Biology Commons^™

West Coast Demersal Scalefish Resource Harvest Strategy 2021-2025 : Version 1.0, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Integrated Fisheries Management Draft Allocation Report – West Coast Demersal Scalefish, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Large Variability In Feeding Behavior Among Crossbred Growing Cattle, David N. Kelly, Roy D. Sleator, Craig P. Murphy, Stephen B. Conroy, Michelle M. Judge, Donagh P. Berry

Department of Biological Sciences Publications

The purpose of this study was to define an extensive suite of feeding behavior traits in growing crossbred cattle and to investigate their phenotypic inter-relationships as well as relationships with other performance and efficiency traits. Time-series feeding behavior data, as well as feed intake and liveweight records, were available for 624 growing crossbred cattle, of which 445 were steers and 179 were heifers. Feeding behavior repeatability estimates were calculated using linear mixed models. Additionally, partial Spearman correlations were estimated among 14 feeding behavior traits, as well as between feeding behavior with both performance and feed efficiency traits, using residuals retained …

Effectiveness Of Current Hygiene Practices On Minimization Of Listeria Monocytogenes In Different Mushroom Production-Related Environments, Vincenzo Pennone, Kenneth Lyonel Dygico, Aidan Coffey, Cormac G.M. Gahan, Helen Grogan, Olivia Mcauliffe, Catherine M. Burgess, Kieran Jordan

Department of Biological Sciences Publications

Background: The commercial production of Agaricus bisporus is a three stage process: 1) production of compost, also called “substrate”; 2) production of casing soil; and 3) production of the mushrooms. Hygiene practices are undertaken at each stage: pasteurization of the substrate, hygiene practices applied during the production of casing soil, postharvest steam cookout, and disinfection at the mushroom production facilities. However, despite these measures, foodborne pathogens, including Listeria monocytogenes, are reported in the mushroom production environment. In this work, the presence of L. monocytogenes was evaluated before and after the application of hygiene practices at each stage of mushroom production …

Feeling Out Your Food: A Histological Analysis Of The Whisker System In Seals, Cameron Cooper

Master's Theses

The vibrissal (whisker) system is present in nearly all mammals and is especially important in deep-diving mammals. Pinnipeds (seals, sea lions, and walruses) have highly sensitive whiskers that are used to follow hydrodynamic trails created by their swimming prey. Each pinniped vibrissa is surrounded by a tripartite blood sinus system composed of an upper cavernous sinus (UCS), a ring sinus (RS), and a lower cavernous sinus (LCS). The UCS has been hypothesized to play a thermoregulatory role, insulating temperature sensitive mechanoreceptors located within the vibrissal follicle. The aim of this study was to examine this hypothesis by measuring and comparing …

Changes In Gene Expression Profiles In Müller Glia Following Exposure To An Α7 Nicotinic Acetylcholine Receptor Agonist, Megan L. Stanchfield

Masters Theses

Previous studies from this lab have determined that dedifferentiation of Müller glia (MG) occurs after application of an α7 nicotinic acetylcholine receptor agonist, PNU-282987 (PNU), to retinal pigment epithelial (RPE) cells in adult rodents. This study was designed to explore the role of the HB-EGF/Ascl1/Lin28a signaling pathway in MG dedifferentiation to retinal progenitor cells. RNAseq was performed on MG following contact with RPE-J cells treated with PNU-282987. Up- or down-regulated genes were compared with published literature of MG dedifferentiation that occurs in lower vertebrate regeneration or with transcript profiles during early mammalian development. Between 8-12 hours, up-regulation was observed in …

5-Ht Receptor Subtype May Mediate Crh Production In Hypothalamus, Bailey Underwood

Lawrence University Honors Projects

Increased levels of corticotropin releasing hormone (CRH) are associated with anxiety, as are decreased levels of serotonin (5-HT). Do 5-HT levels influence CRH production and anxiety? The ventral hippocampus is associated with anxiety behavior, contains cells expressing 5-HT receptors (including 5HT7R), and extends axons into CRH producing regions of the hypothalamus (Jalewa et al., 2014; Jiminez et al., 2018). Therefore, 5-HT responsive neurons may play a role in the anxiety response and CRH production. To analyze how 5-HT may influence anxiety, 5dpf Danio rerio were examined following application of a 5-HT7R agonist (AS-19) and antagonist (SB-258179). A distance assay was …

High Diversity Of Testate Amoebae (Amoebozoa, Arcellinida) Detected By Hts Analyses In A New England Fen Using Newly Designed Taxon-Specific Primers, Alistaire Ruggiero, Jean David Grattepanche, Agnes K.M. Weiner, Laura A. Katz

