Digital Commons Network^™

Social Networks In The Single Cell, Moira Rodriguez, Ana Martinez-Hottovy, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial DNA (mtDNA) can become damaged in many ways. A major repair mechanism is homologous recombination, which requires an undamaged DNA template. Presumably, this template comes from a different mitochondrion in the same cell. Plant mitochondria undergo fission and fusion to form transient networks which could allow the exchange of genetic information. To test this hypothesis, Chustecki et al. (2022) used msh1 mutants with defective DNA repair, and showed that mitochondrial interactions increased, revealing a link between the physical and genetic behavior of mitochondria.

Late Pleistocene Megafauna Extinction Leads To Missing Pieces Of Ecological Space In A North American Mammal Community, Felisa A. Smith, Emma A. Elliott Smith, Amelia Villaseñor, Catalina P. Tomé, S. Kathleen Lyons, Seth D. Newsome

School of Biological Sciences: Faculty Publications

The conservation status of large-bodied mammals is dire. Their decline has serious consequences because they have unique ecological roles not replicated by smaller-bodied animals. Here, we use the fossil record of the megafauna extinction at the terminal Pleistocene to explore the consequences of past biodiversity loss. We characterize the isotopic and body-size niche of a mammal community in Texas before and after the event to assess the influence on the ecology and ecological interactions of surviving species (>1 kg). Preextinction, a variety of C₄ grazers, C₃ browsers, and mixed feeders existed, similar to modern African savannas, with …

Fishing Regulations, Sexual Dimorphism, And The Life History Of Harvest, Lyndsie S. Wszola, Zachary S. Feiner, Christopher J. Chizinski, Jamilynn B. Poletto, John P. Delong

School of Biological Sciences: Faculty Publications

Freshwater recreational fisheries regulations are a vital tool for achieving social and ecological fisheries objectives. However, angler behavior and fish biology may interact to influence regulation efficacy in unexpected ways. We combined models of fish growth and angler behavior to explore how angler behavior interacts with fish life history to shape the probability of fish harvest given capture across ages, life stages, and sexes of walleye (Sander vitreus). Compared to females, males grew more quickly as juveniles, matured earlier, and reached smaller maximum sizes. Male walleye were therefore vulnerable to harvest for more of their reproductive lives than …

Forage Database: A Compilation Of Functional Responses For Consumers And Parasitoids, Stella Uiterwaal, Ian T. Lagerstrom, Shelby R. Lyon, John Delong

School of Biological Sciences: Faculty Publications

Functional responses, the relationships between consumer foraging rate and resource (prey) density, provide key insights into consumer–resource interactions while also being a major driver of population dynamics and food web structure. We present a global database of 2598 standardized functional responses and parameters extracted from the published literature. We refit the functional responses with a Type II model using standardized methods and report the fitted parameters along with data on experimental conditions, consumer and resource taxonomy and type, as well as the habitat and dimensionality of the foraging interaction. The consumer and resource species covered here are taxonomically diverse, from …

An Empiricist’S Guide To Using Ecological Theory, Tess N. Grainger, Athmanathan Senthilnathan, Po-Ju Ke, Matthew A. Barbour, Natalie T. Jones, John Delong, Sarah P. Otto, Mary I. O'Connor, Kyle E. Coblentz, Nikunj Goel, Jawad Sakarchi, Megan C. Szojka, Jonathan M. Levine, Rachel M. Germain

School of Biological Sciences: Faculty Publications

A scientific understanding of the biological world arises when ideas about how nature works are formalized, tested, refined, and then tested again. Although the benefits of feedback between theoretical and empirical research are widely acknowledged by ecologists, this link is still not as strong as it could be in ecological research. This is in part because theory, particularly when expressed mathematically, can feel inaccessible to empiricists who may have little formal training in advanced math. To address this persistent barrier, we provide a general and accessible guide that covers the basic, step-by-step process of how to approach, understand, and use …

