and motivate them to seek college education in the STEM fields. Furthermore, developed DLOs will be available for any instructor interested to implement them in their courses through the Canvas LMS (Learning Management System).

The following projects are not currently actively soliciting help, but if students are interested, please contact the faculty director for more information:

  1. Project: CHEM 211 (Organic Laboratory I) Prof. Anne J. McNeil Topic: Creating REAL (Research Experiences in Authentic Laboratories) Science Students often cite uninspiring introductory courses as a reason for leaving the STEM fields. At the University of Michigan (UM), we teach an introductory organic chemistry lab to approximately 2000 first- year students per academic year. We therefore have an extraordinary opportunity to nurture and/or transform how these students view science. Teaching organic chemistry to first semester first-year students, a tradition at Michigan since 1989, has led to the exceptional challenge that most students enrolled in the corresponding introductory laboratory course have no prior lab experience. Over the past two years, we have completely overhauled this course into an active- learning adventure for the undergraduate students. We would like to make improvements to this existing curriculum. In addition, to keep the labs fresh, we imagine a suite of new labs that could rotate in. We are therefore looking for a FFGSI to help revise existing materials and develop additional lab modules for the CHEM 211 curriculum
  2. Project: CHEM 260 (Physical Chemistry) Prof. Dominika Zgid Topic: Demonstrations and In-Class Experiments for “Real World” chemistry The project will develop demonstrations and experiments to be performed during lecture that will illustrate concepts from the suite of physical chemistry courses. The purpose of the demonstrations will be to help students visualize challenging concepts and connect them with “the real world.”
  3. Project: CHEM 225/226 (Physical Chemistry) Dr. Amy Gottfried Topic: Developing a New Laboratory Course to accompany CHEM 230 Currently CHEM 125/126 accompanies the CHEM 130 lecture course and there is no laboratory course affiliated with CHEM 230. What would a 200-level general chemistry lab course (CHEM 225/226) look like? How would the course serve students not just in increasing their knowledge and their skills but along their academic career path (or what students would the course be targeted to?)
  4. Project: CHEM 463 (Advanced Laboratory) Prof. Paul Zimmerman Topic: Sustainability Projects Chem 463 exposes students to fundamental principles of thermodynamics and statistical mechanics. Although the models presented in such courses are simple, they are powerful enough to provide insight into problems of climate change, sustainable energy, and other challenges faced by modern society. In lieu of traditional discussion sections, students are trained in these concepts and apply this knowledge to their own sustainability projects. The projects, which include a paper and an oral presentation, require that students present a model for understanding or predicting the behavior of a challenging contemporary problem in sustainability. Students’ perceptions of sustainability are evaluated both at the beginning and end of the course to determine how the projects impact their views.
  5. Project: Chem 454 (Biophysical Chemistry) Prof. Julie Biteen Prof. A. Ramamoorthy Topic: Learning through the literature In Chemistry 454, students learn about the modern techniques that are used to characterize the structure and dynamics of biological molecules. In order to deepen the students’ understanding of these approaches in the context of real-world applications, we will develop a set of readings from the current literature. The FFGSI will need to select recent, high-impact publications, which are exciting while understandable to a junior-level undergraduate. Furthermore, the selection will need to span the topics covered in the course. The FFGSI will also create a rubric for evaluating student comprehension of the literature.

ARCHIVE OF PAST PROJECTS (RETIRED, but can be used to inspire new ideas)


METHODS

Course Description

We conducted this study at a research university during one semester of a large-enrollment Introductory Biology course for science majors. The course is part of a two-semester introductory biology sequence and focuses on principles of genetics, evolution, and ecology. This course is currently the subject of a comprehensive reform aimed at implementing evidence-based, learner-centered instructional practices (Handelsman et al., 2004 Smith et al., 2005 Handelsman et al., 2006). There are no mathematics pre- or corequisites for this course beyond the requirements for entrance to the university (3 yr of high school math, including 2 yr of algebra and 1 yr of geometry).