Biological Sciences: Faculty Publications

Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2–10, 10–35, 35–100, and 100–300 μm). Analyses of these data show the following: (1) …

From Aristotle To Wunderkammer: The Development Of Entomology And Insect Collections, Erica Fischer

Honors Projects

This project aimed to analyze the development of insect classification and the shift from the realm of the amateur naturalist to professional science. It looked to address questions regarding entomology as a developing science and how effectively it reflects larger changes in the field of biology and the development of natural history collections. This work was for a synthesis of time periods from the beginnings of classification in the ancient world through the 20th century, a more general timeline than is typically approached. The research needed for the completion of this paper was based on secondary source research in the …

Interactions Of Deet And Novel Repellents With Mosquito Odorant Receptors, Gariel G. Grant, Rachel R. Estrera, Narendra Pathak, C. Dennis Hall, Maia Tsikolia, Kenneth J. Linthicum, Ulrich R. Bernier, Adam C. Hall

Neuroscience: Faculty Publications

The carboxamide N,N-di-ethyl-meta-Toluamide (DEET) is the most effective and widely used insect repellent today. However, drawbacks concerning the efficacy and the safety of the repellent have led to efforts to design new classes of insect repellents. Through quantitative structure-Activity relationships, chemists have discovered two chemical groups of novel repellents: The acylpiperidines and the carboxamides, with the acylpiperidines generally more potent in biological assays. Although the exact mechanism of action of DEET and other repellents has not yet been thoroughly elucidated, previous research shows that the activity of insect odorant receptors are inhibited in the presence of repellents. The present electrophysiological …

Potent Inhibition Of Mandelate Racemase By Boronic Acids: Boron As A Mimic Of A Carbon Acid Center, Amar Nath Sharma, Lia Grandinetti, Erin R. Johnson, Martin St. Maurice, Stephen L. Bearne

Biological Sciences Faculty Research and Publications

Boronic acids have been successfully employed as inhibitors of hydrolytic enzymes. Typically, an enzymatic nucleophile catalyzing hydrolysis adds to the electrophilic boron atom forming a tetrahedral species that mimics the intermediate(s)/transition state(s) for the hydrolysis reaction. We show that para-substituted phenylboronic acids (PBAs) are potent competitive inhibitors of mandelate racemase (MR), an enzyme that catalyzes a 1,1-proton transfer rather than a hydrolysis reaction. The K_i value for PBA was 1.8 ± 0.1 μM, and p-Cl-PBA exhibited the most potent inhibition (K_i = 81 ± 4 nM), exceeding the binding affinity of the substrate by ∼4 …

Light And Temperature Mediate Algal Simulation Of Heterotrophic Activity On Decomposing Leaf Litter, Cody A. Pope, Halvor M. Halvorson, Robert H. Findlay, Steven N. Francoeur, Kevin A. Kuehn

Faculty Publications

1. Recent evidence suggests that periphytic algae stimulate plant litter heterotrophs (fungi and bacteria) in the presence of light, but few studies have tested whether this stimulation varies across gradients of light, which may covary with temperature.
2. We exposed field‐conditioned Typha domingensis litter to fully‐crossed, short‐term gradients of temperature (15, 20, 25, and 30°C) and light (0, 25, 53, 123, and 388 µmol quanta m⁻² s⁻¹) and measured responses of litter‐associated algal, fungal, and bacterial production rates and β‐glucosidase, β‐xylosidase, and phenol oxidase enzyme activities in the laboratory.
3. Increased light stimulated algal production rates, from immeasurable production under …

Enzymatic In-Situ Transesterification Of Neutral Lipids From Simulated Wastewater Cultured Chlorella Emersonii And Pseudokirchneriella Subcapitata To Sustainably Produce Fatty Acid Methyl Esters, Priyanka Priyanka, Gemma K. Kinsella, Gary Henehan, Barry J. Ryan

Articles

Alternative, more sustainable and environmentally positive, sources of energy are one of the current global challenges. One approach to achieving more sustainable sources of energy is to use waste from one system as a raw material for energy production, following the circular biosystem philosophy. This study successfully adopted this approach whereby microalgae strains Chlorella emersonii and Pseudokirchneriella subcapitata were bioprospected and metabolically engineered in simulated wastewater supplemented with glucose to produce neutral lipids. Using a two-step cultivation approach neutral lipid content was enhanced in Chlorella emersonii and Pseudokirchneriella subcapitata biomass. Via in-situ transesterification, these neutral lipids were subsequently bioconverted to …