Towards An Integrative View Of Virus Phenotypes, John P. Delong, Maitham A. Al-Sammak, Zeina Al-Ameeli, David Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack

School of Biological Sciences: Faculty Publications

Understanding how phenotypes emerge from genotypes is a foundational goal in biology. As challenging as this task is when considering cellular life, it is further complicated in the case of viruses. During replication, a virus as a discrete entity (the virion) disappears and manifests itself as a metabolic amalgam between the virus and the host (the virocell). Identifying traits that unambiguously constitute a virus’s phenotype is straightforward for the virion, less so for the virocell. Here, we present a framework for categorizing virus phenotypes that encompasses both virion and virocell stages and considers functional and performance traits of viruses in …

Predator Functional Responses And The Biocontrol Of Aphids And Mites, John Delong, Stella Uiterwaal

School of Biological Sciences: Faculty Publications

Biocontrol with predators is a key tool for controlling agricultural pests and preserving the productive efficiency of crops. Determining which predators to use for biocontrol often involves measuring their functional response—the relationship between foraging rate and prey abundance, yet comparisons of functional responses across predators are complicated by differences in experimental procedures. Here we use a compilation of functional responses standardized for time and space units to illustrate key sources of variation in functional responses for predators being tested for control of aphids and mites. Our results show that arena size (as a proxy for habitat structure) is a crucial …

Arctic Stream Characteristics And Diet Analysis Choice Impact Condition And Diet Estimates Of Ninespine Stickleback (Pungitius Pungitius), Adam Kuhrt

Theses and Dissertations (Comprehensive)

Ninespine stickleback (Pungitius pungitius) are ubiquitous in circumpolar freshwaters, but their ecological role is not well understood. Little research has been conducted on the influence of environmental variables on ninespine stickleback in stream environments, and while they are understood to be generalist feeders, their diet in stream environments is equally understudied. Determining diet is difficult due to biases inherent in all standard diet analysis methods. Morphological gut-content analysis (M-GCA), DNA metabarcoding of gut contents (D-GCA), and stable isotope analysis (SIA) are currently three of the most frequently conducted diet analyses; and while combinations of these methods are commonly …

Effects Of 17Α-Ethinylestradiol (Ee2) On Gonadal Development And Gene Expression In Larval Mummichog (Fundulus Heteroclitus), Carly Sing-Judge

Theses and Dissertations (Comprehensive)

The mummichog (Fundulus heteroclitus) is a small-bodied estuarine fish that inhabits the North American east coast and is often used as a model adult saltwater fish in environmental bioassays. This study aimed to describe gonadal development and gene expression levels in five-week-old mummichog under control conditions and following 17α-ethinylestradiol (EE₂) treatment in order to better understand the susceptibility of sex determination (SD) and gonadal differentiation (GD) processes following contaminant exposure. In the first experiment, eggs were fertilized, collected and incubated in the laboratory for three weeks, then yolk-sac larvae were grown out for five weeks and …

Toxicity Of The Technology Critical Elements Germanium And Yttrium To Daphnia Magna And Hyalella Azteca And The Influence Of Toxicity Modifying Factors, Rashid Shah

Theses and Dissertations (Comprehensive)

Technology critical elements (TCEs) are increasingly used in high and green technologies but there is little aquatic toxicity data for TCEs, particularly in fresh water. The objective of this study was to investigate the toxicity of two TCEs, Ge and Y, to Daphnia magna and Hyalella azteca and to understand the role of natural organic matter and cations on toxicity modification. Testing followed standard methods. The 48 h EC50 for D. magna was 11.6 (95% CI of 9.64-13.8) mg Ge/L based on measured dissolved concentrations at test end. The addition of NOM at 10 mg DOC/L resulted in a significant …

Assessment Of Temperature Optimum Signatures Of Corals At Both Latitudinal Extremes Of The Red Sea, Guilhem Banc-Prandi, Nicolas R. Evensen, Daniel J. Barshis, Gabriela Perna, Youssouf Moussa Omar, Maoz Fine

