Cell and Developmental Biology Commons^™

The Phytoremediative Effects Of Cilantro (Coriandrum Sativum) In Lead Contaminated Soil, Sierra D. Garrett, Timothy D. Trott

Research in Biology

Environmental exposure to heavy metals such as lead pose a significant health threat. The goal of this project was to evaluate the effectiveness of Coriandrum sativum (Cilantro) as a potential lead (II), Pb²⁺, phytoremediator. C. sativumplants were allowed to grow for 43 days while exposed to with different amounts of lead nitrate, Pb(NO₃)₂. Lead exposure was accomplished by regular watering with a concentration series of lead nitrate solutions. The roots and shoots of these plants were separated and dried. Ground plant material was liquefied by nitric acid digestion. The amount of lead absorbed …

Regeneration Data: Rna Sequences, Abijeet Singh Mehta, Amit Singh

Regeneration data

Abstract for paper for which this research was collected: Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, we identified a novel family of 5 protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. Due to absence of transgenic approaches in the Notophthalmus, and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress these genes.

Samples for RNA sequencing were collected at third instar larval (L3) developmental stage. Out of the total 36,099 …

Hydrogen-Based Metabolism As An Ancestral Trait In Lineages Sibling To The Cyanobacteria, Paula B. Matheus Camevali, Frederik Schulz, Cindy J. Castelle, Rose S. Kantor, Patrick M. Shih, Itai Sharon, Joanne M. Santini, Matthew R. Olm, Yuki Amano, Brian C. Thomas, Karthik Anantharaman, David Burstein, Eric D. Becraft, Ramunas Stepanauskas, Tanja Woyke, Jillian F. Banfield

Biology

The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use …

Molecular Mechanism Of Neurodegeneration Induced By 4-Nonylphenol, Michelle Alejandra Aranda

Open Access Theses & Dissertations

Neurodegeneration, a progressive loss of nerve cells, occurs in many neurological disorders, including Alzheimer's disease (AD) and Parkinson's diseases (PD), as well as in dementia. The pathogenesis of these diseases is unknown, and recent evidence suggests that environmental factors, which act as endocrine-disrupting compounds (EDCs) could play a significant role in developing the disease process. 4-Nonylphenol (4-NP), an EDC, and a ubiquitous environmental toxin has been shown to affect brain development and may cause neurodegeneration. 4-NP is produced in large quantities in the U.S. and used as raw materials for making detergents, pesticides, plastics, paints, cosmetics, rubber, and other industrial/household …

Hspg2 Mediates Mandibular Jaw Joint Development, Barbara Samantha Castellanos

Open Access Theses & Dissertations

We present a patient diagnosed with a multiple congenital anomaly syndrome characterized by scoliosis, intellectual disabilities, and craniofacial defects. Trio-based whole exome sequencing identified compound heterozygous variants in the HSPG2 gene: a maternally inherited c.5998-7A>G variant in the promoter region and a paternally inherited c.4916C>T variant in the coding sequence. HSPG2 encodes for perlecan, a large proteoglycan that plays an important role in cartilage formation, cell adhesion, and basement membrane stability. Mutations in HSPG2 have been associated with Schwartz-Jampel syndrome and Dyssegmental Dysplasia Silverman-Handmaker Type, two disorders characterized by skeletal abnormalities (1). These data indicate a function for …

Bioinformatic And Experimental Analyses Of Axolotl Regeneration, Nour W. Al Haj Baddar

Theses and Dissertations--Biology

Salamanders have an extraordinary ability to regenerate appendages after loss or amputation, irrespective of age. My dissertation research explored the possibility that regenerative ability is associated with the evolution of novel, salamander-specific genes. I utilized transcriptional and genomic databases for the axolotl to discover previously unidentified genes, to the exclusion of other vertebrate taxa. Among the genes identified were multiple mmps (Matrix metalloproteases) and a jnk1/mapk8 (c-jun-N-terminal kinase) paralog. MMPs function in extracellular matrix remodeling (ECM) and tissue histolysis, processes that are essential for successful regeneration. Jjnk1/mapk8 plays a pivotal role in regulating transcription in response to cellular stress stimuli, …

Tgf-Β, Wnt, And Fgf Signaling Pathways During Axolotl Tail Regeneration And Forelimb Bud Development, Qingchao Qiu

Theses and Dissertations--Neuroscience

Tgf-β, Wnt, and Fgf signaling pathways are required for many developmental processes. Here, I investigated the requirement of these signaling pathways during tail regeneration and limb development in the Mexican axolotl (Ambystoma mexicanum).

