Biology Commons^™

Oxidative Stress Responses And Nutrient Starvation In Mchm Treated Saccharomyces Cerevisiae, Michael C. Ayers, Zachary N. Sherman, Jennifer E. G. Gallagher

Faculty & Staff Scholarship

In 2014, the coal cleaning chemical 4-methylcyclohexane methanol (MCHM) spilled into the water supply for 300,000 West Virginians. Initial toxicology tests showed relatively mild results, but the underlying effects on cellular biology were underexplored. Treated wildtype yeast cells grew poorly, but there was only a small decrease in cell viability. Cell cycle analysis revealed an absence of cells in S phase within thirty minutes of treatment. Cells accumulated in G1 over a six-hour time course, indicating arrest instead of death. A genetic screen of the haploid knockout collection revealed 329 high confidence genes required for optimal growth in MCHM. These …

Temporal Variability Of Polycyclic Aromatic Hydrocarbons In Deep-Sea Cephalopods Of The Northern Gulf Of Mexico, Isabel C. Romero, Heather L. Judkins, Michael Vecchione

USF St. Petersburg Campus Faculty Publications

As part of the effort to understand the effects of the Deepwater Horizon Oil Spill (DWHOS), we analyzed tissue from five species of midwater oceanic cephalopods in the northern Gulf of Mexico (GoM) during three time periods, including one period sampled fortuitously just before the spill (2010), and two periods sampled after the spill (2011 and 2015–2016). The species, Japetella diaphana, Abralia redfieldi, Histioteuthis corona, Leachia atlantica, and Onychoteuthis banksii were collected in three geographic areas in the GoM (east, south and southeast of the Macondo wellhead). Results indicate a shift in the composition of polycyclic aromatic hydrocarbons (PAHs) in …

Small Herbaria Contribute Unique Biogeographic Records To County, Locality, And Temporal Scales, Travis D. Marsico, Erica R. Krimmel, J. Richard Carter, Emily L. Gillespie, Phillip D. Lowe, Ross Mccauley, Ashley B. Morris, Gil Nelson, Michelle Smith, Diana L. Soteropoulos, Anna K. Monfils

Scholarship and Professional Work - LAS

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

Using Northern Pike And Yellow Perch To Attempt A Trophic Cascade, Bryan Sea

Journal of Earth and Life Science

In the midwestern USA, water clarity has decreased in shallow lakes as a result of large populations of Fathead Minnow Pimephales promelas and agriculture that impact the life that depend on shallow habitats, such as waterfowl, fish, and aquatic plants. Northern Pike Esox lucius and Yellow Perch Perca flavescens were stocked in a few lakes in attempt to create a tropic cascade and reduce populations of nuisance Fathead Minnows. Northern Pike were stocked as fry and Yellow Perch were stocked as adults either pre-spawn or post-spawn. Lake managers hypothesized adult Yellow Perch would spawn and the age-0 Perch would feed …

Salamander Stress And Duress: The Relationship Between Cort, Autotomy And Regeneration, And Exploratory Behaviour, Aaron M. Sullivan, Jacquelyn L. Lewis

Faculty Publications - Department of Biological & Molecular Science

Responses to stress are generally mediated through the production of glucocorticoids by the hypothalamic-pituitary-adrenal (or -interrenal) axis. The prolonged production of stress hormones can contribute to delayed wound healing and growth, but little is known about their influence on regeneration following tail autotomy, or exploratory behaviour in autotomized individuals. Here we examined the relationship between stress, re-generation, and exploratory behaviour in Allegheny Mountain dusky salamanders (Desmognathus ochrophaeus) by manipulating corticosterone (CORT) levels via cutaneous patch. First, we measured tail regeneration in salamanders with elevated CORT for 13 weeks after the induction of tail autotomy. Test subjects received a weekly patch …

Evaluating Volatile Organic Compound Emissions From Cross-Laminated Timber Bonded With A Soy-Based Adhesive, Michael Yauk, Jason Stenson, Micah T. Donor, Kevin Van Den Wymelenberg