Biological Sciences Faculty Publications

Rising ocean temperatures are pushing reef-building corals beyond their temperature optima (T_opt), resulting in reduced physiological performances and increased risk of bleaching. Identifying refugia with thermally resistant corals and understanding their thermal adaptation strategy is therefore urgent to guide conservation actions. The Gulf of Aqaba (GoA, northern Red Sea) is considered a climate refuge, hosting corals that may originate from populations selected for thermal resistance in the warmer waters of the Gulf of Tadjoura (GoT, entrance to the Red Sea and 2000 km south of the GoA). To better understand the thermal adaptation strategy of GoA corals, …

Determinants Of Population Genetic Structure In Chamaecrista Fasciculata (Michx.) Greene (Fabaceae) In The Southeastern United States, Mahboubeh Hosseinalizadeh Nobarinezhad, Lisa E. Wallace

Biological Sciences Faculty Publications

Chamaecrista fasciculata is a widely distributed, phenotypically variable species in the eastern U.S. Whereas studies have demonstrated genetic structure and local adaptation in northern areas of its distribution, there has been no comparison of genetic variability among populations at the southern extent where phenotypic variation is more complex. We characterized genetic variation at 14 microsatellite loci for populations in Mississippi and Alabama and compared this to variation in a phenotypic trait, leaf pubescence. Geographic distance, climatic variables, and elevation were evaluated as factors to explain the observed patterns of genetic diversity. A significant amount of variation (19%) resided among populations, …

The Challenges Of Growing Orchids From Seeds For Conservation: An Assessment Of Asymbiotic Techniques, Devani Jolman, Martín I. Batalla, Alexis Hungerford, Pryce Norwood, Noah Tait, Lisa E. Wallace

Biological Sciences Faculty Publications

Lewis Knudson first successfully germinated orchid seeds asymbiotically on artificial medium in 1922. While many orchid species have since been grown asymbiotically, the tremendous variation in how species respond to artificial medium and growth conditions ex situ has also become apparent in the past century. In this study, we reviewed published journal articles on asymbiotic orchid seed germination to provide a summary of techniques used and to evaluate if these differ between terrestrial and epiphytic species, to identify areas where additional research is needed, and to evaluate whether asymbiotic germination could be used more often in ex situ conservation. We …

Effects Of Elevated Temperature, Reduced Hydroperiod, And Invasive Bullfrog Larvae On Pacific Chorus Frog Larvae, Bailey R. Tasker, Karli Honebein, Allie M. Erickson, Julia E. Misslin, Paul Hurst, Sarah Cooney, Skylar Riley, Scott A. Griffith, Betsy A. Bancroft

Biology Faculty Scholarship

Climate change and invasive species threaten many ecosystems, including surface freshwater systems. Increasing temperatures and reduced hydroperiod due to climate change may promote the persistence of invasive species and facilitate new invasions due to potentially higher tolerance to environmental stress in successful invaders. Amphibians demonstrate high levels of plasticity in life history characteristics, particularly those species which inhabit both ephemeral and permanent water bodies. We tested the influence of two projected effects of climate change (increased temperature and reduced hydroperiod) on Pacific chorus frog (Pseudacris regilla) tadpoles alone and in combination with the presence of tadpoles of a …

Understanding The Cellular And Physiological Mechanisms Of Fertilization And Early-Stage Seed Development, Mohammad Foteh Ali

Theses and Dissertations--Plant and Soil Sciences

Flowering plants have evolved a unique double-fertilization process. Two sperm cells fuse with two female gametophytic cells, the egg and central cells within the ovule, giving rise to the embryo and endosperm, respectively. Sperm cells in flowering plants are nonmotile and delivered in close proximity to the egg and central cells by the pollen tube. Flowering plants have established filamentous actin (F-actin) based sperm nuclear migration system for successful fertilization. Prior to fertilization, the female gamete forms a mesh-like structure of F-actin that shows constant inward movement from the plasma membrane periphery to the center of the cell where the …