Using small chemical inhibitors during tail regeneration, I found that the Tgf-β signaling pathway was required from 0-24 and 48-72 hours post tail amputation (hpa), the Wnt signaling pathway was required from 0-120 hpa, and the Fgf signaling pathway was required from 0-12hpa. Tgf-β1 was upregulated after amputation and thus may mediate Tgf-β signaling pathway during tail regeneration. Both Smad-mediated and non-Smad mediated Tgf-β signaling …

Ultrasound/Elastography Techniques, Lipidomic And Blood Markers Compared To Magnetic Resonance Imaging In Non-Alcoholic Fatty Liver Disease Adults, Irene Cantero, Mariana Elorz, Itziar Abete, Bertha Araceli Marin, Jose Ignacio Herrero, Jose Ignacio Monreal, Alberto Benito, Jorge Quiroga, Ana Martínez, Pilar Huarte, Juan Isidro Uriz-Otano, Josep Antoni Tur, John Kearney, J. Alfredo Martinez, M. Angeles Zulet

Articles

Introduction: Non-alcoholic fatty liver disease (NAFLD) may progress to steatohepatitis, cirrhosis and complicated hepatocellular carcinoma with defined differential symptoms and manifestations. Objective: To evaluate the fatty liver status by several validated approaches and to compare imaging techniques, lipidomic and routine blood markers with magnetic resonance imaging in adults subjects with non-alcoholic fatty liver disease. Materials and methods: A total of 127 overweight/obese with NAFLD, were parallelly assessed by Magnetic Resonance Imaging (MRI), ultrasonography, transient elastography and a validated metabolomic designed test to diagnose NAFLD in this cross-sectional study. Body composition (DXA), hepatic related biochemical measurements as well as the Fatty …

Examining The Effects Of Fadrozole, An Aromatase Inhibitor, On Testosterone And Estrogen Production Of Domestic Chicken Embryos (Gallus Gallus), Abby E. Joseph

Honors Theses

The hypothalamic-pituitary-gonadal (HPG) axis is responsible for the production of the hormones testosterone and estradiol, and testosterone is thought to contribute to regulation of the axis through a negative feedback mechanism. Regulation by negative feedback involves the product of a pathway turning off that pathway when enough product is made. However, because the enzyme P450 aromatase converts testosterone to estradiol, estradiol may also contribute to regulation of the HPG axis and other phenomena that have been attributed to testosterone, like the inhibition of immune function. Previous studies have injected birds with an aromatase inhibitor (presumably reducing estradiol production) and shown …

Exploring The Efficacy Of Natural Products In Alleviating Alzheimer’S Disease Using Animal Models, Prajakta Deshpande, Neha Gogia, Amit Singh

Biology Faculty Publications

Alzheimer’s disease (hereafter AD) is a progressive neurodegenerative disorder that affects the central nervous system. There are multiple factors that cause AD, viz., accumulation of extracellular Amyloid-beta 42 plaques, intracellular hyper-phosphorylated Tau tangles, generation of reactive oxygen species due to mitochondrial dysfunction and genetic mutations. The plaques and tau tangles trigger aberrant signaling, which eventually cause cell death of the neurons. As a result, there is shrinkage of brain, cognitive defects, behavioral and psychological problems. To date, there is no direct cure for AD. Thus, scientists have been testing various strategies like screening for the small inhibitor molecule library …

Disruption Of Cul3-Mediated Ubiquitination Causes Proximal Tubule Injury And Kidney Fibrosis, Turgay Saritas, Catherina A. Cuevas, Mohammed Z. Ferdaus, Christophe Kuppe, Rafael Kramann, Marcus J. Moeller, Jurgen Floege, Jeffrey Singer, James A. Mccormick

Biology Faculty Publications and Presentations

Cullin 3 (CUL3) is part of the ubiquitin proteasomal system and controls several cellular processes critical for normal organ function including the cell cycle, and Keap1/Nrf2 signaling. Kidney tubule-specific Cul3disruption causes tubulointerstitial fibrosis, but little is known about the mechanisms. Therefore, we tested the hypothesis that dysregulation of the cell cycle and Keap1/Nrf2 pathway play a role in initiating the kidney injury upon Cul3 disruption. Cul3 deletion increased expression of cyclin E and p21, associated with uncontrolled proliferation, DNA damage, and apoptosis, all of which preceded proximal tubule injury. The cdk2-cyclin E inhibitor roscovitine did not prevent the effects …

