Developmental Biology Commons^™

The Impact Of Maternal Age On The Expression Of Transgenerational Plasticity In Daphnia Pulicaria, Calvin Nguyen

2025 Spring Honors Capstone Projects - Archive

Transgenerational plasticity refers to heritable, non-genetic changes in phenotype that persist across multiple generations and can enhance offspring survivability in variable environments. In Daphnia, increasing maternal age has been associated with maladaptive plasticity. To investigate this relationship, six clones were collected from two Wisconsin lakes and acclimated to laboratory conditions through a common garden rearing process. For each clone, ten replicates were generated and evenly divided between young (clutches 2–4) and old (clutches 5–8) maternal age groups. Offspring were exposed to three dietary treatments for three experimental generations: one fed only green algae, one fed only cyanobacteria (a nutritionally …

Optimizing Decision-Making In A Cerebral Palsy Model Using Reinforcement Learning, Richard Ampah

Pitzer Senior Theses

This study presents an original interdisciplinary investigation into how reinforcement learning (RL) can model motor and cognitive defects and potentially improve motor and cognitive functions in individuals with cerebral palsy (CP), a non-progressive neurological disorder that impairs movement and adaptability. Integrating computational neuroscience and machine learning, the research applies policy gradient methods and Markov Decision Processes (MDPs) to simulate adaptive learning in agents with and without CP-related constraints.

The central aim is to compare the cumulative rewards of optimal policies, derived from value iteration, and human-like learning policies using the REINFORCE algorithm, both with and without the Bellman baseline. The …

Towards A New Role Of Mitochondrial Hydrogen Peroxide In Synaptic Function, Cliyahnelle Z. Alexander

Student Theses and Dissertations

Aerobic metabolism is known to generate damaging ROS, particularly hydrogen peroxide. Reactive oxygen species (ROS) are highly reactive molecules containing oxygen that have the potential to cause damage to cells and tissues in the body. ROS are highly reactive atoms or molecules that rapidly interact with other molecules within a cell. Intracellular accumulation can result in oxidative damage, dysfunction, and cell death. Due to the limitations of H₂O₂ (hydrogen peroxide) detectors, other impacts of ROS exposure may have been missed. HyPer7, a genetically encoded sensor, measures hydrogen peroxide emissions precisely and sensitively, even at sublethal levels, during …

Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report, Eden Pope, Matthew Huertas, Amar Paul, Braden Cunningham, Matthew Jennings, Ryan Perry, Stephanie Chavez, John A. Kriak, Kyle B. Bills, David W. Sant

Annual Research Symposium

Hypothesis/Purpose: In this report we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of 17p13.3, and the deletion was not present in either parent. This deletion has not previously been characterized, but mutations on the p-arm of chromosome 17 are responsible for Miller-Dieker Syndrome and Isolated Lissencephaly Sequence, both of which share symptoms in common with the patient.

Methods: Peripheral mononuclear cells (PBMCs) were used for karyotyping and competitive genetic hybridization (CHG). Bioinformatic analysis was carried out using the Genome Data Viewer (ncbi.nlm.nih.gov/genome/gdv).

Results: Karyotype was …

Therapies For Mitochondrial Disorders, Kayli Sousa Smyth, Anne Mulvihill

SURE Journal: Science Undergraduate Research Experience Journal

Mitochondria are cytoplasmic, double-membrane organelles that synthesise adenosine triphosphate (ATP). Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is maternally inherited from the oocyte. Mitochondrial proteins are encoded by either nuclear DNA (nDNA) or mtDNA, and both code for proteins forming the mitochondrial oxidative phosphorylation (OXPHOS) complexes of the respiratory chain. These complexes form a chain that allows the passage of electrons down the electron transport chain (ETC) through a proton motive force, creating ATP from adenosine diphosphate (ADP). This study aims to explore current and prospective therapies for mitochondrial disorders (MTDS). MTDS are clinical syndromes coupled with abnormalities …

Genetically Explicit Model May Explain Multigenerational Control Of Emergent Turing Patterns In Hybrid Mimulus, Emily Simmons

Biology and Medicine Through Mathematics Conference

No abstract provided.