Study Population and Research Context

Approximately 80% of the students enrolled in the course were in their first or second year of college (48 and 32%, respectively). Life science majors (e.g., zoology, plant biology, biochemistry) and prehealth or preveterinary students made up 60% of the course population (Table 1 and Supplemental Material). For this study, we analyzed and reported data from students in one course section who completed pre- and postinstruction assessment of QL skills (n = 175).

Table 1. Students by major

This study was conducted in the context of a broader initiative aimed at reforming the introductory biology curriculum. The research was reviewed and classified as exempt by the university's Institutional Review Board.

Instructional Design

Instructors responsible for three of the course sections (150–190 students per section) met weekly to collaborate in all aspects of course design. Weekly meetings focused on constructing common learning objectives and creating learning activities and assessments used in all three sections of the course. We designed all class meetings to engage students through active, inquiry-based pedagogy. At the beginning of the course, we discussed with students the broad course goals, which included learning about the nature of science and knowing how to build scientific knowledge. To achieve these goals, students actively engaged in the activities of scientists, such as collaborative problem solving, creating and interpreting conceptual models, and articulating and evaluating scientific arguments.

Our strategy for infusing quantitative thinking in the normal course of instruction was through iterative assessment of students' QL skills, followed by feedback. We designed and administered (at the beginning of the course and then repeatedly throughout the semester) formative and summative assessments, which incorporated quantitative problems that complemented and supported learning of the biology concepts in the course. These assessments allowed us to rapidly determine whether students were fluent in QL skills directly relevant to biology. Based on the assessment outcomes, we tailored instruction in all three sections to provide students with feedback and further practice, if necessary.

Throughout the semester, we articulated specific QL objectives (Table 2) that complemented the existing course content and learning objectives. Rather than developing stand-alone QL modules, we designed instructional modules, homework, and quiz and exam items that incorporated QL objectives. In the course, students encountered multiple opportunities (Table 3) to apply quantitative thinking in the context of problems about genetics, evolutionary biology, and ecology. All classroom activities and assessments were followed by instructor feedback.

Table 2. QL objectives incorporated into introductory biology

Perform simple manipulations of numerical data and express data in graphical form

1a. Carry out basic mathematical operations (i.e., calculate averages, percentages, frequencies, proportions)

1b. Represent data in graphs (e.g., choose the appropriate type of graph, correctly label axes and units, provide informative captions and legends)

Describe and interpret graphs

2a. Interpret the meaning of simple statistical descriptors, such as error bars and trend lines

2b. Use graphs to formulate predictions and explanations

Use numerical evidence to generate and test hypotheses

3a. Formulate null and alternative hypotheses

3b. Accept or reject null hypotheses based on statistical tests of significance

Articulate scientific arguments based on numerical evidence

4a. Articulate complete and correct claims based on data

4b. Use appropriate reasoning (i.e., experimental design and/or statistics) to support the validity of data-based claims

Exemplars of QL-infused Instruction

In the first week of the course, we implemented a module—the “termite activity”—that addressed the nature of science and incorporated several quantitative aspects. In class, students observed termites following the trace of an ink pen on a sheet of paper. Working in collaborative groups, students observed a small number of termites and the termites' responses to different inks. Students quickly made the observation that termites prefer the ink traces from certain pens while ignoring others. We asked students how a scientist would start from this simple observation to generate evidence to build a scientific claim regarding the termites' behavior (e.g., “what would you need to do to demonstrate that termites prefer ink A to ink B?”). Students worked at developing testable hypotheses about the termites' ink preferences and designed simple experiments to collect quantifiable data about this behavior. To do so, students needed to devise a reproducible method for gathering quantitative data about the termites' ink preferences conduct an experiment and record, analyze, and interpret the data.

