Anne Walter | St. Olaf College (original) (raw)

Papers by Anne Walter

Exploring Mathematical Modeling in Biology Through Case Studies and Experimental Activities

Abstract This section is for instructors and laboratory support personnel. It includes practical ... more Abstract This section is for instructors and laboratory support personnel. It includes practical information for setting up and carrying out the lab activities presented in the text including safety precautions. Alternate lab activities that meet the same mathematical modeling goals are also presented including some “dry labs.” These guidelines are meant to help those adapting this text to adjust course activities in ways that can easily be supported at their institutions. It is also meant to catalyze new ideas and new projects that might be done independently by students or simply be added to the repertoire of supporting activities.

Exploring Mathematical Modeling in Biology Through Case Studies and Experimental Activities, 2020

Abstract Numerical solutions to differential equations and optimization algorithms to estimate pa... more Abstract Numerical solutions to differential equations and optimization algorithms to estimate parameters are implemented in this unit. Sensitivity analysis is introduced to measure the effect of changes in the parameters on the model output as a means for system control, experimental design, and model validation. These tools are applied to the familiar logistic growth and tumor growth models in the background before being explored more deeply in systems with more complex interactions. A model of the Ebola virus, infected cells, and uninfected cells is used to understand the progression of each of these, and sensitivity analysis helps us determine which model parameters can be estimated from virus data. The classic SIR (susceptible, infected, removed) model is applied to the 2009 influenza pandemic, and vaccination strategies are tested. The growth of prostate cancer cells and the immune response are modeled, and ways the immune system can be used as cancer therapy are investigated. Models are used to study quorum sensing and to understand how extracellular conditions can lead to a switch such as bioluminescence. In the lab, a glucose–insulin feedback model is used to predict insulin behavior under several typical biological circumstances.

This section provides a brief introduction to mathematical modeling in biology and basic programm... more This section provides a brief introduction to mathematical modeling in biology and basic programming and lab skills. The purpose of this section is to build the reader's confidence and skill set in R and the lab before they engage in the modeling process. The R Basics section is for those who are new or relative novices in the use of R or other programming languages and introduces data structures, plotting, importing data, and linear regression. Exercises engage students with the material and reinforce the concepts presented. This section of the book may be extremely helpful on its own or to any course or team project that requires R. The Prelab Lab introduces pipettes, units, spectrophotometry, dilutions, and data analysis. Again, exercises are embedded to help users practice using the equipment and thinking about the methods they are using to collect data.

Comparative Biochemistry and Physiology Part A: Physiology, 1978

Total body water (TBW) volume and TBW turnover rate were measured by tritiated water (THO) disapp... more Total body water (TBW) volume and TBW turnover rate were measured by tritiated water (THO) disappearance rate in glaucous-winged gulls, Larus gfaucescens drinking either fresh water or sea water. These measurements were compared allometrically to values reported for other birds. 2. TBW volume was 792 3% BW and TBW turnover 0.064-tO.006 ml/g day in birds given fresh water. These values did not change when these birds were later adapted to sea water. 3. TBW volume is large in gulls compared to other species. TBW turnover rate of gulls is similar to that of other species.

PRIMUS, 2015

St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core ... more St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core course, Mathematics of Biology, was redesigned to include a wet laboratory. The labs required students to collect data and implement the essential modeling techniques of formulation, implementation, validation, and analysis. The four labs investigated population growth, enzyme kinetics, glucose-insulin feedback and random walks/diffusion. Based on assessment data, having the lab and class juxtaposed was an effective way to reinforce mathematical concepts and encourage collaboration among students with different majors. We discuss key factors that permitted this course's development, the continuing challenges and how this model might be adapted to other venues.