The Role Of Rna Helicase Rhau In Immunoglobulin Class Switch Recombination, Sabine Jean Guillaume

Dissertations and Theses

B cells alter the expression of immunoglobulin isotypes through a process known as class switch recombination (CSR). In these cells, activation induced cytidine deaminase (AID) binds Gquadruplex (G4) switch transcripts, which serve as guide RNAs to target AID to the immunoglobulin heavy chain switch (S) regions in the DNA for CSR. Sequence alignment revealed homology between the AID G4 binding domain and the RNA helicase associated with AU-rich element (RHAU) specific motif (RSM), which allows RHAU binding to G4 RNAs and subsequent unwinding of G4 RNA into single-stranded transcripts. We hypothesize that RHAU functions in CSR by binding G4 S …

Exosome- And Microrna-Based Therapeutic Approach For Tendinopathy, Angela Wang Ilaltdinov

Dissertations and Theses

Tendinopathy, characterized by degeneration and chronic inflammation, is a significant clinical burden. Current treatments focus on symptom management but do not sufficiently address its underlying pathology; however, stem cell-based approaches aimed at repairing diseased tissues may overcome this limitation. Therapeutic effects of stem cells may be due in part to paracrine actions, including some mediated by exosomes – extracellular vesicles secreted by cells that play a role in cell communication. MicroRNA (miRNA), small non-coding RNA carried by exosomes, are likely responsible for many exosome effects. Exosomes and miRNA therapies show promise in treating diseases such as cancer and arthritis, but …

Response Of Antarctic Soil Fauna To Climate-Driven Changes Since The Last Glacial Maximum, Andre L.C. Franco, Byron J. Adams, Melisa A. Diaz, Nathan P. Lemoine, Nicholas B. Dragone, Noah Fierer, W. Berry Lyons, Ian Hogg, Diana H. Wall

Biological Sciences Faculty Research and Publications

Understanding how terrestrial biotic communities have responded to glacial recession since the Last Glacial Maximum (LGM) can inform present and future responses of biota to climate change. In Antarctica, the Transantarctic Mountains (TAM) have experienced massive environmental changes associated with glacial retreat since the LGM, yet we have few clues as to how its soil invertebrate-dominated animal communities have responded. Here, we surveyed soil invertebrate fauna from above and below proposed LGM elevations along transects located at 12 features across the Shackleton Glacier region. Our transects captured gradients of surface ages possibly up to 4.5 million years and the soils …

The Mitospecific Domain Of Mrp7 (Bl27) Supports Mitochondrial Translation During Fermentation And Is Required For Effective Adaptation To Respiration, Jessica M. Anderson, Jodie M. Box, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

We demonstrate here that mitoribosomal protein synthesis, responsible for the synthesis of oxidative phosphorylation (OXPHOS) subunits encoded by the mitochondrial genome, occurs at high levels during glycolysis fermentation and in a manner uncoupled from OXPHOS complex assembly regulation. Furthermore, we provide evidence that the mitospecific domain of Mrp7 (bL27), a mitoribosomal component, is required to maintain mitochondrial protein synthesis during fermentation but is not required under respiration growth conditions. Maintaining mitotranslation under high-glucose-fermentation conditions also involves Mam33 (p32/gC1qR homologue), a binding partner of Mrp7’s mitospecific domain, and together they confer a competitive advantage for a cell’s ability to adapt to …

Histological Comparison Of Shark Dermis Across Various Ecomorphologies, Olivia Schuitema

