Digital Commons Network^™

Parallel Quorum-Sensing System In Vibrio Cholerae Prevents Signal Interference Inside The Host., Samit Watve, Kelsey Barrasso, Sarah A Jung, Kristen J Davis, Lisa A Hawver, Atul Khataokar, Ryan G Palaganas, Matthew B Neiditch, Lark Perez, Wai-Leung Ng

College of Science & Mathematics Departmental Research

Many bacteria use quorum sensing (QS) to regulate virulence factor production in response to changes in population density. QS is mediated through the production, secretion, and detection of signaling molecules called autoinducers (AIs) to modulate population-wide behavioral changes. Four histidine kinases, LuxPQ, CqsS, CqsR and VpsS, have been identified in Vibrio cholerae as QS receptors to activate virulence gene expression at low cell density. Detection of AIs by these receptors leads to virulence gene repression at high cell density. The redundancy among these receptors is puzzling since any one of the four receptors is sufficient to support colonization of V. …

Draft Management Plan For The South Coast Nearshore Net Managed Fishery, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Draft Management Plan For The South Coast Line And Fish Trap Managed Fishery, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Lionfish (Pterois Volitans) As Biomonitoring Species For Oil Pollution Effects In Coral Reef Ecosystems, Peter Van Den Hurk, Ian Edhlund, Ryan David, Jacob J. Hahn, Michel J. Mccomb, Elizabeth L. Rogers, Emily Pisarski, Katy Chung, Marie Delorenzo

Publications

With oil spills, and other sources of aromatic hydrocarbons, being a continuous threat to coral reef systems, and most reef fish species being protected or difficult to collect, the use of the invasive lionfish (Pterois volitans) might be a good model species to monitor biomarkers in potentially exposed fish in the Caribbean and western Atlantic. The rapid expansion of lionfish in the Caribbean and western Atlantic, and the unregulated fishing for this species, would make the lionfish a suitable candidate as biomonitoring species for oil pollution effects. However, to date little has been published about the responses of …

The Natural Selection Game: Incorporating Active Learning In Evolution Curricula For General Biology, Shabnam Mohammadi, Nicholas M. Kiriazis, Lorin A. Neuman-Lee

School of Biological Sciences: Faculty Publications

Teaching evolution in high school and in entry-level college courses can be challenging due to the inherent misinformation, misunderstanding, and biases with which students approach the topic. In this setting, it is critical to both teach the basic concepts and address common student misconceptions about evolution. We present two paired activities that allow students to (1) explore the processes of natural selection in a direct and experiential way and (2) address common misconceptions in evolutionary theory. The first activity, the “Natural Selection Game,” has students simulate a bird population and experience shifts in phenotype frequency as a result of selective …

De Novo Sequencing, Assembly, And Annotation Of The Transcriptome For The Free-Living Testate Amoeba Arcella Intermedia, Giulia M. Ribeiro, Alfredo L. Porfírio-Sousa, Xyrus X. Maurer-Alcalá, Laura A. Katz, Daniel J.G. Lahr

Biological Sciences: Faculty Publications

Arcella, a diverse understudied genus of testate amoebae is a member of Tubulinea in Amoebozoa group. Transcriptomes are a powerful tool for charac- terization of these organisms as they are an efficient way of characterizing the protein-coding potential of the genome. In this work, we employed both sin- gle-cell and clonal populations transcriptomics to create a reference transcrip- tome for Arcella. We compared our results with annotations of Dictyostelium discoideum, a model Amoebozoan. We assembled a pool of 38 Arcella inter- media transcriptomes, which after filtering are composed of a total of 14,712 translated proteins. There are GO categories enriched …

Trait Differentiation And Modular Toxin Expression In Palm-Pitvipers, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson

Publications

Background

Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis …

Maternal Weight Affects Placental Dna Methylation Of Genes Involved In Metabolic Pathways In The Common Marmoset Monkey (Callithrix Jacchus), Laren Narapareddy, Derek E. Wildman, Don L. Armstrong, Amy Weckle, Aleeca F. Bell, Crystal L. Patil, Suzette D. Tardif, Corinna N. Ross, Julienne N. Rutherford

