Biology Commons^™

The Nlrp3 Inflammasome: A New Player In Neurological Diseases, Eli̇f Eren, Nesri̇n Özören

Turkish Journal of Biology

Inflammasomes are supramolecular protein complexes implicated in the detection of pathogens or danger-associated molecules and are responsible for mounting the first line of innate immune response to counteract these signals and restore tissue homeostasis. Among different inflammasomes identified so far, NLRP3 is of main interest since mutations in Nlrp3 gene are associated with autoinflammatory diseases such as Muckle-Wells syndrome, neonatal onset multisystem inflammatory disease, and familial cold urticaria/autoinflammatory syndrome. On the other hand, whereas other inflammasomes are mainly detectors of specific molecular motifs, NLRP3 is acting as a general sensor of cellular perturbations including potassium efflux, lysosomal damage, and ROS …

In Vitro Study On Chondrogenic Differentiation Of Human Adipose-Derived Stem Cells On Treated Bovine Pericardium, My Thi Ngoc Nguyen, Vu Nguyen Doan, Ha Le Bao Tran

Turkish Journal of Biology

Bovine pericardium has been proposed as an available material for tissue engineering and bioprosthetic reconstruction. In this study, bovine pericardium was fabricated into a scaffold for culturing and chondrogenic differentiation of human adipose-derived stem cells (hADSCs). Bovine pericardium was treated in 10 mM Tris-HCl and 0.15% SDS, followed by crosslinking in 0.1% glutaraldehyde. Treated bovine pericardium (tBP) was characterized as a slight yellowish thin membrane with enhanced tensile strength and strain property. The membrane maintained stability under enzymatic conditions for up to 16 days of incubation. The results confirmed tBP as a cell-friendly scaffold for hADSCs due to low cytotoxicity …

In Silico Approach To The Analysis Of Snps In The Human Apaf1 Gene, Tuğba Kaman, Ömer Faruk Karasakal, Ebru Özkan Oktay, Korkut Ulucan, Muhsi̇n Konuk

Turkish Journal of Biology

The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this study was to predict deleterious/damaging SNPs in the APAF1 gene via in silico analysis. To this end, APAF1 missense SNPs were obtained from the NCBI dbSNP database. In silico analysis of the missense SNPs was carried out by using publicly available online software tools. The stabilization and three-dimensional modeling of mutant proteins were also determined by using the …

Crosstalk Between Autophagy And Apoptosis Induced By Camphor Inschizosaccharomyces Pombe, Hizlan Hincal Ağuş, Sedanur Yilmaz, Cansin Ogeday Şengöz

Turkish Journal of Biology

Camphor is widely used in pharmacy, the food industry, and cosmetics. In this study, we evaluate inhibitory and cytotoxic effects of camphor in the fission yeast (Schizosaccharomyces pombe), which presents a unicellular model in mechanistic toxicology and cell biology. Low-dose camphor exposure (0.4 mg/mL) activated autophagy, which was shown by GFP-Atg8 dots and transcriptional upregulation of Atg6 (Beclin-1 ortholog). Autophagy was also confirmed by using autophagy-deficient cells, which showed reduction in GFP-Atg8 dot formation. However, high-dose camphor exposure (0.8 mg/mL) caused dramatic cell death ratios, demonstrated by spot and colony-forming assays, even in autophagy-deficient cells. To unravel the underlying mechanism, …

Identification Of Watermelon Heat Shock Protein Members And Tissue-Specific Gene Expression Analysis Under Combined Drought And Heat Stresses, Yasemi̇n Çeli̇k Altunoğlu, Merve Keleş, Tevfi̇k Hasan Can, Mehmet Cengi̇z Baloğlu

Turkish Journal of Biology

Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformatics analysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed. In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to the Hsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100 family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar …

Effects Of Potassium Source And Rate On Yield, Quality, And Leaf Chemistry Of Dark And Burley Tobacco, And Residual Effects Of Soil K Levels, Andrea Brooke Keeney