Faculty Publications - Department of Biological & Molecular Science

Volatile organic compound (VOC) emissions from indoor sources are large determinants of the indoor air quality (IAQ) and occupant health. Cross-laminated timber (CLT) is a panelized engineered wood product often left exposed as an interior surface finish. As a certified structural building product, CLT is currently exempt from meeting VOC emission limits for composite wood products and confirming emissions through California Department of Public Health (CDPH) Standard Method testing. In this study, small chamber testing was conducted to evaluate VOC emissions from three laboratory-produced CLT samples: One bonded with a new soy-based cold-set adhesive; a second bonded with a commercially …

Rapid Determination Of Activation Energies For Gas-Phase Protein Unfolding And Dissociation In A Q-Im-Tof Mass Spectrometer, Micah T. Donor, Samantha O. Shepherd, James S. Prell

Faculty Publications - Department of Biological & Molecular Science

Ion mobility-mass spectrometry has emerged as a powerful tool for interrogating a wide variety of chemical systems. Collision-induced unfolding (CIU), typically performed in time-of-flight instruments, has been utilized to obtain valuable qualitative insight into protein structure and illuminate subtle differences between related species. CIU experiments can be performed relatively quickly, but unfolding energy information obtained from them has not yet been interpreted quantitatively. While several methods can determine quantitative dissociation energetics for small molecules, clusters, and peptides, these methods have rarely been applied to proteins, and never to study unfolding. Here, we present a method to rapidly determine activation energies …

Protonation Isomers Of Highly Charged Protein Ions Can Be Separated In Faims-Ms, J. Diana Zhang, Micah T. Donor, Amber D. Rolland, Michael G. Leeming, Huixin Wang, Adam J. Trevitt, K.M. Mohibul Kabir, James S. Prell, William A. Donald

Faculty Publications - Department of Biological & Molecular Science

High-field asymmetric waveform ion mobility spectrometry-mass spectrometry (FAIMS-MS) can resolve over an order of magnitude more conformers for a given protein ion than alternative methods. Such an expansion in separation space results, in part, from protein ions with masses of >29 kDa undergoing dipole alignment in the high electric field of FAIMS, and the resolution of ions that adopt pendular vs free rotor states. In this study, FAIMS-MS, collision-induced dissociation (CID), and travelling wave (TW) IMS-MS were used to investigate the pendular and free rotor states of protonated carbonic anhydrase II (CAII, 29 kDa). The electrospray ionization additive 1,2-butylene carbonate …

Increasing Collisional Activation Of Protein Complexes Using Smaller Aperture Source Sampling Cones On A Synapt Q-Im-Tof Instrument With A Stepwave Source, Jesse W. Wilson, Micah T. Donor, Samantha O. Shepherd, James S. Prell

Faculty Publications - Department of Biological & Molecular Science

Quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometers have revolutionized investigation of native biomolecular complexes. High pressures in the sources of these instruments aid transmission of protein complexes through damping of kinetic energy by collisional cooling. Since adducts are removed through collisional heating (declustering), excessive collisional cooling can prevent removal of non-specific adducts from protein ions, leading to inaccurate mass measurements, broad mass spectral peaks, and obfuscation of ligand binding. We show that reducing the source pressure using smaller aperture source sampling cones (SC) in a Waters Synapt G2-Si instrument increases protein ion heating by decreasing collisional cooling, providing a simple way to …

Correlated Clusters Of Closed Reaction Centers During Induction Of Intact Cells Of Photosynthetic Bacteria, Péter Maróti, István A. Kovács, Mariann Kis, James L. Smart, Ferenc Iglói

Faculty Publications - Department of Biological & Molecular Science

Antenna systems serve to absorb light and to transmit excitation energy to the reaction center (RC) in photosynthetic organisms. As the emitted (bacterio)chlorophyll fluorescence competes with the photochemical utilization of the excitation, the measured fluorescence yield is informed by the migration of the excitation in the antenna. In this work, the fluorescence yield concomitant with the oxidized dimer (P+ ) of the RC were measured during light excitation (induction) and relaxation (in the dark) for whole cells of photosynthetic bacterium Rhodobacter sphaeroides lacking cytochrome c2 as natural electron donor to ­P+ (mutant cycA). The relationship between the fluorescence yield and …

