Biology Commons^™

The Value Of Support: Stem Intervention Programs Impact Student Persistence And Belonging., Erin E. Shortlidge, Mackenzie J. Gray, Suzanne Estes, Emma C. Goodwin

Biology Faculty Publications and Presentations

In response to unwaveringly high attrition from STEM pathways, STEM Intervention Programs (SIPs) support STEM students in effort to increase retention. Using mixed methods (survey and focus groups), we studied students at one university who were either supported or unsupported by SIPs to understand how students may differ in experiences believed to contribute to STEM persistence. We evaluated: sense of belonging, scientific self-efficacy, scientific community values, scientific identity, and STEM involvement. The enrollment status of students two and a half years postsurvey was also tracked. SIP students reported significantly higher science identity and sense of belonging and were more involved …

Oil Identification Of Harp Seal And Other Select Marine Mammals, Meghan Pinedo, Deborah A. Duffield, Dalin N. D’Alessandro, Erin R. Price, Edgard O. Espinoza

Biology Faculty Publications and Presentations

Because of the rich omega-3 fatty acids content, harp seal (Pagophilus groenlandicus) oil is a popular supplement that is packaged as pills in Canada and sold for medicinal purposes, although this practice is banned in the United States. Due to US regulations, it is important to be able to distinguish between fish oil and seal oil, but the taxonomic determination of oils provenance has been a difficult problem to solve. In this study, Direct Analysis in Real Time time-of-flight mass spectrometry (DART TOFMS) was used to analyze the chemotypes of blubber samples collected from seven species of …

Autism Risk Gene Cul3 Alters Neuronal Morphology Via Caspase-3 Activity In Mouse Hippocampal Neurons, Qiang-Qiang Xia, Anju Singh, Jing Wang, Zhong Xin Xuan, Jeffrey D. Singer, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders (NDDs) in which children display differences in social interaction/communication and repetitive stereotyped behaviors along with variable associated features. Cul3, a gene linked to ASD, encodes CUL3 (CULLIN-3), a protein that serves as a key component of a ubiquitin ligase complex with unclear function in neurons. Cul3 homozygous deletion in mice is embryonic lethal; thus, we examine the role of Cul3 deletion in early synapse development and neuronal morphology in hippocampal primary neuronal cultures. Homozygous deletion of Cul3 significantly decreased dendritic complexity and dendritic length, as well as axon formation. Synaptic spine density significantly …

Effective Dispersal Patterns In Prairie Plant Species Across Human-Modified Landscapes., Elizabeth C. Hendrickson, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Effective dispersal among plant populations is dependent on vector behaviour, landscape features and availability of adequate habitats. To capture landscape feature effects on dispersal, studies must be conducted at scales reflecting single-generation dispersal events (mesoscale). Many studies are conducted at large scales where genetic differentiation is due to dispersal occurring over multiple generations, making it difficult to interpret the effects of specific landscape features on vector behaviour. Genetic structure at the mesoscale may be determined by ecological and evolutionary processes, such as the consequences of vector behaviour on patterns of gene flow. We used chloroplast haplotypes and nuclear genome SNP …

Rhizobia-Legume Symbiosis Mediates Direct And Indirect Interactions Between Plants, Herbivores And Their Parasitoids, Carlos Bustos-Segura, Adrienne L. Godschalx, Lucas Malacari, Sergio Rasmann, Fanny Deiss, Daniel Ballhorn, Betty Benrey

Biology Faculty Publications and Presentations

Microorganisms associated with plant roots significantly impact the quality and quantity of plant defences. However, the bottom-up effects of soil microbes on the aboveground multitrophic interactions remain largely under studied. To address this gap, we investigated the chemically- mediated effects of nitrogen-fixing rhizobia on legume-herbivore-parasitoid multitrophic interactions. To address this, we initially examined the cascading effects of the rhizobia bean association on herbivore caterpillars, their parasitoids, and subsequently investigated how rhizobia influence on plant volatiles and extrafloral nectar. Our goal was to understand how these plant- mediated effects can affect parasitoids. Lima bean plants (Phaseoulus lunatus) inoculated with rhizobia exhibited …