Theses and Dissertations--Plant and Soil Sciences

Field trials were conducted in 2016, 2017 and 2018 with dark fire-cured, dark air-cured, and burley tobacco at Princeton, Murray and Lexington Kentucky. Tobacco variety used in 2016 was a low converter (LC) variety, varieties used in 2017 and 2018 were LC and higher converter (HC) varieties. Potassium sources used at all locations and in all years were potassium sulfate (K₂SO₄) and potassium chloride (KCl). Application rates used at all locations and in all years were 93, 186, 279 kg K ha^-1along with an untreated control that received no potassium. In all trials, tobacco …

Priming By Arbuscular Mycorrhizal Fungi Of Plant Antioxidant Enzyme Production: A Meta-Analysis, Ami Lokhandwala, Jason D. Hoeksema

Faculty and Student Publications

Priming of antioxidant enzyme production of plants, which can act as a defense against pathogens and other stresses, is an under-appreciated benefit often provided by arbuscular mycorrhizal (AM) fungi. Although numerous experiments have demonstrated this phenomenon, this literature has not been synthesized, and we understand little about the factors that may drive variation in the magnitude of this priming phenomenon. We gathered data from 81 original publications in which antioxidant enzyme production of plants was measured in the presence and absence of AM fungi, including factors that varied among studies, such as the identity of plants and fungi, number of …

Weak Warning Signals Can Persist In The Absence Of Gene Flow, J. P. Lawrence, Bibiana Rojas, Antoine Fouquet, Johanna Mappes, Annelise Blanchette, Ralph A. Saporito, Renan Janke Bosque, Elodie A. Courtois, Brice Noonan

Faculty and Student Publications

Aposematic organisms couple conspicuous warning signals with a secondary defense to deter predators from attacking. Novel signals of aposematic prey are expected to be selected against due to positive frequency-dependent selection. How, then, can novel phenotypes persist after they arise, and why do so many aposematic species exhibit intrapopulation signal variability? Using a polytypic poison frog (Dendrobates tinctorius), we explored the forces of selection on variable aposematic signals using 2 phenotypically distinct (white, yellow) populations. Contrary to expectations, local phenotype was not always better protected compared to novel phenotypes in either population; in the white population, the novel phenotype evoked …

The Ecology Of Central Florida's Thief Ants (Hymenoptera: Formicidae: Solenopsis), Leo Ohyama

Electronic Theses and Dissertations

Thief ants of the genus Solenopsis are a diverse group of ants that are found in ant communities throughout the world. They have long been purported to practice lestobiosis, an interaction between small and larger-bodied ants, where small ants cryptically tunnel into larger-bodied ant nests within the subterranean environment and steal brood or eggs for consumption. Thief ants are extremely small, measuring 1-2 mm in length and many of the species within this group practice a subterranean life history, where they live the entirety of their lives exclusively belowground. Due to these key characteristics, the ecology and natural history of …

Multiple Connections Between Amazonia And Atlantic Forest Shaped The T Phylogenetic And Morphological Diversity Of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae), Rafael O. De Sá, João Filipe Riva Tonini, Hannah Van Huss, Alex Long, Travis Cuddy, Mauricio C. Forlani, Pedro L.V. Peloso, Hussam Zaher, Célio F.B. Haddad

Biology Faculty Publications

Chiasmocleis is the most species-rich genus of Neotropical microhylids. Herein, we provide the first comprehensive multilocus phylogeny for the genus, including all but 3 of the 34 recognized species and multiple individuals per species. We discuss cryptic speciation, species discovery, patterns of morphological evolution, and provide a historical biogeographic analysis to account for the current distribution of the genus. Diversification of Chiasmocleis from other New World microhylids began during the Eocene, app. 40 mya, in forested areas, and current diversity seems to be a product of recurrent connections between the Atlantic Forest and Amazonia. Small-sized species evolved independently three times …