An Ortholog Of The Vasa Intronic Gene Is Required For Small Rna-Mediated Translation Repression In Chlamydomonas Reinhardtii, Xinrong Ma, Fadia Ibrahim, Eun-Jeong Kim, Scott Shaver, James Becker, Fareha Razvi, Ronald L. Cerny, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular alga Chlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show that Chlamydomonas VIG1, an ortholog of the Drosophila melanogaster Vasa intronic gene (VIG), is required for this process. VIG1 localizes predominantly in the cytosol and comigrates with monoribosomes and …

Mitochondrial Dna Repair In An Arabidopsis Thaliana Uracil N-Glycosylase Mutant, Emily L. Wynn, Emma Purfeerst, Alan Christensen

School of Biological Sciences: Faculty Publications

Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were …

Temperature Alters The Shape Of Predator–Prey Cycles Through Effects On Underlying Mechanisms, John P. Delong, Shelby Lyon

School of Biological Sciences: Faculty Publications

Background: Predicting the effects of climate warming on the dynamics of ecological systems requires understanding how temperature influences birth rates, death rates and the strength of species interactions. The temperature dependance of these processes—which are the underlying mechanisms of ecological dynamics—is often thought to be exponential or unimodal, generally supported by short-term experiments. However, ecological dynamics unfold over many generations. Our goal was to empirically document shifts in predator–prey cycles over the full range of temperatures that can possibly support a predator–prey system and then to uncover the effect of temperature on the underlying mechanisms driving those changes.

Methods: We …

Identification And Characterization Of Differentially Expressed Genes In Caenorhabditis Elegans In Response To Pathogenic And Nonpathogenic Stenotrophomonas Maltophilia, Leah J. Radeke, Michael A. Herman

School of Biological Sciences: Faculty Publications

Background: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, …

Divergent Density Feedback Control Of Migratory Predator Recovery Following Sex-Biased Perturbations, Daisuke Goto, Martin J. Hamel, Mark A. Pegg, Jeremy J. Hammen, Matthew L. Rugg, Valery E. Forbes

School of Biological Sciences: Faculty Publications

Uncertainty in risks posed by emerging stressors such as synthetic hormones im-pedes conservation efforts for threatened vertebrate populations. Synthetic hor-mones often induce sex-biased perturbations in exposed animals by disrupting gonad development and early life-history stage transitions, potentially diminishing per capita reproductive output of depleted populations and, in turn, being manifest as Allee effects. We use a spatially explicit biophysical model to evaluate how sex-biased perturbation in life-history traits of individuals (maternal investment in egg production and male-skewed sex allocation in offspring) modulates density feedback control of year-class strength and recovery trajectories of a long-lived, migratory fish—shovelnose sturgeon (Scaphirhynchus platorynchus)—under spatially …

Multiple True-False Questions Reveal More Thoroughly The Complexity Of Student Thinking Than Multiple-Choice Questions: A Bayesian Item Response Model Comparison, Chad Brassil, Brian A. Couch

School of Biological Sciences: Faculty Publications

Background: Within undergraduate science courses, instructors often assess student thinking using closed-ended question formats, such as multiple-choice (MC) and multiple-true-false (MTF), where students provide answers with respect to predetermined response options. While MC and MTF questions both consist of a question stem followed by a series of options, MC questions require students to select just one answer, whereas MTF questions enable students to evaluate each option as either true or false. We employed an experimental design in which identical questions were posed to students in either format and used Bayesian item response modeling to understand how responses in each …

Mammal Community Structure Through The Paleocene-Eocene Thermal Maximum, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Human-mediated species invasion and climate change are leading to global extinctions and are predicted to result in the loss of important axes of phylogenetic and functional diversity. However, the long-term robustness of modern communities to invasion is unknown, given the limited timescales over which they can be studied. Using the fossil record of the Paleocene- Eocene Thermal Maximum (PETM; ~ 56 Ma) in North America, we evaluate mammalian community-level response to a rapid global warming event (5° to 8°C) and invasion by three Eurasian mammalian orders and by species undergoing northward range shifts. We assembled a database of 144 species …

Lithological Constraints On Resource Economies Shape The Mycorrhizal Composition Of A Bornean Rain Forest, Monique Weemstra, Kabir G. Peay, Stuart J. Davies, Mohizah Mohamad, Akira Itoh, Sylvester Tan, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

• Arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) produce contrasting plant–soil feedbacks, but how these feedbacks are constrained by lithology is poorly understood.