UNF Graduate Theses and Dissertations

The integument plays essential roles in the structural support, protection, and hydrodynamic capability among fishes. Most shark skin research has been done on the external epidermal layer containing the dermal denticles, while the larger dermis layer has been mostly ignored. The dermis layer in sharks is composed of two layers, the upper stratum laxum and the lower stratum compactum, holding supportive collagen and elastin fibers. There may be morphological and compositional differences in the dermis layers across various species of sharks, although the extent of such is unknown. These potential differences may be represented by various dermal thicknesses and different …

Toward Building Science Literacy, Kathryn Rafferty

UNLV Best Teaching Practices Expo

Reading scientific literature is a critical science competency that proves difficult to “teach.” Students enter our classes with varying science vocabularies, and many suffer imposter syndrome when reading technical reports because they do not yet identify as capable scientists. The “Science Literacy” assignment guides students to develop and expand strategies to read science articles. Over the semester, students read 5 to 6 articles ranging from peer-reviewed manuscripts to popular science magazines to science blogs about sequencing Ozzy Osbourne's DNA. In Canvas Discussion boards, they a guiding set of questions and then respond to their peers. This assignment is a low-stakes …

Documenting The Rapidly Expanding Distribution Of Invasive Ravenna Grass (Tripidium Ravennae) Eastern In Kansas, Rachel A. Styers

Electronic Theses & Dissertations

Invasive species cause significant ecological losses in the United States where they cost approximately $21 billion dollars a year to manage (Fantle-Lepczyk et al., 2022). Early detection of new invasive species, coupled with a rapid response of management efforts, can help to slow the ecological and economic impacts caused by these habitat invaders. Tripidium ravennae (L.) H. Scholz (or Ravenna grass) is a tall, robust, cespitose grass known to occur in Kansas, although its distribution remained poorly documented prior to this study. Given its known invasive tendencies, it has been declared noxious in at least six US states. Coupled with …

Impacts Of Plastic Pollution On A Pelagic Marine Mammal, The Northern Elephant Seal, Lauren M. Kashiwabara

University of the Pacific Theses and Dissertations

As plastic pollution increases, top marine predators such as marine mammals are becoming increasingly susceptible to plastic particles and their additives. Plastic particles have been found in gastrointestinal tracts and scat of many marine mammals, and quantifying plastic pollution in those that are pelagic can provide insight into plastic pollution in mesopelagic ecosystems that are just beginning to be analyzed. Adapting well-developed laboratory techniques for microplastic (MP) isolation (i.e. density separation and chemical digestion), I isolated MPs from the scat of the deepest diving pinniped, the northern elephant seal (NES), and found that100% of scat samples (n=11) contained high counts …

The Bgs 13 Mutant Of Pichia Pastoris And Its Effect On Structural Changes Of The Reporter Protein B-Lactogolbulin, Bushra Irshad

University of the Pacific Theses and Dissertations

Pichia pastoris, a methylotrophic yeast, is an ideal host for recombinant protein expression. It has the capability of performing many eukaryotic post-translational modifications and grows to high cell densities. However, P. pastoris’s secretion properties are not always efficient, and its secretory pathway mechanisms have not been thoroughly elucidated. A previously identified mutant strain, bgs13, was found to efficiently secrete most recombinant proteins tested, raising the possibility that this bgs13 mutant is a universal super secreter and understanding its secretion process is needed. In this study, we used a reporter protein, ?-lactoglobulin (b-LG), to perform structural analysis and comparisons of protein …

Stomatal Conductance And Reed Canary Grass Suppression Traits Of Native Michigan Trees, David E. Martinez, Dave Warners

Student Papers and Reports

Reed canary grass (Phalaris arundinacea), a prominent invasive understory species, threatens native Michigan biodiversity statewide. A notable affected area includes a stretch of agricultural land along Schooley Drain in Caledonia, MI, located in the headwaters of the Plaster Creek watershed. Our study pursues the following questions: “Do native trees provide enough shade to reduce the growth of Reed canary grass?” and “Which native trees best transpire water from a floodplain?”: To answer these questions, we continued the evaluation of seven different species of native Michigan trees to investigate which species best inhibits the growth of reed canary grass …