Role Of Moa-1, An Anti-Phosphatase, And Apl-1, An App-Related Protein, In Morphogenesis And Mating Behavior In Caenorhabditis Elegans, Valerie C. Moscoso

Dissertations and Theses

Alzheimer's disease is a neurodegenerative disease that affects more than 30 million people globally. The disease is characterized by an accumulation of extracellular beta-amyloid peptide plaques and intracellular neurofibrillary tangles in the brain. The beta-amyloid peptide is derived from a larger precursor protein, the amyloid precursor protein (APP). Mutations in APP have been correlated with Alzheimer's disease. Due to the presence of two paralogues, APLP1 and APLP2, which have overlapping functions, the normal function of APP is difficult to elucidate. Knockout of the entire APP gene family in mice results in lethality and developmental defects, indicating that the APP gene …

Application Strategy For An Anthraquinone-Based Repellent And The Protection Of Soybeans From Canada Goose Depredation, Scott J. Werner, Matthew Gottlob, Charles D. Dieter, Joshua D. Stafford

Human–Wildlife Interactions

Agricultural crops can sustain extensive damage caused by Canada geese (Branta canadensis) when these crops are planted near wetlands or brood-rearing sites. From 2000 to 2015, South Dakota Game, Fish and Parks spent >$5.6 million to manage damages caused by Canada geese to agricultural crops (primarily soybeans) in South Dakota, USA. For the purpose of developing a repellent application strategy for nonlethal goose damage management, we comparatively evaluated the width of anthraquinone applications (i.e., 9.4 L Flight Control^® Plus goose repellent/ha [active ingredient: 50% 9,10-anthraquinone] at 0–36 m versus 0–73 m perpendicular to the edge of wetlands …

Foraging Preferences Of Barnacle Geese On Endophytic Tall And Red Fescues, Tuuli-Marjaana Koski, Kari Saikkonen, Tero Klemola, Marjo Helander

Human–Wildlife Interactions

Many grasses (Poaceae) have symbiotic fungal endophytes, which affect livestock by producing unpalatable or harmful secondary compounds. Less is known about the repelling effects of fungal endophytes on avian grazers despite potential wildlife management implications. Herbivorous goose (Branta spp.) species may become a nuisance in recreational use areas via fecal littering. Planting these areas with grasses that avian grazers avoid may help mitigate this damage. In 2016, we studied the foraging preference of the barnacle geese (B. leucopsis) with endophytic (E+) or endophyte-free (E-) red fescue (Festuca rubra) and/or tall fescue (Schedonorus phoenix) in …

Wildlife Damage To Crops Adjacent To A Protected Area In Southeastern Mexico: Farmers’ Perceptions Versus Actual Impact, Gabriel Can-Hernández, Claudia Villanueva-García, Elías José Gordillo-Chávez, Coral Jazvel Pacheco-Figueroa, Elizabeth Pérez-Netzahual, Rodrigo García-Morales

Human–Wildlife Interactions

Human–wildlife conflicts occur when wildlife has an adverse effect on human activities (e.g., predation of livestock, crop raiding). These conflicts are increasing, particularly in areas surrounding natural protected areas, where villagers engage in subsistence agriculture. Crop damage may cause farmers to retaliate and harm wildlife species considered responsible for the damage. Among the factors that determine the intensity of the conflict are the frequency of the damage and the amount of biomass consumed relative to the perceptions, values, and cultural history of the farmers affected. To better understand the conflicts between farmers and wildlife, we compared farmer perceptions of wildlife …

Fluvastatin And Microrna-146a Alter Interleukin-33 Mediated Mast Cell Functions., Marcela Taruselli

Theses and Dissertations

Mast cells are tissue-resident immune cells known as effector cells for the innate and adaptive immune systems. Mast cells contribute to host defenses against parasites such as large roundworm parasites, bacterial pathogens, and toxins, and participate in wound healing, but they are mostly known for their role in allergic diseases. It has been well established that during allergic diseases, mast cells are stimulated by IgE cross-linkage to release proinflammatory mediators. However, a newly discovered cytokine, IL-33 has also been implicated in allergic disease. Recently, IL-33 has been implicated as a driver of several Type I sensitivities and previous studies have …