• We investigated the hypothesis that lithological drivers of soil fertility filter plant resource economic strategies in ways that influence the relative fitness of trees with AMF or EMF symbioses in a Bornean rain forest containing species with both mycorrhizal strategies.

• Using forest inventory data on 1245 tree species, we found that although AMF-hosting trees had greater relative dominance on all soil types, with declining lithological soil fertility EMF-hosting trees became more dominant. Data on …

A High-Throughput Method To Quantify Feeding Rates In Aquatic Organisms: A Case Study With Daphnia, Jessica L. Hite, Alaina C. Pfenning-Butterworth, Rachel E. Vetter, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

1. Food ingestion is one of the most basic features of all organisms. However, obtaining precise—and high-throughput—estimates of feeding rates remains challenging, particularly for small, aquatic herbivores such as zooplankton, snails, and tadpoles. These animals typically consume low volumes of food that are time-consuming to accurately measure.

2. We extend a standard high-throughput fluorometry technique, which uses a microplate reader and 96-well plates, as a practical tool for studies in ecology, evolution, and disease biology. We outline technical and methodological details to optimize quantification of individual feeding rates, improve accuracy, and minimize sampling error.

3. This high-throughput assay offers several …

Adaptations Of Interferon Regulatory Factor 3 With Transition From Terrestrial To Aquatic Life, Monica Angeletti, Wan-Ling Nicole Hsu, Nashaat Majo, Hideaki Moriyama, Etsuko Moriyama, Luwen Zhang

School of Biological Sciences: Faculty Publications

Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and the major factors for the induction of interferons, a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of those IRFs to the environments. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned fish lineage, while …

Functional Responses Are Maximized At Intermediate Temperatures, Stella F. Uiterwaal, John Delong

School of Biological Sciences: Faculty Publications

Functional responses describe how consumer foraging rates change with resource density. Despite extensive research looking at the factors underlying foraging interactions, there remains ongoing controversy about how temperature and body size control the functional response parameters space clearance (or attack) rate and handling time. Here, we investigate the effects of temperature, consumer mass, and resource mass using the largest compilation of functional responses yet assembled. This compilation contains 2,083 functional response curves covering a wide range of foragers and prey types, environmental conditions, and habitats. After accounting for experimental arena size, dimensionality of the foraging interaction, and consumer taxon, we …

Presence Of Fruits Decreases Probability Of Retaining Flowers In A Sequentially Flowering Plant, Shivani Jadeja, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Both intrinsic and extrinsic plant processes affect the fate of flowers along an inflorescence in sequen- tially flowering plants. We investigated whether the intrinsic process of competition for limited resource between fruits and flowers owing to resource preemption or sink strength of basal fruits, or architectural effects due to posi- tional differences in the probability of retaining flowers, explains a lower probability of retaining distal flowers inYucca glauca. Further, we investigated how the extrinsic process of seed herbivory interacts with the plant’s intrinsic processes of flower retention. We carried out a field experiment to compare flower retention among nine combi- …

Invited Commentaries On Shizuka & Johnson 2020, & Response From The Authors, Adriana A. Maldonado-Chaparro, Damien R. Farine, Amiyaal Ilany, Orr Spiegel, Noa Pinter-Wollman, Ipek G. Kulahci, Eric Vander Wal, Quinn M.R. Webber, Daniel I. Rudenstein, Daizaburo Shizuka, Allison E. Johnson

School of Biological Sciences: Faculty Publications

Adriana A. Maldonado-Chaparro and Damien R. Farine, Demographic processes in animal networks are a question of time

Amiyaal Ilany, Complex societies, simple processes

Orr Spiegel and Noa Pinter-Wollman, Placing the effects of demography on networks in ecological context

Ipek G. Kulahci, Individual differences can affect how networks respond to demography

Eric Vander Wal and Quinn M.R. Webber, Density dependence and eco-evolutionary dynamics of animal social networks