Ubiquitous Filter Feeders Shape Open Ocean Microbial Community Structure And Function, Anne W. Thompson, Györgyi Nyerges, Kylee M. Brevick, Kelly Sutherland

Biology Faculty Publications and Presentations

The mechanism of mortality plays a large role in how microorganisms in the open ocean contribute to global energy and nutrient cycling. Salps are ubiquitous pelagic tunicates that are a well-known mortality source for large phototrophic microorganisms in coastal and high-latitude systems, but their impact on the immense populations of smaller prokaryotes in the tropical and subtropical open ocean gyres is not well quantified. We used robustly quantitative techniques to measure salp clearance and enrichment of specific microbial functional groups in the North Pacific Subtropical Gyre, one of the largest ecosystems on Earth. We discovered that salps are a previously …

A Genus In The Bacterial Phylum Aquificota Appears To Be Endemic To Aotearoa-New Zealand, Jean F. Power, Carlo R. Carere, Holly E. Welford, Daniel T. Hudson, Kevin C. Lee, John W. Moreau, Anna-Louise Reysenbach, Thijs J.G. Ettema, Multiple Additional Authors

Biology Faculty Publications and Presentations

Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and …

Preparing Teaching Assistants To Facilitate Course-Based Undergraduate Research Experiences (Cures) In The Biological Sciences: A Call To Action, Erin Shortlidge, Amie M. Kern, Emma Goodwin, Jeffrey T. Olimpo

Biology Faculty Publications and Presentations

Course-based undergraduate research experiences (CUREs) offer an expanding avenue to engage students in real-world scientific practices. Increasingly, CUREs are instructed by graduate teaching assistants (TAs), yet TAs may be underprepared to facilitate and face unique barriers when teaching CUREs. Consequently, unless TAs are provided professional development (PD) and resources to teach CUREs effectively, they and their students may not reap the assumed benefits of CURE instruction. Here, we describe three perspectives – that of the CURE TA, the CURE designer/facilitator, and the CURE student – that are collectively intended to inform the development of tentative components of CURE TA PD. …

Germ Cell Recovery, Cryopreservation And Transplantation In The California White Sturgeon, Acipenser Transmontanus, Amie L. Romney, Danielle M. Myers, Fatima R. Martin, Tawney N. Scanlan, Stuart A. Meyers

Biology Faculty Publications and Presentations

The white sturgeon (Acipenser transmontanus) is the largest freshwater fish in North America. Because of the unique life history characteristics of sturgeon, including longevity, late maturation and long spawning intervals, their aquaculture can be a significant investment of resources. As a result of habitat loss and overharvesting, natural populations of white sturgeon are threatened and there is a growing effort to improve conservation aquaculture programs. Germ cell transplantation is an innovative technology previously demonstrated in a variety of fish species to be able to produce a surrogate broodstock. The technique relies upon optimal donor germ cell recovery and transplantation into …

Drivers Of Plankton Community Structure In Intermittent And Continuous Coastal Upwelling Systems–From Microbes And Microscale In-Situ Imaging To Large Scale Patterns, Moritz Schmid, Su Sponaugle, Anne W. Thompson, Kelly T. Sutherland, Robert Cowen

Biology Faculty Publications and Presentations

Eastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. Studies that integrate the classic trophic web based on new production with the microbial loop are rare due to the range in body forms and sizes of the taxa. Underwater imaging can overcome this limitation, and with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California …

Big Boned: How Fat Storage And Other Adaptations Influenced Large Theropod Foraging Ecology, Cameron Pahl, Luis A. Ruedas

Biology Faculty Publications and Presentations

Dinosaur foraging ecology has been the subject of scientific interest for decades, yet much of what we understand about it remains hypothetical. We wrote an agent-based model (ABM) to simulate meat energy sources present in dinosaur environments, including carcasses of giant sauropods, along with living, huntable prey. Theropod dinosaurs modeled in this environment (specifically allosauroids, and more particularly, Allosaurus Marsh, 1877) were instantiated with heritable traits favorable to either hunting success or scavenging success. If hunter phenotypes were more reproductively successful, their traits were propagated into the population through their offspring, resulting in predator specialists. If selective pressure favored scavenger …