Manufactured By Nature: Growing Generatively Designed Products, Mohammad Jawad

Theses and Dissertations

Mass production and assembly lines are yesterday’s manufacturing methods. They have exhausted Earth’s resources and limited the possibilities of design in terms of both form and material, prompting designers to search for new processes. A new generation of making includes biomimicry-inspired technologies such as 3D printing and parametric simulation, which have transformed the production paradigm. Utilizing nature as industry, this thesis explores the possibility of “growing” designed objects by employing nature’s own processes and resources. It integrates bio materials, generative design and additive manufacturing to produce objects for a post-industrial world. The project outcomes employ natural minerals, crystallization and 3D …

Spatial And Temporal Distributions Of Larval Clupeid Fishes In A Tidal Freshwater Marsh Complex, Philip Reid Anderson

Theses and Dissertations

Tidal freshwater wetlands provide valuable ecosystem services such as nutrient cycling, coastal flood control, and reproductive habitat for early life stages of economically and ecologically important fishes. The nutrient rich environments that tidal freshwater wetlands occur in support high levels of primary productivity of phytoplankton and vegetation that provide essential reproductive habitat for anadromous clupeid fishes (Alosa spp., Brevoortia tyrannus) in Chesapeake Bay tributaries. Seasonal retention of clupeid eggs and larvae within tidal freshwater habitats may enhance early growth, survival, and year class strength. The primary goal of the present study was to characterize the relative importance of …

Mechanisms Underlying Production Stability In Temperate Deciduous Forests, Shea B. Wales

Theses and Dissertations

A persistent and reliable future terrestrial carbon (C) sink will depend on how stable forest production is under more variable climate conditions. We examined how age, forest structure, and disturbance history relate to the interannual variability of above-ground wood net primary production (NPPw). Our site in northern Michigan spans two experimental forest chronosequences and three late successional stands; the chronosequences have distinct disturbance histories, originating following either clear cut harvesting (“Cut Only”) or clear cut harvesting and fire (“Cut and Burn”), and range from 21 to 108 years old. Annual NPPw was estimated using dendrochronology and site specific allometric equations. …

Regulatory T Cells Promote Breast Cancer Progression Through Inhibiting Classical Activation Of Macrophages, Nicholas M. Clark

Theses and Dissertations

Transient ablation of regulatory T cells has been shown to be effective at hindering tumor growth and metastasis in murine breast cancer model. Based on our lab’s previous work, we have demonstrated that NK cells and CD8+ cytotoxic T cells were not required for the protective effect of Treg cell ablation. However, we also reported that CD4+ helper T cells and IFN-γ were required for the protective effect of Treg cell ablation. Furthermore, we observed that CD11B+ cells responded to Treg ablation therapy by up-regulating target genes of IFN-γ. Therefore, this study aimed to investigate the connection between the myeloid …

Business In The Estuary, Party In The Sea: Migration Patterns Of Striped Mullet (Mugil Cephalus) Within The Indian River Lagoon Complex, Olivia Myers

Electronic Theses and Dissertations

Commercial and recreational environmental enterprises in the Indian River Lagoon (IRL), Florida supply nearly 10,000 jobs and produce $1.6 billion dollars a year in revenue. These waters contain iconic species of sportfish, including red drum, snook, and sea trout, as well as their lower trophic level prey such as snapper and mullet. Striped mullet (Mugil cephalus) are both commercially valuable as well as an indicator species for overall ecosystem health. From September to December, mullet in the IRL undergo an annual migration from their inshore foraging habitats to oceanic spawning sites. However, their actual migratory pathways remain unknown. To address …

Hydrodynamic Limitations And The Effects Of Living Shoreline Stabilization On Mangrove Recruitment Along Florida Coastlines, Christian Pilato