The Emma Cole Project: Reevaluating The Flora Of Grand Rapids, William Hofmann, Hayden Janssen, Martin Vanderschoot, Garrett Crow, Dave Warners

Student Papers and Reports

In 1901, botanist and teacher Emma Cole published an account of all the vascular plants in the Grand Rapids area, which is the most comprehensive documentation of the flora in the area today. The vicinity of Grand Rapids has been developed significantly since then, and with it the surrounding natural spaces have also been greatly altered. Over the past 7 years, Calvin University’s Emma Cole Project has been inventorying the flora of greater Grand Rapids and comparing modern plant life with the flora during Cole’s time 120 years ago. This project strives to both verify species’ presence around Grand Rapids …

Plaster Creek Stewards - Urban Habitat Restoration With Green Team, Jia Luchs, Clare Doss, Rachel Warners, Dave Warners, Deanna Geelhoed

Student Papers and Reports

Plaster Creek, though its watershed is home to many potential stewards in Grand Rapids, is the most polluted creek in West Michigan. The Green Team, a branch of Plaster Creek Stewards, is a group of students that work during the summer with a focus on research, education, and working directly to restore the Plaster Creek Watershed. The Green Team works toward this goal through urban green infrastructure, utilizing native plants to manage stormwater. Two Calvin students, Jia Luchs and Clare Doss, and twenty high school students living in the Plaster Creek watershed were hired by Plaster Creek Stewards this summer …

Urban Insect Biodiversity - Effects Of Native Landscaping, Caedmon Morgret, Dave Warners

Student Papers and Reports

Urban development comes with the cost of destroyed natural habitats. Urban infrastructure flattens entire ecosystems, replacing them with impervious, life-inhibiting constructions.

Alleviating the impacts of urbanization is possible. Green infrastructure mitigates habitat loss by restoring native habitats within urbanized areas. One benefit of green infrastructure is the reestablishment of biodiversity, benefitting plants, animals, and insects alike. Biodiversity creates a healthier habitat and location than urban infrastructure –and lack of biodiversity –does.

To investigate this benefit we performed a pilot study, sampling lawns and curb-cut rain gardens (CCRGs). We compared biodiversity between restored and unrestored urban habitats.

Botanical Inventory And Management Consideration For Potential Park At 32 Nd Street Property: City Of Grand Rapids Parks And Recreation, David Warners, William Hofmann, Hayden Janssen, Martin Vanderschoot, Garrett Crow

Faculty and Professional Research

During the spring and summer of 2022, a botanical inventory and floristic quality assessment was carried out by Calvin University students and faculty for the 32 nd Street Property proposed as a 17-acre potential City Park, located at 2163 32 nd Street SE in Grand Rapids, Michigan. The purpose of this inventory was to inform the staff of the Grand Rapids Parks and Recreation Department of the botanical significance of this newly sectioned property and also to provide information for the City to share with neighbors of the plants that could be found in this parcel. The research conducted as …

Botanical Assessments Of High-Quality Southern Shrub-Carr And Hardwood Swamp Wetlands In The Undeveloped Lowell Regional Greenspace, Kent County, Michigan, Garrett Crow, Dave Warners, Haley R. Weesies, Jonathon D. Walt, Zachary Hartwig, Carolyn H. Koehn

Faculty and Professional Research

The 2019–2023 Masterplan for Kent County Parks includes the future development of acquired properties that have been designated as the Lowell Regional Greenspace (528 acres), occupying nearly the entirety of Section 22 of Lowell Charter Township in Kent County, Michigan. Four wetlands located in the same drainage basin along Karen Creek in the Lowell Regional Greenspace were inventoried for floristic quality assessments during the summers of 2016, 2018, 2019, and 2021. One of the wetlands was forested and determined to be a southern hardwood swamp community type. The other three wetlands are best classified as shrub-carr communities. In the southern …