Exosomes Mediate Zika Virus Transmission Through Smpd3 Neutral Sphingomyelinase In Cortical Neurons, Wenshuo Zhou, Michael Woodson, Michael B. Sherman, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

The harmful effects of ZIKA virus (ZIKV) infection are reflected by severe neurological manifestations such as microcephaly in neonates and other complications associated with Guillain-Barre syndrome in adults. The transmission dynamics of ZIKV in or between neurons, or within the developing brains of the foetuses are not fully understood. Using primary cultures of murine cortical neurons, we show that ZIKV uses exosomes as mediators of viral transmission between neurons. Cryo-electron microscopy showed heterogeneous population of neuronal exosomes with a size range of 30-200 nm. Increased production of exosomes from neuronal cells was noted upon ZIKV infection. Neuronal exosomes contained both …

Put Your Money Where Your Mouth Is: Reforming Organized Dentistry To Address Persistent Oral Health Disparities In The U.S., Aparna Chintapalli

Pomona Senior Theses

The importance of oral health has been largely neglected from the conventional standards of healthcare in terms of public understanding & prioritization, the industrial infrastructure, and the scope of prevention & early-intervention services. Its adjunctive locus to the field of medicine has lead to the bifurcation of the oral cavity from the rest of the human body. As a result of this divide, there have been multiple factors that have allowed socially stratified oral health outcomes to manifest. This thesis examines the determinants of oral health disparities through a multidisciplinary lens (i.e. biology, public policy, infrastructure), and offers evidence of …

The Effects Of A Ketone Body On Synaptic Transmission, Alexandra Elizabeth Stanback

Theses and Dissertations--Biology

The ketogenic diet is commonly used to control epilepsy, especially in cases when medications cannot. The diet typically consists of high fat, low carb, and adequate protein and produces a metabolite called acetoacetate. Seizure activity is characterized by glutamate excitotoxicity and therefore glutamate regulation is a point of research for control of these disorders. Acetoacetate is heavily implicated as the primary molecule responsible for decreasing glutamate in the synapse; it is believed that acetoacetate interferes with the transport of glutamate into the synaptic vesicles. The effects on synaptic transmission at glutamatergic synapses was studied in relation to the ketogenic diet …

Canonical Wnt Mechanisms In Neural Crest Induction, Mark Stephen Perfetto

Graduate Theses, Dissertations, and Problem Reports (ETD)

Canonical Wnt signaling is a pathway that is critical for normal development and the progression of disease. The canonical Wnt signaling pathway was put together carefully by synthesizing decades of research. Over those decades, canonical Wnt signaling was found to be crucial for nearly all aspects of development, but of importance to this thesis, is a key regulatory factor for the development of the highly migratory multipotent stem cells, the neural crest. As our knowledge of the importance of canonical Wnt signaling grew, research is being conducted to further our understanding of how canonical Wnt signaling communicates with other signaling …

Effects Of Aquatic Acidification On Calcium Uptake In White River Shrimp Litopenaeus Setiferus Gills, Maria-Flora Jacobs

UNF Graduate Theses and Dissertations

Previous research regarding aquatic acidification has examined the protonation of the carbonate and does not consider calcium to be a limiting factor. This is the first study to suggest that pH may affect the uptake of calcium in crustacean gills. This project describes ion transport mechanisms present in the cell membranes of white river shrimp Litopenaeus setiferus gill epithelium, and the effects of pH on the uptake of calcium by these means. Partially purified membrane vesicles (PPMV) of shrimp gills were prepared through a homogenization process that has been used previously to define ion transport in crab and lobster gill …

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 …

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 …

Visceral Adipose Tissue Modulates Radiosensitivity In Oesophageal Adenocarcinoma, Ann Marie Mongan, Niamh Lynam-Lennon, Suzanne Doyle, Rory Casey, Eibhlin Carr, Aoife Cannon, Melissa J Conroy, Graham P Pidgeon, Lorraine Brennan, Joanne Lysaght, John V. Reynolds, Jacintha O’Sullivan