Computational Analysis Of Plasma Lipidomics From Mice Fed Standard Chow And Ketogenic Diet, Amy L. Seufert, James W. Hickman, Jaewoo Choi, Brooke A. Napier

Biology Faculty Publications and Presentations

Dietary saturated fatty acids (SFAs) are upregulated in the blood circulation following digestion. A variety of circulating lipid species have been implicated in metabolic and inflammatory diseases; however, due to the extreme variability in serum or plasma lipid concentrations found in human studies, established reference ranges are still lacking, in addition to lipid specificity and diagnostic biomarkers. Mass spectrometry is widely used for identification of lipid species in the plasma, and there are many differences in sample extraction methods within the literature. We used ultra-high performance liquid chromatography (UPLC) coupled to a high-resolution hybrid triple quadrupole-time-of-flight (QToF) mass spectrometry (MS) …

Diverse And Variable Community Structure Of Picophytoplankton Across The Laurentian Great Lakes, John Gale, Carey P. Sweeney, Sarah Paver, Maureen L. Coleman, Anne W. Thompson

Biology Faculty Publications and Presentations

The Laurentian Great Lakes provide economic support to millions of people, drive biogeochemical cycling, and are an important natural laboratory for characterizing the fundamental components of aquatic ecosystems. Small phytoplankton are important contributors to the food web in much of the Laurentian Great Lakes. Here, for the first time, we reveal and quantify eight phenotypically distinct picophytoplankton populations across the Lakes using a multilaser flow cytometry approach, which distinguishes cells based on their pigment phenotype. The distributions and diversity of picophytoplankton flow populations varied across lakes and depths, with Lake Erie standing out with the highest diversity. By sequencing sorted …

Cullin 3–Mediated Regulation Of Intracellular Iron Homeostasis Promotes Thymic Invariant Nkt Cell Maturation, Emily L. Yarosz, Ajay Kumar, Jeffrey Singer, Cheong-Hee Chang

Biology Faculty Publications and Presentations

The E3 ubiquitin ligase cullin 3 (Cul3) is critical for invariant NKT (iNKT) cell development, as iNKT cells lacking Cul3 accumulate in the immature developmental stages. However, the mechanisms by which Cul3 mediates iNKT cell development remain unknown. In this study, we investigated the role of Cul3 in both immature and mature thymic iNKT cells using a mouse model with a T cell–specific deletion of Cul3. We found that mature iNKT cells lacking Cul3 proliferated and died more than wild-type cells did. These cells also displayed increased glucose metabolism and autophagy. Interestingly, we found that tight regulation of iron homeostasis …

Effects Of Heterozygous Deletion Of Autism-Related Gene Cullin-3 In Mice, Qiang-Qiang Xia, Angela K. Walker, Chenghu Song, Jing Wang, James A. Mobley, Jeffrey Singer, Anju Singh, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In …

Embryonic Development Of Natural Annual Killifish Populations Of The Genus Austrolebias: Evolutionary Parallelism And The Role Of Environment, Hellen Schlueb, Daniel Blanco, Daniel García, Jason Podrabsky

Biology Faculty Publications and Presentations

1. Repeated, independent emergence of the same trait within different phylogenetic lineages is termed parallel evolution. It typically occurs as a result of similar selective pressures. Annual killifish have adapted to survive in the extreme habitat of temporary pools on three continents and present an especially amenable system for studying fundamental principles of evolutionary parallelism. When the pools dry, annual killifish embryos survive through the dry phase in the bottom substrate in a stage of dormancy—a diapause. The diapause is a complex set of three different developmental stages, none of which is obligate, thus leading to a multitude of potential developmental …

Evolutionary Codependency: Insights Into The Mitonuclear Interaction Landscape From Experimental And Wild Caenorhabditis Nematodes, Suzanne Estes, Zachary P. Dietz, Vaishali Katju, Ulfar Bergthorsson