Instruction throughout the semester followed in this manner. Although it is beyond the scope of this article to illustrate in detail each activity, we direct the reader to Ebert-May et al. (2010) and to an example of a teaching and learning module that we implemented in the course (a case study on evolution of antibiotic-resistant bacteria http://serc.carleton.edu/42411).

After the termite activity, we assessed students' learning about the nature of science on the first in-class quiz, which included the Frog problem (Figure 1), designed to assess both students' understanding of the nature of science and QL skills. The Frog problem presented students with an experimental scenario and a data set. Students were asked to calculate means (objective [Obj.] 1a), represent the data graphically (Obj. 1b), draw conclusions based on the evidence (Obj. 4a), justify their claim (Obj. 4b), and deduce from the experimental setup what hypothesis that experiment was testing (Obj. 3).

Figure 1. The Frog problem, adapted from an original problem (http://first2.plantbiology.msu.edu/resources/inquiry_activities/frog_activity.htm). This problem was developed by D. L. and D.E.M., based on the work of Kiesecker (2002), and includes text quoted from Miller (2002).

In the context of the unit on evolution, we taught about Hardy–Weinberg equilibrium by using a classroom simulation that required students to calculate allele and genotype frequencies (Obj. 1a) and to make predictions based on observed and calculated data (Obj. 3a). Within the ecology unit, students investigated the impact of invasive species on aquatic ecosystems by exploring the case of sea lampreys in the Great Lakes (www.glfc.org/lampcon.php). Students generated a graph of population growth (Obj. 1b) developed a null hypothesis (Obj. 3a) interpreted a chi-squared value (Obj. 2a) and articulated a complete scientific argument, including a claim (Obj. 4a) and warrant (Obj. 4b).

The final exam was structured around the case of the moose and wolves of Isle Royale, Michigan (www.isleroyalewolf.org/wolfhome/home.html). Students answered questions on genetics, evolution, and ecology within the context of the Isle Royale ecosystem, with particular emphasis on the moose and wolves. One item on the exam (Wolf problem Figure 2) presented students with a data set and asked them to calculate frequency values (Obj. 1a), represent the frequency data in a graph (Obj. 1b), and predict what kind of warrant would be necessary to support a claim based on those data (Obj. 4b).

Figure 2. The Wolf problem. The data that guided design of this problem are publicly available through the “Wolves and Moose of Isle Royale” website (www.isleroyalewolf.org/overview/overview/wolf%20bones.html).

Analysis of Students' QL Skills

Graphing the calculated data (means for the Frog problem frequencies for the Wolf problem)

Appropriately labeling the y-axis

Appropriately labeling the x-axis

Using an appropriate type of graph for the data (a bar graph, in both cases)

Each graph received a composite score, the sum of all four elements. For example, a score of 4 means a student graphed the calculated data using a bar graph and labeled both axes correctly. Scores of ≤3 indicate an error in one or more areas. We compared students' scores at the beginning (Frog problem) and at the end of the course (Wolf problem) by using a paired sample Wilcoxon signed rank test. Statistical analysis was conducted in the R statistical environment (R Development Core Team, 2009).

The Frog problem asked students to formulate a claim based on the given evidence and to provide appropriate reasoning (warrant) to support the claim. We assigned a score of 1 or 0 for presence/absence of each of these following elements in the students' claims:

Student stated that atrazine alone has no effect.

Student stated that trematodes alone have an effect.

Student stated that the combined effect of trematodes and atrazine is greater than that of trematodes alone.

Each claim therefore received a score between 0 and 3 a score of 3 indicates a complete and correct claim. Students' warrants were analyzed for explicit reference to elements of experimental design. We scored students' warrants as correct based on whether they mentioned at least one of the following elements of the experimental setup:

Large number of frog eggs used

Number of replicates − three for each treatment

Use of the appropriate experimental controls

The Wolf problem provided quantitative evidence and a claim, and asked students what kind of warrant would support that claim. Students' warrants were scored as correct if they explicitly stated that a statistical test of significance (such as the chi-squared test) should be performed on the data to support the claim.