Biochimica et Biophysica Acta (BBA) - Biomembranes, 1980

Keyhole limpet hemocyanin has been shown by others (Alvarez, O., Diaz, E. and Latorre, R. (1975) ... more Keyhole limpet hemocyanin has been shown by others (Alvarez, O., Diaz, E. and Latorre, R. (1975) Biochim. Biophys. Acta 389, 444-448) to form single conductance channels in black lipid membranes. In an attempt to visualize how the large (300 ~) water-soluble hemocyanin molecule interacts with lipid bilayers, we have examined hemocyanin in the presence of lipids with the electron microscope. We find that incubation of lipids with keyhole limpet hemocyanin produces a characteristic 70 /~ in diameter, ring-shaped particle or annulus associated with the bilayer. This annulus, which appears to be quite distinct from previously observed aggregated and dissociated forms of hemocyanin, may be responsible for the channel formation in black lipid membranes.

College recently restructured its Summer Bridge Program (SBP) course for incoming lowincome (LI) ... more College recently restructured its Summer Bridge Program (SBP) course for incoming lowincome (LI) and first-generation (FG) college students from a non-majors’ biology course, “Issues in Biology,” to an interdisciplinary “Explorations in Science” course. Two significant changes were made with the intention of giving students more agency as scholars: a) lab-based research projects vs. library projects and b) explicitly taught quantitative skills. Both courses used a coherent theme, outside readings and provided opportunities to practice study and exam taking skills. Here we describe the “Explorations” course in detail and compare the outcomes of its first two offerings to those of the original “Issues” class. Both SBP cohorts were compared to students who were neither LI nor FG. We learned that global outcomes such as average retention rate and major selection were not affected by the new format. However, students in “Explorations” mastered more quantitative skills, succeeded in their...

American Journal of Reproductive Immunology, 1995

It has been proposed that antibodies against phospholipid-dependent antigens (aPLs), induce recur... more It has been proposed that antibodies against phospholipid-dependent antigens (aPLs), induce recurrent pregnancy loss and thrombosis through modulation of endothelial cell function, yet aPLs have not been conclusively shown to bind with endothelial cells. Using indirect immunofluorescence we investigated the anti-endothelial cell reactivity of three monoclonal antibodies that differentiate between the phospholipids cardiolipin (CL) and phosphatidylserine (PS): BA3B5C4 (CL+/PS+); 3SB9b (CL-/PS+); and D11A4 (CL+/PS-). Cultured umbilical cord endothelial cells were prepared without fixation or with cold acetone fixation. None of the aPLs reacted with endothelial cells prepared without fixation. 3SB9B reacted strongly with cytoskeletal-like components in acetone-fixed cells, whereas BA3B5C4 and D11A4 were unreactive. The cytoskeletal-like binding of 3SB9b was completely blocked by a monoclonal antibody against vimentin, whereas antibodies against tubulin or actin were not inhibitory. Lipid extraction of the cells destroyed the 3SB9b reactive antigen without affecting the reactivity of anti-vimentin. These results suggest that phospholipid-dependent antigenic determinants are not expressed on the surface of resting endothelial cells but that a PS-dependent antigenic determinant is associated with endothelial cell intermediate filaments.

Chloride Transport in Biological Membranes, 1982

The Journal of biological chemistry, Jan 5, 1988

Fusion of vesicular stomatitis virus (VSV) with Vero cells was measured after exposure of the vir... more Fusion of vesicular stomatitis virus (VSV) with Vero cells was measured after exposure of the virus to low pH under a variety of experimental conditions. The method of relief of fluorescence self-quenching of the probe octadecylrhodamine was used to monitor fusion. Incubation of the virus at pH 5.5 prior to binding to cells led to significant enhancement of fusion at the plasma membrane, whereas fusion via the endocytic pathway was inhibited. Fusion of pH 5.5-pretreated VSV showed a similar pH threshold for fusion as nontreated virus, and it was blocked by antibody to VSV G protein. Activation of VSV by pretreatment at low pH was only slightly dependent on temperature. In contrast, when VSV was first bound to target cells and subsequently exposed at 4 degrees C to the low pH, activation of the fusion process did not occur. The pH 5.5-mediated activation of VSV could be reversed by returning the pH to neutral in the absence of target membranes. The low pH pretreatment also led to agg...