Exploring The Effects Of Varied Land Use On Elemental Concentrations Within Streams, Logan Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

It is well documented that human activity influences the chemistry of surrounding waters. As such, it is possible that there is a link between land use within a watershed and the chemical composition of the stream. The objectives of this study are to determine if varied land use does affect the concentrations of macronutrients and trace elements present in the streams of Northwest Arkansas, and if so, to determine what extent urban and agricultural development are responsible for these changes. Water samples were collected across 19 streams in the Northwest Arkansas region between January and March of 2022. Water samples …

Maternal Social Status, Offspring 2d:4d Ratio And Postnatal Growth, In Macaca Mulatta (Rhesus Macaques), Juan Pablo Arroyo

USF Tampa Graduate Theses and Dissertations

Early life exposure to stressors can disrupt growth and development, resulting in long-term compromised function and increased risk for disease throughout the lifecourse. Maternal exposure to psychosocial stressors (i.e., stressors derived from social status, social inequalities, and social interactions) during pregnancy has been associated with reduced fetal growth, adverse birth outcomes, and increased morbidity for the offspring later in life. Maternal hormonal responses to stress, such as fluctuations in glucocorticoids (e.g., cortisol) and androgens (e.g., testosterone), can result in increased developmental instability, interfere with offspring growth in-utero, and may alter developmental processes of sexual dimorphism. Second digit to fourth digit …

Spreading Mechanics And Differentiation Of Astrocytes During Retinal Development, Tracy Stepien, Timothy W. Secomb

Biology and Medicine Through Mathematics Conference

No abstract provided.

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.

Using A Novel Cell- Penetrating Peptide Technology To Induce Pluripotency, Laura-Maria Oja

Master of Science in Chemical Sciences Theses

Somatic stem cells have been used as a regenerative medicine tool to treat diseases like leukemia for decades, but they are limited in their ability to self-renew and differentiate. A better alternative, induced pluripotent stem cells (iPSCs), has the ability to generate cells from all three germ layers and avoid tissue rejection as well as bypass the ethical concerns related to embryonic stem cells. In 2006, Takahashi and Yamanaka discovered that only four genes were required to induce pluripotency: Oct4, Sox2, Klf4, and c-Myc (OSKM). Since then, pluripotency has been induced with OSKM most effectively by transfection or transduction. However, …

The Bioethical Significance Of “The Origin Of Man’S Ethical Behavior” (October 1941, Unpublished) By Ernest Everett Just And Hedwig Anna Schnetzler Just, Theodore Walker Jr.

Journal of the South Carolina Academy of Science

Abstract –

E. E. Just (1883-1941) is an acknowledged “pioneer” in cell biology, and he is perhaps the pioneer in study of egg cell fertilization. Here we discover that Just also made pioneering contributions to general biology and evolutionary bioethics.

Within Just’s published contributions to observational cell biology, there are substantial fragments of his theory of ethical behavior, a theory with roots in cell biology. In addition to such previously available fragments, Just’s fully developed theory is now available. This recently discovered unpublished book-length manuscript argues for the biological origins of ethical behavior (evolving from cells to humans, within a …

Modeling Collective Migration Of Neural Crest Cells With A Cucker-Smale Velocity Alignment Process, Claire Evensen

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Network Analyses Of Glomerular Capillaries, Jason Cory Brunson, Justin Sardi, Mark Terasaki

Biology and Medicine Through Mathematics Conference

No abstract provided.

Study Of The Effects Of Silver Ions And Silver Nanoparticles On Embryonic Development, Martha Sharisha Johnson

Biomedical Sciences Theses & Dissertations

This dissertation focuses on the study of the toxicity of metal nanoparticles (NPs) and their ions on the development of zebrafish embryos, aiming to understand unique biological effects of NPs and ions, and design new in vivo assays to characterize the toxicity of these metal NPs and metal ions. Currently, the underlying molecular mechanisms of biological effects of nanomaterials are partially understood. Some studies assume that the toxic effects of NPs can be attributed to the release of their ions. We investigate the effects of silver NPs (Ag NPs) and silver ions (Ag+ ions) on the embryonic development of zebrafish …

Analyzing Neuronal Dendritic Trees With Convolutional Neural Networks, Olivier Trottier, Jonathon Howard

Yale Day of Data

In the biological sciences, image analysis software are used to detect, segment or classify a variety of features encountered in living matter. However, the algorithms that accomplish these tasks are often designed for a specific dataset, making them hardly portable to accomplish the same tasks on images of different biological structures. Recently, convolutional neural networks have been used to perform complex image analysis on a multitude of datasets. While applications of these networks abound in the technology industry and computer science, use cases are not as common in the academic sciences. Motivated by the generalizability of neural networks, we aim …

Modeling Microtubule-Based Transport In The Frog Egg Cell, Maria-Veronica Ciocanel

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Using Remote Site Incubators For Re-Introduction Of Arctic Graylng (Thymallus Arcticus) To The Big Manistee Watershed, Sunflower Wilson