Based on patterns we observed in the students' warrants, we also identified elements that characterized incorrect reasoning. In this study, we focused on two kinds of “incorrect reasoning”: a) the student restated the claim and (b) the student restated the evidence, by either pointing at the raw data or at the graph. We scored students' warrants for presence (or absence) of these elements.


APPENDIX A

Pretest and posttest questions used to measure learning gains in the F'03 and S'04 courses. The 12 questions that were also used in the S'05 course are marked with an asterisk. The answers scored as correct are in bold-face type.

The five most commonly studied metazoan model organisms: C. elegans, Drosophila, Xenopus, chick, and mouse, are important for biomedical research because all of them

are simpler and/or experimentally more convenient than humans.

are descended from a common metazoan ancestor.

are representative of five different phyla.

use many of the same developmental and physiological mechanisms as humans, though they appear superficially very different.

have one or more characteristics that facilitate study of certain aspects of development.

* We still don't understand very well how genes control the construction of complex structures, like the antennae of the fruit fly, Drosophila melanogaster. If you wished to identify genes that control antennal development and find out what proteins they encode, the best way to begin would be to:

isolate a gram of D. melanogaster antennae and extract mRNAs to make cDNA clones.

find another Drosophila species with different antennal morphology and genetically map the genes responsible for the difference.

obtain a large population of embryos at the stage when antennae are beginning to form, label them with 32 P, extract the labeled mRNAs, make the corresponding cDNAs, and sequence them.

mutagenize a population of D. melanogaster wild type and screen their progeny for mutants with no antennae or altered antennal morphology then genetically map the mutations responsible.

search the database of sequenced D. melanogaster genes for homologs of antennal genes in other organisms.

* Drosophila strains carrying a mutation in a gene you have named ant have no antennae. You suspect that ant could encode a known transcription factor called PT3. The PT3 gene has been cloned and sequenced. A good test of whether ant is the PT3 gene would be to:

determine whether a PT3 gene probe will hybridize to any mRNAs from an ant mutant.

determine whether the cloned PT3 gene injected into an ant mutant embryo could rescue (correct) the antennal defect.

determine whether double-stranded RNA made from the cloned PT3 gene and injected into the embryo causes lack of antennae.

isolate the PT3 gene from ant mutant fly DNA and determine whether its sequence is different from that of the normal PT3 gene.

use PT3 DNA to probe Southern blots of digested genomic DNA from wild-type and ant mutant embryos, and ask whether the hybridization patterns are different.

* Which of the following statements about ligands and receptors is/are true?

Components of the extracellular matrix never serve as signaling ligands.

The receptors for steroid ligands are membrane bound.

Many ligands interact with receptors in target cell membranes to activate signaling pathways.

Juxtacrine signaling involves diffusible ligands and membrane bound receptors.

Two cells with the same receptor will always respond identically to a given ligand.

* The number of different signaling pathways involved in embryonic development is

The position and orientation of the cleavage furrow that separates two mitotically dividing cells during cytokinesis are

usually determined by external cues.

equidistant from the two poles of the mitotic spindle and orthogonal to it.

equidistant from the two poles of the dividing cell and orthogonal to a line connecting them.

often orthogonal to the cleavage plane of the preceding division.

controlled by interaction of microtubules with the cortex of the dividing cell.

* Epithelial cells are different from mesenchymal cells in that epithelial cells:

have polarity, defined by an apical and basal side.

are tightly adherent to each other.

are loosely adherent to each other.

are usually defined as migratory.

typically comprise the linings of organs.

Which of the following is/are likely to bind to specific DNA response elements and activate or repress the transcription of specific genes?

A steroid hormone receptor.

From the numerical choices below, pick the one experimental technique that could best be used to answer each of the questions 9-11.