Articles

Oesophageal adenocarcinoma (OAC) is an exemplar model of obesity-associated cancer. Response to neoadjuvant chemoradiotherapy (NA CRT) is a clinical challenge. We examined if visceral adipose tissue and obesity status alter radiosensitivity in OAC. The radioresistant (OE33R) and radioresponsive (OE33P) OAC isogenic model was cultured with adipose tissue conditioned media from three patient cohorts: non-cancer patients, surgery only OAC patients and NA CRT OAC patients. Cell survival was characterised by clonogenic assay, metabolomic profiling by nuclear magnetic resonance spectroscopy and adipokine receptor gene expression by qPCR. A retrospective in vivo study compared tumour response to NA CRT in normal weight (n=53) …

Investigating The Antiviral Effects Of Vig-3 From Rainbow Trout, Shanee Herrington-Krause

Theses and Dissertations (Comprehensive)

Rainbow trout is the most farmed fish in Ontario, and thus is economically important to the province. Despite this, there is a lack of understanding regarding fish innate immunity, specifically with regards to interferon-stimulated genes (ISGs) and their antiviral effector functions. ISGs are the workhorses of the innate antiviral response, operating together to limit each step of virus replication. The Viral Hemorrhagic Septicemia Virus (VHSV) induced gene (Vig)-3 is a newly identified ISG within many fish species and is homologous to ISG-15 in mammals. It is a small ubiquitin-like protein inducible by type I interferon (IFN-I), and is suggested to …

Regulation Of Canonical And Non-Canonical Hippo Pathway Components In Mitosis And Cancer, Seth Stauffer

Theses & Dissertations

The Hippo pathway is conserved regulator of organ size through control of proliferation, apoptosis, and stem-cell self-renewal. In addition to this important function, many of the canonical signaling members have also been shown to be regulated during mitosis. Importantly, Hippo pathway components are frequently dysregulated in cancers and have attracted attention as possible targets for improved cancer therapeutics. Further exploration of Hippo-YAP (yes-associated protein) signaling has revealed new regulators and effectors outside the canonical signaling network and has revealed a larger non-canonical network of signaling proteins in which canonical Hippo pathway components crosstalk with important cellular homeostasis and apoptosis signaling …

Investigating The Impact Of Oxidative Stress On Tetrahymena Thermophila Sirtuin,Thd 18, Emmanuel Dubuisson

Publications and Research

Sirtuins are a family of enzymes that fulfill various important biological functions. Investigators have looked for the implication of Sirtuin genes in cell signaling mechanisms, in the formation and silencing of heterochromatin, in the regulation of ion channels, and in the modulation of the cellular redox reactions[2]. Different model organisms have been previously used to conduct these studies; among them, there are yeasts, nematodes, and fruit flies. Each one has made some valuable contribution into the vast body of knowledge related to this field.

However, gaps in the understanding of Sirtuins functions still remain to be filled. In this optic, …

Polyglutamine Repeat Proteins Disrupt Actin Structure In Drosophila Photoreceptors., Annie Vu, Tyler Humphries, Sean Vogel, Adam Haberman

Biology: Faculty Scholarship

Expansions of polygutamine-encoding stretches in several genes cause neurodegenerative disorders including Huntington's Disease and Spinocerebellar Ataxia type 3. Expression of the human disease alleles in Drosophila melanogaster neurons recapitulates cellular features of these disorders, and has therefore been used to model the cell biology of these diseases. Here, we show that polyglutamine disease alleles expressed in Drosophila photoreceptors disrupt actin structure at rhabdomeres, as other groups have shown they do in Drosophila and mammalian dendrites. We show this actin regulatory pathway works through the small G protein Rac and the actin nucleating protein Form3. We also find that Form3 has …

Characterization Of A Basement Membrane Associated Protein Encoding Gene In Drosophila Melanogaster, Aref Ranjbar, Ajay Srivastava

Posters-at-the-Capitol

Title: Characterization of a Basement Membrane Associated Protein Encoding Gene in Drosophila melanogaster

Authors: Aref Ranjbar, Mayank Kapadia, Ajay Srivastava, PhD(faculty member, mentor)