Daniel I. Rubenstein, On assessing the importance of demographic change for social structure

Daizaburo Shizuka and Allison E. Johnson, The long view on demographic effects on social networks: A response to comments on Shizuka …

An Evaluation Of Availability And Adequacy Of Multi-Hazard Early Warning Systems In Asian Countries: A Baseline Study, Ignacio Aguirre-Ayerbe, Maria Merino, Seinn Lei Aye, Ranjith Dissanayake, Fathmath Shadiya, Crisanto M. Lopez

Biology Faculty Publications

Early warning systems are widely considered as one of the more important aspects to reduce the impacts and consequences that hazardous natural events pose to societies. Similar to the other terms related to disaster risk reduction, this concept has evolved over time to eventually result in a comprehensive framework, that includes features from the upstream phase, such as detection and forecasting tools and models, to the downstream phase that considers a people-centred approach.

Based on this holistic conceptual framework, this paper attempts to assess the degree of adequacy and integration of early warning systems with reference to international standards using …

In Memoriam: Ignacio Ribera (1963–2020), Emmanuel D. Delocado, Michael Balke, Hendrik Freitag

Biology Faculty Publications

No abstract provided.

First Genome Sequence Of The Gunnison’S Prairie Dog (Cynomys Gunnisoni), A Keystone Species And Player In The Transmission Of Sylvatic Plague, Mirian T. N. Tsuchiya, Rebecca B. Dikow, Loren Cassin-Sackett

Integrative Biology Faculty and Staff Publications

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both …

Genetic Analysis Of The Endangered Gray Bat Species (Myotis Grisescens), Emma Fitzgerald

Lewis Honors College Capstone Collection

This study attempts to analyze the genetics using specific haplotype sequences of the endangered gray bat to determine genetic events that have happened in the past as well as determining how the species population has changed over time. We were able to conduct a Tajima’s D test to investigate whether a potential bottleneck has occurred. A linear regression of the genetic vs. geographical distance was produced to investigate the patterns of haplotype distribution. The species past distribution was compared to the current distribution using known collected specimens. A map of future predictions was constructed using present and future climate layers …

Painted Turtle (Chrysemys Picta) Home Range And Habitat Use In A Dam Impoundment, Bria Spalding

Senior Honors Theses and Projects

Habitat fragmentation, including damming rivers, is a major threat to species conservation in urban areas causing reduced dispersal and biodiversity. Dam removal is typically beneficial to many species because dams restrict the movement of many organisms. However, the dam removal may negatively impact some species. The purpose of our study was to assess the potential effects that the removal of the Peninsular Paper Dam (Huron River, Ypsilanti) may have on painted turtles (Chrysemys picta) by monitoring their habitat use prior to dam removal. Chrysemys picta is a native species abundant in lentic systems (ponds and lakes) with muddy …

Characterization Of Cofilin Function In Xenopus Laevis, Verginio Persicone

Senior Honors Theses and Projects

Proper cell migration is necessary for healthy embryonic development. The EphA4 receptor, when activated, triggers a cell migration response away from the signal molecule ephrin that is displayed by surrounding cells. Little is known about how the EphA4 receptor interacts with the actin cytoskeleton to trigger the migration response. We hypothesize that cofilin is key to downstream actin cytoskeleton regulation by the EphA4 pathway. In this study, we observed cofilin gene expression across several stages of early Xenopus laevis embryonic development by using RT-PCR. We observed cofilin protein presence across those same embryonic stages by using Western Blot. We also …

Examination Of The Relationship Between Biot 303 Students’ Achievement Goals And Metacognitive Reflective Writing, Anna Pathammavong

Senior Honors Theses and Projects

Our motivation for engaging in certain behaviors, like the metacognitive process, is driven by the type of achievement goals we set for ourselves. Reflective writing is critical in the metacognitive process because it engages how we communicate our thoughts to others. In this study we classified twenty-one future elementary school educators as having set either mastery achievement goals or performance achievement goals for themselves in a science teaching methods course. Our study focused on the relationship between the type of achievement goals each student identified with and their engagement in metacognitive processes following specific learning activities. We hypothesized that students …