Biology Faculty Publications and Presentations

Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these …

Novel Viruses Of The Family Partitiviridae Discovered In Saccharomyces Cerevisiae, Angela M. Crabtree, Ignacio De La Higuera, Kenneth Stedman, Multiple Additional Authors

Biology Faculty Publications and Presentations

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite …

Predation Of Lepidophyma Flavimaculatum (Squamata: Xantusiidae) By Basiliscus Plumifrons (Squamata: Corytophanidae), Mauricio Quirós Rosales, José Manuel Mora, Randy Alvarado

Biology Faculty Publications and Presentations

Lizards are the most diversified group of living reptiles with 7176 species worldwide (Uetz 2022). They play key roles in ecosystems where they are prey to a wide variety of predators, including snakes, other lizards, mammals, birds, and invertebrates (Pianka and Vitt 2006). The tropical forests of the new world contain a high variety of species of different sizes, shapes, and colors. In Costa Rica in particular, at least 80 species of lizards have been reported (Leenders 2019). They occupy highly diverse habitat types where they participate in food webs that involve many other species of vertebrates and invertebrates.

A New Frontier For Fat: Dietary Palmitic Acid Induces Innate Immune Memory, Amy L. Seufert, Brooke A. Napier

Biology Faculty Publications and Presentations

Dietary saturated fats have recently been appreciated for their ability to modify innate immune cell function, including monocytes, macrophages, and neutrophils. Many dietary saturated fatty acids (SFAs) embark on a unique pathway through the lymphatics following digestion, and this makes them intriguing candidates for inflammatory regulation during homeostasis and disease. Specifically, palmitic acid (PA) and diets enriched in PA have recently been implicated in driving innate immune memory in mice. PA has been shown to induce long-lasting hyper-inflammatory capacity against secondary microbial stimuli in vitro and in vivo, and PA-enriched diets alter the developmental trajectory of stem cell progenitors in …

Inference And Reconstruction Of The Heimdallarchaeial Ancestry Of Eukaryotes, Laura Eme, Daniel Tamarit, Eva F. Caceres, Courtney W. Stairs, Valerie De Anda, Max E. Schön, Kiley W. Seitz, Nina Dombrowski, Anna-Louise Reysenbach, Multiple Additional Authors

Biology Faculty Publications and Presentations

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors— members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage …

Chi Sequences Switch The Recbcd Helicase–Nuclease Complex From Degradative To Replicative Modes During The Completion Of Dna Replication, Avery E. Jehru, Charmain Courcelle, Justin Courcelle, Multiple Additional Authors

Biology Faculty Publications and Presentations

Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase–nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with crossover hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced replication is processive but uncoupled with respect to leading and lagging strand synthesis and can be suppressed by ter sites …

Paternity Patterns In A Long-Term Resident Bottlenose Dolphin Community, Debbie Duffield, Randall Wells

Biology Faculty Publications and Presentations

Genetic analyses, initiated in 1984, have played a major role in our understanding of the structure and social relationships of the long-term resident community of common bottlenose dolphins (Tursiops truncatus) in Sarasota Bay, Florida (SBDC). One component of our ongoing study of the community’s social system involves using blood samples from periodic catch-and-release sampling for life history and health assessment studies, as well as skin from biopsy dart sampling studies and strandings, to investigate paternity and mating strategies in this community. These analyses, covering a span of four generations of calves, were originally based on chromosomes and protein electrophoresis, but …

Methanocaldococcus Lauensis Sp. Nov., A Novel Deep-Sea Hydrothermal Vent Hyperthermophilic Methanogen, Stéphane L'Haridon, Steven Goulaouic, Emily St John, Stephanie Fouteau, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

Three hyperthermohphilic methanogens, designated strain SG7T, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7T, SG1 and SLH were affiliated with the genus Methanocaldococcus within the family Methanocaldococcaceae, order Methanococcales. They shared 95.5–99.48 % 16S rRNA gene sequence similarity to other Methanocaldococcus species and were most closely related to Methanocaldococcus bathoardescens. Cells of strains SG7T, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between …