Isolation And Characterization Of Bacteriophages Infecting Enterobacter Cloacae To Reduce Bloater Defect In Cucumber Fermentations, Samantha Thompson

Master of Science in Integrative Biology Theses

Fermented cucumbers are one of the most important fermented vegetables consumed worldwide. During cucumber fermentations, certain undesirable changes may occur. One of such changes is known as bloater defect (hollow cavities in fermented cucumbers), which is primarily caused by gas-producing bacteria including Enterobacter cloacae. Bloater defect lowers product quality and leads to significant economic loss to the pickle industry, and effective preventative methods are needed. Bacteriophages (phages) are highly host-specific bacteria killers. Use of phages to control unwanted bacteria in foods is a promising approach because phages do not change food properties. The goals of this research were to …

Inactivation Of Hippo And Cjun-N-Terminal Kinase (Jnk) Signaling Mitigate Fus Mediated Neurodegeneration In-Vivo, Ankita Sarkar, Abijeet Singh Mehta, Prajakta Deshpande, Madhuri Kango-Singh, Udai Bhan Pandey, Amit Singh

Biology Faculty Publications

Amyotrophic Lateral Sclerosis (ALS), a late-onset neurodegenerative disorder characterized by the loss of motor neurons in the central nervous system, has no known cure to-date. Disease causing mutations in human Fused in Sarcoma (FUS) leads to aggressive and juvenile onset of ALS. FUS is a well-conserved protein across different species, which plays a crucial role in regulating different aspects of RNA metabolism. Targeted misexpression of FUS in Drosophila model recapitulates several interesting phenotypes relevant to ALS including cytoplasmic mislocalization, defects at the neuromuscular junction and motor dysfunction. We screened for the genetic modifiers of human FUS-mediated neurodegenerative phenotype using molecularly …

Optimal Allocation Of Two Resources In Annual Plants, David Mcmorris

Department of Mathematics: Dissertations, Theses, and Student Research

The fitness of an annual plant can be thought of as how much fruit is produced by the end of its growing season. Under the assumption that annual plants grow to maximize fitness, we can use techniques from optimal control theory to understand this process. We introduce two models for resource allocation in annual plants which extend classical work by Iwasa and Roughgarden to a case where both carbohydrates and mineral nutrients are allocated to shoots, roots, and fruits in annual plants. In each case, we use optimal control theory to determine the optimal resource allocation strategy for the plant …

Plasticity Of Least Tern And Piping Plover Nesting Behaviors In Response To Sand Temperature, Alicia K. Andes, Mark H. Sherfy, Terry L. Shaffer, Susan N. Ellis-Felege

Biology Faculty Publications

Birds that nest on the ground in open areas, such as Piping Plovers (Charadrius melodus) and Interior Least Terns (Sternula antillarum athalassos), are exposed to high temperatures in thermally stressful environments. As a result, some ground-nesting avian species have adapted behavioral strategies to maintain thermal regulation of eggs and themselves. We assessed the impact of sand temperature on shorebird nesting behaviors by installing video cameras and thermocouples at 52 Least Tern and 55 Piping Plover nests on the Missouri River in North Dakota during the 2014–2015 breeding seasons. Daily duration and frequency of shading behaviors exhibited …

Mechanisms Of Atp-Dependent Substrate Reduction In The Nitrogenase-Like Dpor Complex, Elliot Irwin Corless

Dissertations (1934 -)

Iron-Sulfur ([Fe-S]) clusters are the most common transient electron carriers in cells and are necessary for basic metabolism of all life. Bacterial systems use two operons (isc and suf ) for the biogenesis and delivery of [Fe-S] clusters to various proteins. Once delivered, they serve as transient electron carriers necessary for both heterotrophic and autotrophic metabolism and reduction/oxidation chemistry. This work utilizes the hetero-octameric Dark operative Protochlorophyllide Oxido-Reductase (DPOR) complex as a platform to investigate [Fe-S] cluster biogenesis and the concerted action of its multiple [Fe-S] clusters and protein subunits. DPOR catalyzes the penultimate step in bacterial chlorophyll synthesis and …

Characterization Of The Mir-44 Family Of Micrornas In The C. Elegans Germline, Katherine Ann Maniates

Dissertations (1934 -)

While numerous individual miRNAs have been detected in the germline, the functions of most other specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. Analysis of newly generated mir-44 family mutants has identified a group of miRNAs that modulate the pathway of germline sex determination in C. elegans. Mutants produce fewer sperm and display an earlier switch to producing oocytes. In the germline, cell fate decisions are made for germline …