Dissertations, Master's Theses and Master's Reports

Remote Site Incubators (RSIs) were developed for the incubation of salmonid eggs directly at a field site to enhance success and imprinting of young. These have been employed in the re-establishment of Arctic Grayling in Montana and are being laboratory tested for possible reintroduction of this species in the Big Manistee River, MI. Arctic Grayling, Rainbow and Brook Trout eggs, obtained from state hatcheries, were reared in a laboratory using flow through lake water to assess egg and fry survival using RSIs. Dead eggs and fry were removed daily and observations of developmental stages recorded. Rainbow Trout eggs were evaluated …

Mathematical Analysis Of Feedback Targets Of Bmp Signaling In Drosophila Embryonic Development, Yan Luo

Open Access Theses

Bone morphogenetic proteins (BMPs) drive a range of cellular processes especially in the early stages of embryonic development. This family of proteins acts as one of the most important extracellular signals in development pattern formation across the animal kingdom. Cells in embryos differentiate into different cell types in response to the concentration level of BMP. This complex process is regulated by multiple regulators that serve to tune the signal response.

Extensive experimental and computational research has been performed to analyze BMP regulation in Drosophila, a widely studied model organism, and has advanced our understanding of animal development. Because of …

The Effects Of Sulfuric Acid Deposition On The Growth And Development Of Pond Breeding Salamanders In The Genus Ambystoma, Kenneth J. Anderson

Masters Theses & Specialist Projects

In terrestrial habitats with a history of mining activity and previous or ongoing reclamation efforts, understanding the effects of acidification on the ecology of amphibians is an important part of the restoration process and the conservation of local amphibian populations. Pond-breeding amphibians spend much of their post metamorphic life history in direct contact with the soil in upland habitat adjacent to aquatic breeding sites. I reared recently metamorphosed marbled salamanders (Ambystoma opacum) to evaluate the role of soil acidity on determinants of fitness such as growth and survival. My results indicate that a substrate of pH 4 was lethal to …

Modelling The Polarization, Migration And Neuromast Deposition In The Zebrafish Posterior Lateral Line System, Hildur Knutsdottir

Biology and Medicine Through Mathematics Conference

No abstract provided.

Developmental Toxicity Of Tetrakis (Hydromethyl) Phosphonium Chloride (Thpc) In Zebrafish (Danio Rerio) Embryos, Lan L. Nguyen

Honors College Theses

Tetrakis (hydromethyl) phosphonium chloride (THPC) is a tetrakis (hydromethyl) phosphonium salt commonly used by the textile industry and is polymerized onto cotton fabrics to provide a flame-retardant finish. Traces of THPC were found in the Ogeechee River, a 294 mile-long black river in Georgia, and could have been a toxin contributing to the mass killing of aquatic animals in May 2011. THPC has been known to be carcinogenic and cause other systemic toxicity in various mammalian animals. However given that the chemical is mostly discharged in natural waters, the environmental impact of the discharge on water quality and there by …

Ontogenetic Scaling Patterns And Functional Anatomy Of The Pelvic Limb Musculature In Emus (Dromaius Novaehollandiae), Luis P. Lamas, Russell P. Main, John R. Hutchinson

Department of Basic Medical Sciences Faculty Publications

Emus (Dromaius novaehollandiae) are exclusively terrestrial, bipedal and cursorial ratites with some similar biomechanical characteristics to humans. Their growth rates are impressive, as their body mass increases eighty-fold from hatching to adulthood whilst maintaining the same mode of locomotion throughout life. These ontogenetic characteristics stimulate biomechanical questions about the strategies that allow emus to cope with their rapid growth and locomotion, which can be partly addressed via scaling (allometric) analysis of morphology. In this study we have collected pelvic limb anatomical data (muscle architecture, tendon length, tendon mass and bone lengths) and calculated muscle physiological cross sectional area …

Data Completion Methods For Improved Developmental Stage Annotation Of Drosophila Embryos In Images, Chitsanu Janyalikit

Electrical & Computer Engineering Theses & Dissertations

Drosophila melanogaster is a dominant model organism for studying the function of animal genes in initial stages of embryogenesis. Usually, images containing Drosophila gene expression patterns are captured at different developmental stages to study the interconnection of animal genes. To achieve most biologically meaningful results, gene expression images from a similar stage should be compared. Currently, biologists manually classify embryos in images into different stages, which is time intensive and infeasible for current massively produced gene expression images. Therefore, there is a need to develop an automatic system for the annotation.