Gel mobility shift assay with labeled DNA.

* Which of two tissues contains more of a particular mRNA? 2

* Where is a particular transcript (for which you have an RNA probe) present in an embryo? 3

* What is the phenotype of an embryo in the absence of a particular transcript? 4

* Consider a recessive, maternal-effect C. elegans mutation, m, that causes embryos to die. Which of the following statements is/are true?

Whether an embryo dies will depend on the genotype of the embryo.

Whether an embryo dies will depend on the genotype of the hermaphrodite parent.

If a heterozygous (m/+) hermaphrodite is mated to a heterozygous male 1/4 of the progeny embryos will die.

If a homozygous (m/m) hermaphrodite is mated to a wild-type male, all of the progeny embryos will die.

The experiment in (d) cannot be done, because m/m hermaphrodites will always die as embryos.

* In all animal embryos, the process of gastrulation accomplishes the following important function(s):

Patterning the anterior-posterior axis.

Establishing which side of the embryo will be dorsal.

Bringing endodermal cells into the interior of the embryo.

Bringing ectodermal cells into the interior of the embryo.

Bringing endodermal and ectodermal cells into contact for inductive interactions.

* Targeted alteration (knockout or mutation) of a specific gene in the germ line of an animal requires

that the animal's genome has been completely sequenced.

that the gene in question has been cloned.

a method for introducing DNA into cells that are in or will give rise to the germ line.

homologous recombination of introduced DNA with the resident gene on a chromosome.

nonhomologous recombination of introduced DNA with the resident gene on a chromosome.

* Programmed cell death (apoptosis)

occurs only in invertebrates.

occurs in response to injury.

is necessary to prevent cancer in mammals.

occurs only in certain degenerative disease conditions.

is important in limb morphogenesis.


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Biodiversity as a tree: A "micro" view of life

Instead of the macro view offered by the Scale, Darwin was focused on a "micro" view of biodiversity: What could explain the small variations distinguishing species that actually resembled one another? He came to see that evolutionary changes on the micro level would add up to the differences that were obvious at the macro level. So, instead of a stairway or ladder as a metaphor for understanding the cluster pattern of biodiversity, Darwin pictured a tree.

This was a brilliant insight. Rather than being arrow-like and linear, a tree has many elements that spread out in different directions. Rather than being static, it is dynamic. It grows over time, just as evolution is embedded in time. It sprouts branches, as if it were generating new varieties and new species. Or, it may have branches that do not subdivide. Some branches grow straight up, parallel to the trunk, while most head off in different directions as they develop, resembling alternative adaptations. Some branches grow into stumps and die out, becoming extinct. Others may grow long and last for generations, thousands of years, tens of thousands of years, and even longer. None of the branches of a tree is judged to be any better than others none is superior and none is inferior. They are all simply different.

Crucially important is the fact that all the branches of a tree are interconnected. You can trace their origins from their endpoints to the parent shoots from which they grew, just as you might trace the roots of dogs, or cats, or Galapagos finches to their original ancestral species.

The Origin tree diagram illustrates how a branching pattern of evolution can produce a greater number of species over time than what was there to begin with. It shows how some lines of species, or lineages, split more frequently than others. It shows that some lineages do not split at all but evolve almost like a column. It shows that extinction is a basic property of descent: Many populations are left behind and do not reach the top because they have died out.

Darwin saw evolution as a


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Water Balance of Cells Without Rigid Walls

Unlike plants, animal cells do not have rigid walls surrounding their cellular membranes. If an animal cell is placed in a hypotonic environment, the cell will gain water, swell, and possibly burst. A cell without a rigid wall will lose water and shrivel if placed in a hypertonic environment. A cell without rigid walls may require an isotonic environment to live. Alternatively, this type of cell may also survive through the use of adaptations for osmoregulation. This allows cells to actively regulate the flow of water across the membrane.


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