The Journal of biological chemistry, Jan 5, 1987

We have studied fusion between membranes of vesicular stomatitis virus (VSV) and Vero cells using... more We have studied fusion between membranes of vesicular stomatitis virus (VSV) and Vero cells using an assay for lipid mixing based on the relief of self-quenching of octadecylrhodamine (R18) fluorescence. We could identify the two pathways of fusion by the kinetics of R18 dequenching, effects of inhibitors, temperature dependence, and dependence on osmotic pressure. Fusion at the plasma membrane began immediately after lowering the pH below 6 and showed an approximately exponential time course, whereas fusion via the endocytic pathway (pH 7.4) became apparent after a time delay of about 2 min. Fusion via the endocytic pathway was attenuated by treating cells with metabolic inhibitors and agents that raise the pH of the endocytic vesicle. A 10-fold excess of unlabeled virus arrested R18VSV entry via the endocytic pathway, whereas R18 dequenching below pH 6 (fusion at the plasma membrane) was not affected by the presence of unlabeled virus. The temperature dependence for fusion at pH 7...

Molecular Membrane Biology, 1986

The ability of apocytochrome c and the heme containing respiratory chain component, cytochrome c,... more The ability of apocytochrome c and the heme containing respiratory chain component, cytochrome c, to induce fusion of phosphatidylcholine (PC) small unilamellar vesicles containing 0-50 mol % negatively charged lipids was examined. Both molecules mediated fusion of phosphatidylserine (PS):PC 1:1 vesicles as measured by energy transfer changes between fluorescent lipid probes in a concentration- and pH-dependent manner, although cytochrome c was less potent and interacted over a more limited pH range than the apocytochrome c. Maximal fusion occurred at pH 3, far below the pKa of the 19 lysine groups contained in the protein (pI = 10.5). A similar pH dependence was observed for vesicles containing 50 mol % cardiolipin (CL), phosphatidylglycerol (PG), and phosphatidylinositol (PI) in PC but the apparent pKa values varied somewhat. In the absence of vesicles, the secondary structure of apocytochrome c was unchanged over this pH range, but in the presence of negatively charged vesicles, the polypeptide underwent a marked conformational change from random coil to alpha-helix. By comparing the pH dependencies of fusion induced by poly-L-lysine and apocytochrome c, we concluded that the pH dependence derived from changes in the net charge on both the vesicles and apocytochrome c. Aggregation could occur under conditions where fusion was imperceptible. Fusion increased with increasing mole ratio of PS. Apocytochrome c did induce some fusion of vesicles composed only of PC with a maximum effect at pH 4. Biosynthesis of cytochrome c involves translocation of apocytochrome c from the cytosol across the outer mitochondrial membrane to the outer mitochondrial space where the heme group is attached. The ability of apocytochrome c to induce fusion of both PS-containing and PC-only vesicles may reflect characteristics of protein/membrane interaction that pertain to its biological translocation.

Molecular and Cellular Biochemistry, 1990

Most structural and functional studies of membrane proteins eventually require that the protein b... more Most structural and functional studies of membrane proteins eventually require that the protein be solubilized from its original membrane, isolated and reconstituted into a membrane composed of native or specific phospholipids. The conditions comprising a successful reconstitution protocol often seem both arbitrary and elusive. The solubilization steps as the neutral surfactant octyl glucoside (OG) is added to the negatively charged lipid phosphatidylserine (PS) were followed by several optical techniques. Vesicle leakage, changes in resonance energy transfer between lipid probes and micelle formation were determined as a function of (PS) and temperature. The (OG) needed at these transitions was linear with (PS) so that average compositions and the free (OG) could be calculated for each point. More OG is needed to solubilize at 15 compared to 35 ° C reflecting the temperature dependence of pure OG solubility. Although similar, the average compositions of the mixed surfactant-lipid structure and their temperature dependence were not identical to similar points determined for egg phosphatidylcholine and OG.