Gene expression information in embryo images usually appears as …

Computational Modeling-Driven Study Of Signaling Pathway Affecting Cleft Formation During Submandibular Salivary Gland Development, Shayoni Ray

Legacy Theses & Dissertations (2009 - 2024)

Branching morphogenesis is a conserved mechanism of mammalian organ development (salivary glands, lungs, mammary glands, pancreas, kidney, etc.), and has been a classic topic of study for generations of developmental biologists. During the process of tissue formation, several cellular and molecular and protein signaling events occur at successive stages enabling proper formation of tissue shape and structure. In order to provide a comprehensive understanding of the process of branching morphogenesis, we need a systems level approach to integrate multifactorial information. My overall global hypothesis is that multiple mathematical modeling approaches can be utilized to extract crucial cellular and tissue level …

Effects Of Calcium Availability On The Reproductive Output Of Insectivorous Bats, Christina M. Booher

All-Inclusive List of Electronic Theses and Dissertations

Reproduction is a period of high calcium demand in vertebrates, and calcium deficiency can limit reproductive output in mammals. Insects are a poor calcium source, suggesting that insectivorous species are more likely to be calcium deficient. Pregnant big brown bats (Eptesicus fuscus) consume 10 times less calcium than they are estimated to require. To accommodate calcium demand during pregnancy, many mammals mobilize more calcium from the skeleton, and extensive bone loss has been observed in some bats during pregnancy. A conflict may arise between the female and developing embryo over allocation of limited calcium supplies, which could limit reproductive output …

Rapid Assimilation Of Yolk Enhances Growth And Development Of Lizard Embryos From A Cold Environment, Melissa Ann Blake

All-Inclusive List of Electronic Theses and Dissertations

Selection for rapid growth in cold environments results in a geographic pattern known as countergradient variation. The eastern fence lizard, Sceloporus undulatus, exhibits countergradient variation in growth rate across latitudinal clines. In a common-garden experiment, S. undulatus embryos from cold environments grew more efficiently than embryos warm environments, even when the energetic contents of eggs were equalized. To examine the physiological mechanisms of higher growth efficiency, I measured the energetics of embryos during the first 49 days of incubation. Specifically, I recorded body mass, residual yolk, total respiration, and developmental stage for embyos from two populations (Virginia and South Carolina). …

The Role Of Lipids During Embryonic Development Of The Euphausiids Euphausia Pacifica And Thysanoessa Spinifera, Se-Jong Ju, H. Rodger Harvey, Jaime Gómez-Gutiérrez, William T. Peterson

OES Faculty Publications

To understand the role of lipids during early embryogenesis, major lipid classes together with individual fatty acid and sterol composition were determined in embryos from multiple developmental stages of the euphausiids Euphausia pacifica and Thysanoessa spinifera. Average lipid content in embryos of E. pacifica and T. spiniferafrom the earliest stage (multicell) were 4.45 and 3.69 µg embryo^-1,respectively. During development, the lipid content decreased at similar rates in the embryos of both species. In contrast to many crustacean eggs, phospholipids were the dominant lipid class in all embryonic stages, with decreasing concentrations seen during development. Individual …

Growth Rate Variability And Lipofuscin Accumulation Rates In The Blue Crab Callinectes Sapidus, Se-Jong Ju, David H. Secor, H. Rodger Harvey

OES Faculty Publications

To better understand growth and age-pigment (lipofuscin) accumulation rates of the blue crab Callinectes sapidus under natural conditions, juveniles (33 to 94 mm carapace width) were reared in outdoor ponds for over 1 yr. Growth rates, measured by carapace width, during summer and fall exceeded all those reported in the literature; the initial carapace width of 59 ± 14 mm (mean ± SD) increased to 164 ± 15 mm within a 3 mo period. No growth occurred during winter months (November to April) at low water temperatures. Growth rates of crabs in ponds were substantially higher (von Bertalanffy growth parameter …

Three-Dimensional Reconstructions Of Tadpole Chondrocrania From Histological Sections, Gary P. Radice, Mary Kate Boggiano, Mark Desantis, Peter M. Larson, Joseph Oppong, Matthew T. Smetanick, Todd M. Stevens, James Tripp, Rebecca A. Weber, Michael Kerckhove, Rafael O. De Sá

Biology Faculty Publications

Reconstructing three dimensional structures (3DR) from histological sections has always been difficult but is becoming more accessible with the assistance of digital imaging. We sought to assemble a low cost system using readily available hardware and software to generate 3DR for a study of tadpole chondrocrania. We found that a combination of RGB camera, stereomicroscope, and Apple Macintosh PowerPC computers running NIH Image, Object Image, Rotater. and SURFdriver software provided acceptable reconstructions. These are limited in quality primarily by the distortions arising from histological protocols rather than hardware or software.