Environmental Enrichment Factors Associated With The Activity Level Of Bottlenose Dolphins Under Professional Care, Lisa K. Lauderdale, K. Alex Shorter, Joaquin Gabaldon, Jill D. Mellen, Multiple Additional Authors

Biology Faculty Publications and Presentations

Environmental enrichment can be used to improve the welfare of dolphins in zoos and aquariums. Bottlenose dolphins under professional care are typically provided with a range of enrichment that has a variety of features and levels of complexity at various frequencies. In the present study, a subset of data from a larger study entitled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study) was used to examine the relationship between activity level and enrichment buoyancy as well as enrichment provisioning schedules. Survey data were collected from accredited zoos and aquariums related to the …

Selective And Differential Feeding On Marine Prokaryotes By Mucous Mesh Feeders, Carey P. Sweeney, Kelly R. Sutherland, Anne Thompson

Biology Faculty Publications and Presentations

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer …

The Time Is Right For An Antarctic Biorepository Network, Kristin M. O’Brien, Elizabeth L. Crockett, Bryon J. Adams, Charles D. Amsler, Hannah J. Appiah-Madson, Allen Collins, Thomas Desvignes, Sarah Eppley, Multiple Additional Authors

Biology Faculty Publications and Presentations

Antarctica is a central driver of the Earth’s climate and health. The Southern Ocean surrounding Antarctica serves as a major sink for anthropogenic CO2 and heat (1), and the loss of Antarctic ice sheets contributes significantly to sea level rise and will continue to do so as the loss of ice sheets accelerates, with sufficient water stores to raise sea levels by 58 m (2). Antarctica's marine environment is home to a number of iconic species, and the terrestrial realm harbors a remarkable oasis for life, much of which has yet to be discovered (3). Distinctive oceanographic features of the …

Urban Green Roofs Can Support A Diversity Of Parasitoid Wasps, Aramee C. Diethelm, Susan Masta

Biology Faculty Publications and Presentations

Green roofs are often installed atop buildings to provide ecological services such as mitigating storm water runoff and cooling air within urban heat islands. We found that green roofs in Portland, Oregon, also can support biodiversity, including a diverse assemblage of parasitoid wasps, with 20 morphospecies from 10 families present on the four roofs we surveyed. The roofs with greater plant diversity and structural complexity harbored comparatively more parasitoid morphospecies than the structurally simpler Sedum-dominated roofs. The oldest green roof supported much greater diversity than the younger roofs, including a comparably planted roof three times its size. Parasitoid wasps from …

Upper Temperature Limit Of Larval Pacifc Lamprey Entosphenus Tridentatus: Implications For Conservation In A Warming Climate, Timothy A. Whitesel, Christina T. Uh

Biology Faculty Publications and Presentations

Climate models suggest that by 2100, maximum temperatures where many larval Pacific lamprey, Entosphenus tridentatus, rear now may approach 27–31 °C. Little information exists on whether larval Pacific lamprey can tolerate these temperatures. We used acclimated chronic exposure (ACE) and direct acute exposure (DAE) experiments to determine the water temperature that is lethal to larval Pacific lamprey and whether sublethal water temperatures influence larval burrowing behavior. After 30 days in ACE experiments, all larvae survived in temperatures averaging ≤ 27.7 °C, no larvae survived in temperatures averaging ≥ 30.7 °C and the ultimate upper incipient lethal temperature (UILT) was …

Cruise, A Tool For The Detection Of Iterons In Circular Rep-Encoding Single-Stranded Dna Viruses, Adam Jones, George W. Kasun, Joel Stover, Kenneth M. Stedman, Ignacio De La Higuera

Biology Faculty Publications and Presentations

Iterons are short, repeated DNA sequences that are important for the replication of circular single-stranded DNA viruses. No tools that can reliably predict iterons are currently available. The CRUcivirus Iteron SEarch (CRUISE) tool is a computational tool that identifies iteron candidates near stem-loop structures in viral genomes.