Basement Membranes (BM) are important for normal development and tumor progression. In order to get a better understanding of BM dynamics we identified genes that encoded BM interacting proteins. One such gene is predicted to be involved in vesicle-mediated transport in Drosophila melanogaster. Here we characterize this gene by utilizing molecular biology techniques like immunohistochemistry, RNA in situ hybridization, and Western blot analysis utilizing antibodies generated in the laboratory. Western blot analysis identified this protein to be …

Cell Specific Control Of The Pallidostriatal Pathway, Shubha Verma '19

Student Publications & Research

Parkinson’s Disease is a neurodegenerative disorder of the basal ganglia. The main cause for Parkinson’s Disease is the depletion of dopamine, a neurotransmitter. The basal ganglia contains four major nuclei: the substantia nigra, the subthalamic nucleus, the external globus pallidus, and the striatum. These nuclei communicate with each other by the use of neurons.

Emerging Roles Of The Membrane Potential: Action Beyond The Action Potential, Lina Abdul Kadir, Michael Stacey, Richard Barrett-Jolley

Bioelectrics Publications

Whilst the phenomenon of an electrical resting membrane potential (RMP) is a central tenet of biology, it is nearly always discussed as a phenomenon that facilitates the propagation of action potentials in excitable tissue, muscle, and nerve. However, as ion channel research shifts beyond these tissues, it became clear that the RMP is a feature of virtually all cells studied. The RMP is maintained by the cell's compliment of ion channels. Transcriptome sequencing is increasingly revealing that equally rich compliments of ion channels exist in both excitable and non-excitable tissue. In this review, we discuss a range of critical roles …

Review Of The Family Rivulidae (Cyprinodontiformes, Aplocheiloidei) And A Molecular And Morphological Phylogeny Of The Annual Fish Genus Austrolebias Costa 1998, Marcelo Loureiro, Rafael O. De Sá, Sebastián W. Serra, Felipe Alonso, Luis Esteban Krause Lanés, Matheus Vieira Volcan, Pablo Calviño, Dalton Nielsen, Alejandro Duarte, Graciela Garcia

Biology Faculty Publications

The family Rivulidae is the fourth most diverse clade of Neotropical fishes. Together with some genera of the related African family Nothobranchiidae, many rivulids exhibit a characteristic annual life cycle, with diapausing eggs and delayed embryonic development, which allows them to survive in the challenging seasonal ponds that they inhabit. Rivulidae also includes two species known as the only the self-fertilizing vertebrates and some species with internal fertilization. The first goal of this article is to review the systematics of the family considering phylogenetic relationships and synapomorphies of subfamilial clades, thus unifying information that is dispersed throughout the literature. From …

Small Noncoding Rna Profiles Along Alternative Developmental Trajectories In An Annual Killifish, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of …

Integration Of Bmp And Insulin/Igf-1 Signaling Regulates Multiple Homeostatic Functions In Caenorhabditis Elegans, James F. Clark

Dissertations, Theses, and Capstone Projects

The maintenance of homeostatic functions is key to the survival and well-being of an organism. Regulation of homeostasis relies on varied inputs, both intrinsic and extrinsic, to potentiate a web of interconnected signaling relays. Insulin/IGF-1 signaling (IIS) is a well-known regulator of glucose and lipid metabolism, as well as having far reaching effects in other homeostatic mechanisms. On the other hand, bone morphogenetic protein (BMP), a member of the transforming growth factor beta signaling superfamily, is known for its role in differentiation and development, with only recent studies highlighting potential roles in metabolic homeostasis. Here we elucidate new functions for …

Crispr Knockouts Reveal An Endogenous Role For Ancient Neuropeptides In Regulating Developmental Timing In A Sea Anemone, Nagayasu Nakanishi, Mark Q. Martindale

Biological Sciences Faculty Publications and Presentations

Neuropeptides are evolutionarily ancient peptide hormones of the nervous and neuroendocrine systems, and are thought to have regulated metamorphosis in early animal ancestors. In particular, the deeply conserved Wamide family of neuropeptides—shared across Bilateria (e.g. insects and worms) and its sister group Cnidaria (e.g. jellyfishes and corals)—has been implicated in mediating life-cycle transitions, yet their endogenous roles remain poorly understood. By using CRISPR-Cas9-mediated reverse genetics, we show that cnidarian Wamide—referred to as GLWamide—regulates the timing of life cycle transition in the sea anemone cnidarian Nematostella vectensis. We find that mutant planula larvae lacking GLWamides transform into morphologically normal polyps …