Biology Faculty Publications (Archived)

Accumulating evidence suggests that dysregulation of placental DNA methylation (DNAm) is a mechanism linking maternal weight during pregnancy to metabolic programming outcomes. The common marmoset, Callithrix jaccus, is a platyrrhine primate species that has provided much insight into studies of the primate placenta, maternal condition, and metabolic programming, yet the relationships between maternal weight and placental DNAm are unknown. Here, we report genome-wide DNAm from term marmoset placentas using reduced representation bisulfite sequencing. We identified 74 genes whose DNAm pattern is associated with maternal weight during gestation. These genes are predominantly involved in energy metabolism and homeostasis, including the regulation …

Efficiency Of Using Electric Toothbrush As An Alternative To A Tuning Fork For Artificial Buzz Pollination Is Independent Of Instrument Buzzing Frequency, Mandeep Tayal, Jesus Chavana, Rupesh R. Kariyat

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Background: Breeding programs and research activities where artificial buzz-pollinations are required to have primarily relied upon using tuning forks, and bumble bees. However, these methods can be expensive, unreliable, and inefficient. To find an alternative, we tested the efficiency of pollen collection using electric toothbrushes and compared it with tuning forks at three vibration frequencies—low, medium, and high and two extraction times at 3 s and 16 s- from two buzz—pollinated species (Solanum lycopersicum and Solanum elaeagnifolium).

Results: Our results show that species, and extraction time significantly influenced pollen extraction, while there were no significant differences for the different vibration …

Polyphenol-Rich Purple Corn Pericarp Extract Adversely Impacts Herbivore Growth And Development, Mandeep Tayal, Pavel Somavat, Isabella Rodriguez, Tina Thomas, Bradley O. Christoffersen, Rupesh R. Kariyat

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Plant secondary metabolites such as terpenes, phenolics, glycosides, and alkaloids play various functional roles including pigmentation, foliar and floral volatile synthesis, hormonal regulation, and direct and indirect defenses. Among these, phenolic compounds are commonly found in plants, but vary in the distribution of their specific compounds among plant families. Polyphenols, including anthocyanins and tannins, are widely distributed and have been well documented for their roles- primarily in plant pigmentation and also in plant defenses. However, commercialization of such compounds for use in insect pest management is severely hampered by expensive, inefficient, and time-consuming extraction protocols. Using a recently developed inexpensive …

Small-Molecule Activation Of Lysosomal Trp Channels Ameliorates Duchenne Muscular Dystrophy In Mouse Models, Lu Yu, Xiaoli Zhang, Yexin Yang, Dan Li, Kaiyuan Tang, Zifan Zhao, Wanwan He, Ce Wang, Nirakar Sahoo

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Duchenne muscular dystrophy (DMD) is a devastating disease caused by mutations in dystrophin that compromise sarcolemma integrity. Currently, there is no treatment for DMD. Mutations in transient receptor potential mucolipin 1 (ML1), a lysosomal Ca2+ channel required for lysosomal exocytosis, produce a DMD-like phenotype. Here, we show that transgenic overexpression or pharmacological activation of ML1 in vivo facilitates sarcolemma repair and alleviates the dystrophic phenotypes in both skeletal and cardiac muscles of mdx mice (a mouse model of DMD). Hallmark dystrophic features of DMD, including myofiber necrosis, central nucleation, fibrosis, elevated serum creatine kinase levels, reduced muscle force, impaired motor …

Expression Analysis Of Cnidarian-Specific Neuropeptides In A Sea Anemone Unveils An Apical-Organ-Associated Nerve Net That Disintegrates At Metamorphosis, Hannah Zang, Nagayasu Nakanishi

Biological Sciences Faculty Publications and Presentations

Neuropeptides are ancient neuronal signaling molecules that have diversified across Cnidaria (e.g., jellyfish, corals, and sea anemones) and its sister group Bilateria (e.g., vertebrates, insects, and worms). Over the course of neuropeptide evolution emerged lineage-specific neuropeptides, but their roles in the evolution and diversification of nervous system function remain enigmatic. As a step toward filling in this knowledge gap, we investigated the expression pattern of a cnidarian-specific neuropeptide—RPamide—during the development of the starlet sea anemone Nematostella vectensis, using in situ hybridization and immunohistochemistry. We show that RPamide precursor transcripts first occur during gastrulation in scattered epithelial cells of the …