Characterizing The Mechanisms Of Ectopic Expression Of Dream Complex Target Genes And The Hta Phenotype In C. Elegans, Jerrin Roy Cherian

Dissertations (1934 -)

It is important for organisms to establish and maintain proper gene expression for normal growth and development. In C. elegans, the DREAM repressor complex helps maintain proper gene expression in somatic cells by repressing germline genes. DREAM complex mutants show close to normal gene expression at 20°C; however, at 26°C, DREAM complex mutants display increased misexpression of germline genes ectopically in the soma and display a distinct High Temperature larval Arrest (HTA) phenotype. It is unclear what gene regulatory mechanisms lead to misexpression of germline genes in somatic cells of DREAM complex mutants. My dissertation research investigated three aspects of …

Anthropogenic Drivers And Ecological Concepts Of Antimicrobial Resistance, Rachelle E. Beattie

Dissertations (1934 -)

Antimicrobial resistance (AMR) is a ubiquitous global health issue driven by the overuse and misuse of antimicrobial compounds in healthcare and veterinary medicine. Both natural and built environments have been recognized as reservoirs of antimicrobial resistant bacteria, genes, and pathogens but the factors that drive increases in their abundance are not well understood, especially in natural environments. The primary goal of this work is to characterize the ecological drivers of antimicrobial resistance in freshwater ecosystems impacted by intensive livestock farms, known contributors of environmental resistance. Kewaunee County, Wisconsin served as an ideal study site for the investigation of the impact …

Vertical Transmission And Venereal Transmission Of Zika Virus In A Population Of South Texas Aedes Aegypti, Jeremy Marshall

Theses and Dissertations

Zika virus has become a greater global public health concern from the occurrence of outbreaks in 2007 and its expansion to the Americas in 2015. The presence of Aedes aegypti in the Lower Rio Grande Valley and evidence of local transmission of Zika in Brownsville, Texas provides a need to research transmission dynamics of local populations. In these experiments, a locally acquired, laboratory colony of Aedes aegypti mosquitoes were infected with a blood meal featuring a Mexican isolate of Zika virus to display vector competency, vertical transmission, venereal transmission. Here, we infected 39 females, with 34 of them displaying evidence …

Insect Mediated Species Interactions: Examining Methods To Improve Artificial Buzz Pollination And Testing The Effects Of Plant Based Bioactive Compounds On Herbivore Life-History Traits, Mandeep Tayal

Theses and Dissertations

Pollination and herbivory are two major interactions in insect-plant ecology. Specialized pollination systems such as buzz pollination where pollen grains have to be extracted by bees with special thoracic vibrations and indirect flight muscles, is observed in ~6% of all flowering plants. Breeding and research programs in these species demand artificial pollination, but natural buzz pollinators are unreliable for this purpose. To find an alternative, we tested the pollen extraction efficiency of using inexpensive electric toothbrush over tuning fork (another commonly used device) in two buzz-pollinated species (Tomato and Silverleaf nightshade) at different buzzing frequencies and multiple buzzing time intervals. …

The Arabidopsis Transcription Factor Aintegumenta Orchestrates Patterning Genes And Auxin Signaling In The Establishment Of Floral Growth And Form, Beth A. Krizek, Ivory C. Blakley, Yen Yi Ho, Nowlan Freese, Ann E. Loraine

Faculty Publications

Understanding how flowers form is an important problem in plant biology, as human food supply depends on flower and seed production. Flower development also provides an excellent model for understanding how cell division, expansion and differentiation are coordinated during organogenesis. In the model plant Arabidopsis thaliana, floral organogenesis requires AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE 6 (AIL6)/PLETHORA 3 (PLT3), two members of the Arabidopsis AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor family. Together, ANT and AIL6/PLT3 regulate aspects of floral organogenesis, including floral organ initiation, growth, identity specification and patterning. Previously, we used RNA-Seq to identify thousands of genes with disrupted expression in ant ail6 …

Resources For Teaching And Assessing The Vision And Change Biology Core Concepts, Janet L. Branchaw, Pamela A. Pape-Lindstrom, Kimberly D. Tanner, Sarah A. Bissonnette, Tawnya L. Cary, Brian A. Couch, Alison J. Crowe, Jenny K. Knight, Katharine Semsar, Julia I. Smith, Michelle K. Smith, Mindi M. Summers, Caroline J. Wienhold, Christian D. Wright, Sara E. Brownell