Molecular and Cellular Biochemistry, 1994

The magnesium buffer coefficient (BMg) was calculated for BC3H-1 cells from the rise in cytosolic... more The magnesium buffer coefficient (BMg) was calculated for BC3H-1 cells from the rise in cytosolic Mg2+ activity observed when magnesium was released from ATP after iodoacetate (IAA) and NaCN treatment. The basal cytosolic Mg2+ activity (0.54 +/- 0.1 mM) measured with mag-fura-2 doubled when 4.54 mM magnesium was liberated from ATP: BMg was 12.9 indicating that a 1 mM increase in Mg2+ activity requires an addition of about 13 mM magnesium. The accuracy of this value depends on these assumptions: (a) all of the magnesium released from ATP stayed in the cells; (b) the rise in Mg2+ was not secondary to pH-induced changes in BMg; (c) mag-fura-2 measured Mg2+ and not Ca2+; and (d) the accuracy of the mag-fura-2 calibration. Total magnesium did not change in response to IAA/CN treatment, thus the change in Mg2+ activity reflected a redistribution of cell magnesium. pH changes induced by NH4Cl pulse and removal had little effect on Mg2+ activity and the changes were slower than and opposite to pH-induced changes in Ca2+ activity measured by fura-2. Ca2+ responses were temporally uncoupled from Mg2+ responses when the cells were treated with IAA only and in no cases did Ca2+ levels rise above 1 microM, showing that the mag-fura-2 is responding to Mg2+. Additional studies demonstrated that approximately 90% of the mag-fura-2 signal was cytosolic in origin. The remaining non-diffusible mag-fura-2 either was bound to cytosolic membranes or sequestered in organelles with the fluorescence characteristics of the Mg2(+)-complexed form, even when cytosolic free Mg2+ activity was approximately 0.5 mM. This bound mag-fura-2 would appear to increase the Kd and thus clearly limits the accuracy of our estimmate for BMg. Despite this limitation, we demonstrate that Mg2+ is tightly regulated in face of large changes in extracellular Mg2+, and that interplay observed between pH, Ca2+ and Mg2+ activities strongly supports the hypothesis that these factors interact through a shared buffer capacity of the cell.

Journal of Virological Methods, 1992

Two viruses, respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) were used to ... more Two viruses, respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) were used to evaluate viral purification by an affinity resin column (MatrexTM CellufineTM Sulfate (MCS); Amicon Division, WR Grace & Co.). Viable RSV was purified significantly from crude cell lysate by a single pass through a column containing the anionic MCS resin. Most cell protein and albumin eluted from the MCS resin with phosphate buffered saline (PBS) but RSV eluted at high ionic strength, i.e ., 2 0.6 M NaCl. Further purification was possible by sucrose step gradient centrifugation.

The Journal of Membrane Biology, 1984

The membrane permeability coefficients for the homologous monocarboxylic acids, formic through he... more The membrane permeability coefficients for the homologous monocarboxylic acids, formic through hexanoic, as well as benzoic and salicylic, were determined for egg phosphatidylcholine-decane planar bilayer membranes. The permeabilities of formic, acetic and propionic acid were also determined for "solvent-free" phosphatidylethanolamine bilayers. Permeability coefficients were calculated from tracer fluxes measured under otherwise symmetrical conditions, and precautions were taken to ensure that the values were not underestimated due to unstirred layer effects. The relation between the nonionic (HA) permeability (Pm) and the hexadecane/water partition coefficient (Kp) was: log Pm = 0.90 log Kp + 0.87 (correlation coefficient = 0.996). Formic acid was excluded from the analysis because its permeability was sixfold higher than predicted by the other acids. The permeabilities for "solvent-free" membranes were similar to those for decane-containing membranes. The exceptionally high permeability of formic acid and the high correlation of the other permeabilities to the hexadecane/water partition coefficient is a pattern that conforms with other nonelectrolyte permeabilities through bilayers. Similarly, the mean incremental free energy change per methylene group (delta delta G/-CH2-) was -764 cal mol-1, similar to other homologous solutes in other membrane systems. However, much less negative delta delta G values (-120 to -400 cal mol-1) were previously reported for fatty acids permeating bilayers and biological membranes. These values are due primarily to unstirred layer effects, metabolism and binding to membranes and other cell components.