Electronic Theses and Dissertations

The recruitment success of mangroves is influenced by a variety of factors, including propagule availability, desiccation, herbivory, and hydraulic habitat limitations. Hydrodynamic forces (waves and currents) act as obstacles to mangrove recruitment, restricting the successful colonization of mangrove species. We evaluated the biological and physical limitations to mangrove recruitment through monthly shoreline surveys and lateral pull-tests. Surveys followed mangroves from propagule release through recruitment along the shorelines of De Soto National Memorial (Bradenton, FL), capturing differences in propagule availability and recruitment along natural areas and across differing forms of shoreline stabilization ("living shorelines" and revetments). Propagule densities were highest along …

Fear And Loathing In The Super Organism: Foraging Strategy Doesn't Change Forager Response In A Landscape Of Fear., Philip Schadegg

Electronic Theses and Dissertations

Understanding how predators impact keystone species, like ants, is very important for our understanding of ecology because of ants' importance in shaping community dynamics and ecosystem functions. In this thesis I present research investigating the role of the ant-specialized spider Anasaitis canosa in influencing the foraging behavior of four ant species (Formica pallidefulva, Odontomachus ruginodis, Pheidole obscurithorax & Solenopsis invicta). Collectively, these four species use foraging strategies exhibited by most ants. I conducted two experiments to quantify the impacts of spider predation on ant prey. The first used forty colonies of four ant species to investigate how A. canosa changed …

Assessing The Effects Of Habitat And Manatee Exclusion Devices On Red Drum (Sciaenops Ocellatus) Movement Patterns In Estuarine Impoundments, Steven Baker

Electronic Theses and Dissertations

The Integrate-Transfer-Launch (ITL) complex impoundments located within the Kennedy Space Center security zone are known spawning sites for red drum (Sciaenops ocellatus). However, recent construction of manatee exclusion bollards around culverts leading into these impoundments may impede movement to and from this critical habitat. The goals of this study were to: 1) utilize passive acoustic telemetry to document patterns of red drum movement and habitat use within and around the ITL impoundments to assess how manatee exclusion bollards and environmental conditions may impact movement of red drum; and 2) explore red drum movement in response to environmental disturbance, specifically a …

Comparative Analysis Of Zebrafish And Planarian Model Systems For Developmental Neurotoxicity Screens Using An 87-Compound Library, D. Hagstrom, L. Truong, S. Zhang, R. Tanguay, Eva-Maria S. Collins

Biology Faculty Works

There is a clear need to establish and validate new methodologies to more quickly and efficiently screen chemicals for potential toxic effects, particularly on development. The emergence of alternative animal systems for rapid toxicology screens presents valuable opportunities to evaluate how systems complement each other. In this article, we compare a chemical library of 87-compounds in two such systems, developing zebrafish and freshwater planarians, by screening for developmental neurotoxic effects. We show that the systems’ toxicological profiles are complementary to each other, with zebrafish yielding more detailed morphological endpoints and planarians more behavioral endpoints. Overall, zebrafish was more sensitive to …

Understories: A Common Ground For Art And Science, Scott F. Gilbert, S. R. Gilbert

Biology Faculty Works

No abstract provided.

Expression-Based Cell Lineage Analysis In Drosophila Through A Course-Based Research Experience For Early Undergraduates, John M. Olson, Cory J. Evans, Kathy T. Ngo, Hee Jong Kim, Joseph Duy Nguyen, Kayla G.H. Gurley, Truc Ta, Vijay Patel, Lisa Han, Khoa T. Truong-N, Letty Liang, Maggie K. Chu, Hiu Lam, Hannah G. Ahn, Abhik Kumar Banerjee, In Young Choi, Ross G. Kelley, Naseem Moridzadeh, Awais M. Khan, Omair Khan, Szuyao Lee, Elizabeth B. Johnson, Annie Tigranyan, Jay Wang, Anand D. Gandhi, Manish M. Padhiar, Joseph Hargan Calvopina, Kirandeep Sumra, Kristy Ou, Jessie C. Wu, Joseph N. Dickan, Sabrena M. Ahmadi, Donald N. Allen