School of Biological Sciences: Faculty Publications

The Vision and Change report called for the biology community to mobilize around teaching the core concepts of biology. This essay describes a collection of resources developed by several different groups that can be used to respond to the report’s call to transform undergraduate education at both the individual course and departmental levels. First, we present two frameworks that help articulate the Vision and Change core concepts, the BioCore Guide and the Conceptual Elements (CE) Framework, which can be used in mapping the core concepts onto existing curricula and designing new curricula that teach the biology core concepts. Second, we …

The Role Of Chromatin Remodeling Protein And Transcriptional Repressor, Ing4, In Hematopoiesis Regulation, Melanie Rodriguez

Theses and Dissertations

The hematopoietic compartment is tasked with the establishment and maintenance of the entire blood program. Key to this process are hematopoietic stem cells (HSCs), which possess the unique ability to self-renew and differentiate to replenish blood cells throughout an organism’s lifetime. In a screen for epigenetic regulators of hematopoiesis in zebrafish, we identified chromatin remodeling protein and transcription repressor, Ing4, as a requirement for hematopoietic stem and progenitor cell (HSPC) specification. Ing4, a member of the inhibitor of growth (ING) family, is a subunit of the HB01-JADE-hEAF6 histone acetyltransferase complex responsible for most nucleosomal histone H4 acetylation in eukaryotes. Ing4 …

Characterization And Analysis Of The Avian Epidermal Differentiation Complex And Implications In Feather Evolution, Anthony Chastine Davis

Theses and Dissertations

Since the most recent major mass-extinction event ~65 million years ago, birds have expanded to now occupy a wide range of habitats and exhibit diverse lifestyles. A major reason for this evolutionary success is the mechanical resilience and diversity of their epidermal appendages such as feathers, scales, and beaks. The diversity of these appendages, specifically feathers has played a critical role in their evolutionary success. The feathers of birds vary substantially across different species, as well as at different life stages and anatomical locations on an individual bird. Several of the genetic elements involved in the development and structure of …

Undergraduate Biology Education Research Gordon Research Conference: A Meeting Report, Erin L. Dolan, Michelle Borrero, Kristine Callis-Duehl, Miranda M. Chen Musgrove, Joelyn De Lima, Isi Ero-Tolliver, Laci M. Gerhart, Emma Goodwin, Lindsey R. Hamilton, Meredith A. Henry, Jose Herrera, Bethany Huot, Stacey Kiser, Melissa E. Ko, Marcy E. Kravec, Mark Lee, Lisa B. Limeri, Melanie E. Peffer, Debra Pires, Juan S. Ramirez Lugo, Starlette M. Sharp, Nicole A. Suarez

Biology Faculty Publications and Presentations

The 2019 Undergraduate Biology Education Research Gordon Research Conference (UBER GRC), titled “Achieving Widespread Improvement in Undergraduate Education,” brought together a diverse group of researchers and practitioners working to identify, promote, and understand widespread adoption of evidence-based teaching, learning, and success strategies in undergraduate biology. Graduate students and postdocs had the additional opportunity to present and discuss research during a Gordon Research Seminar (GRS) that preceded the GRC. This report provides a broad overview of the UBER GRC and GRS and highlights major themes that cut across invited talks, poster presentations, and informal discussions. Such themes include the importance of …

Pre-Emptive Detection Of Mature Pine Drought Stress Using Multispectral Aerial Imagery, Nancy Grulke, Jason Maxfield, Phillip Riggan, Charlie Schrader-Patton

Biology Faculty Publications and Presentations

Drought, ozone (O₃), and nitrogen deposition (N) alter foliar pigments and tree crown structure that may be remotely detectable. Remote sensing tools are needed that pre-emptively identify trees susceptible to environmental stresses could inform forest managers in advance of tree mortality risk. Jeffrey pine, a component of the economically important and widespread western yellow pine in North America was investigated in the southern Sierra Nevada. Transpiration of mature trees differed by 20% between microsites with adequate (mesic (M)) vs. limited (xeric (X)) water availability as described in a previous study. In this study, in-the-crown morphological traits (needle chlorosis, …

Using Genetic Diversity To Differentiate Mosquito Populations, Rachel Christine Malampy

Theses and Dissertations

Experiment 1: Little is known about Aedes aegypti females sharing oviposition sites. We examined four different oviposition sites in McAllen, TX. A mitochondrial gene was used to analyze the variation within the oviposition site to understand how many egg-laying females are sharing oviposition sites. These results will aid in the understanding of Aedes. aegypti oviposition behavior and contribute to more effective mosquito control techniques.

Experiment 2: Mosquito flight patterns and movement from habitat to habitat can drastically influence the spread of diseases. The anthropophilic Aedes aegypti mosquito has historically been identified as having a very limited flight range. Studies also …