Biology Faculty Works

A variety of genetic techniques have been devised to determine cell lineage relationships during tissue development. Some of these systems monitor cell lineages spatially and/or temporally without regard to gene expression by the cells, whereas others correlate gene expression with the lineage under study. The GAL4 Technique for Real-time and Clonal Expression (G-TRACE) system allows for rapid, fluorescent protein-based visualization of both current and past GAL4 expression patterns and is therefore amenable to genome-wide expression-based lineage screens. Here we describe the results from such a screen, performed by undergraduate students of the University of California, Los Angeles (UCLA) Undergraduate Research …

Impact Of Industrial Biocides On Bacterial Isolates From Hydraulic Fracturing Produced Water, Waad Ahmed Aljohani

Dissertations, Master's Theses and Master's Reports

Biocides are antimicrobial compounds that are designed to kill diverse groups of microbes in an untargeted fashion. Glutaraldehyde and DBNPA are commonly used to manage microbial growth in different industries. It is possible that biocide use may result in the development of bacterial resistance. However, resistance to DBNPA is believed to be limited under normal use conditions. We isolated a number of bacteria from produced water from a hydraulically fractured site in West Texas. We then tested the ability of these isolates to resist Glutaraldehyde and DBNPA. In this study, we found that these isolates have varying resistance to these …

Tools For Change: Measuring Student Conceptual Understanding Across Undergraduate Biology Programs Using Bio-Maps Assessments, Michelle K. Smith, Sara E. Brownell, Alison J. Crowe, N. G. Holmes, Jennifer K. Knight, Katharine Semsar, Mindi M. Summers, Cole Walsh, Christian D. Wright, Brian A. Couch

School of Biological Sciences: Faculty Publications

Assessing learning across a biology major can help departments monitor achievement of broader program-level goals and identify opportunities for curricular improvement. However, biology departments have lacked suitable tools to measure learning at the program scale. To address this need, we developed four freely available assessments—called Biology-Measuring Achievement and Progression in Science or Bio-MAPS—for general biology, molecular biology, ecology/evolution, and physiology programs. When administered at multiple time points in a curriculum, these instruments can provide departments with information on how student conceptual understanding changes across a major and help guide curricular modifications to enhance learning.

Validation Of A Low-Cost Sensor For Development Of Wearable And Handheld Spectrometers, Justin Leslie Cathey

Graduate Research Theses & Dissertations

This study examined the possibility of creating a quantitative radiometric spectrometer from a low-cost relative radiometric spectrometer sensor through the use of statistical analysis and development of a correction factor (p > 0.05). Radiometric spectrometers are able to measure and fully characterize the radiometric and photometric characteristics of light, while relative spectrometers are not able to fully, quantitatively characterize the radiometric response from a light source, thus they are less expensive. The spectrometer created in this research is able to measure and produce comparative lighting parameters as well as an actual radiometer spectrometer.

The photoreceptors cells within the human eye allow …

Effects Of Habitat Disturbance On The Teeth Of Propithecus Diadema In The Forests Of Tsinjoarivo, Madagascar: Implications For Species Viability And Conservation, Katie Susann Heffernan

Graduate Research Theses & Dissertations

The accelerated transformation of Madagascar’s ecosystems is a direct result of habitat destruction which has devastating consequences for the viability of the island’s animals. This dissertation focuses on the critically endangered diademed sifaka, Propithecus diadema, living in the rainforests of Tsinjoarivo, Madagascar. Tsinjoarivo has been heavily impacted by slash and burn agriculture and transformed into isolated forest fragments. Previous research by Irwin and colleagues has demonstrated that the diet and group dynamics of Propithecus diadema differ between continuous and degraded forests, but whether fragmented landscapes provide tougher foods and lead to behavioral changes through increased tooth wear has not been …