The Development Of Cephalic Armor In The Tokay Gecko (Squamata: Gekkonidae: Gekko Gecko), Rebecca J. Laver, Cristian H. Morales, Matthew P. Heinicke, Tony Gamble, Kristin Longoria, Aaron M. Bauer, Juan D. Daza

Biological Sciences Faculty Research and Publications

Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap-footed lizards) only known to occur in three genera: Geckolepis, Gekko, and Tarentola. The Tokay gecko (Gekko gecko LINNAEUS 1758) is among the best-studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well-known. Likewise, a comparative survey of additional species within the broader Gekko clade to determine the uniqueness of this trait has not …

Hur Ubiquitination By Brca1/Bard1 And Its Role In Controlling Gene Expression During Dna Damage Response, Gamage M. Aruggoda

Dissertations, Theses, and Capstone Projects

Despite our understanding of the biochemistry of the BRCA1/BARD1 E3 ligase, we know very little of the mechanism by which its cellular substrates, how they are chosen, how its E3 Ub ligase activity is regulated, which are the cofactors involved in this regulation, and how the substrates are modified during DDR. In this dissertation, I further evaluate BRCA1/BARD1-mediated E3 ligase activity and how CstF-50 and p97 regulate this reaction working as cofactors. My data show that BRCA1/BARD1 is an E3 ligase that ubiquitinates the RNA binding protein Human antigen R(HuR).

HuR is abundant in the nucleus and is transported to …

A Neural Mechanism For Capnotaxis In The Naked Mole-Rat, Michael Zions

Dissertations, Theses, and Capstone Projects

A Neural Mechanism for Capnotaxis in the Naked Mole-Rat

The Naked Mole-Rat (NM-R) is a small hairless rodent that has thrived underground in the Horn of Africa for the past 40 million years. It was first discovered in 1847, but has only been maintained in captivity and studied as a laboratory animal over the past 40 years. To date, more than 400 scientific papers have been published on this species. This is relatively few compared to established lab animals like rats and mice, but those papers contain a trove of information that has changed our understanding of the constraints of …

Humanized Nog Mice For Intravaginal Hiv Exposure And Treatment Of Hiv Infection, Anna Halling Folkmar Andersen, Stine Sofie Frank Nielsen, Rikka Olesen, Katharine Mack, Frederik Dagnæs-Hansen, N. Uldbjerg, Lars Østergaard, Ole S. Søgaard, Paul Denton, Martin Tolstrup

Biology Faculty Publications

Humanized mice provide a sophisticated platform to study human immunodeficiency virus (HIV) virology and to test antiviral drugs. This protocol describes the establishment of a human immune system in adult NOG mice. Here, we explain all the practical steps from isolation of umbilical cord blood derived human CD34+ cells and their subsequent intravenous transplantation into the mice, to the manipulation of the model through HIV infection, combination antiretroviral therapy (cART), and blood sampling. Approximately 75,000 hCD34+ cells are injected intravenously into the mice and the level of human chimerism, also known as humanization, in the peripheral blood is estimated longitudinally …

Isolated Antibiotic Producing Bacteria In Local Soil Samples Determined To Be Bacillus, Cassidy Potter, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

Nosocomial pathogens are multi-drug resistant to antibiotics that fight bacterial infections posing danger to the public health, the most dangerous of them being the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). This project is a collabortaion with the TIny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from the soil. TEPI allows student-led research on local soil samples from Bettendorf, IA to discover potential novel antibiotic producing bacteria that could potentially treat ESKAPE pathogens and reduce public health risk. Two soil isolates …

Screening For Antibiotic-Producers In Soil From A Garden, Long Tran, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

Multidrug-resistant pathogens are the leading cause of nosocomial infection, which killed more than 30,000 people in the United States every year. Among these, ESKAPE strains bugs, which comprise six highly drug-resistant bacteria, pose the greatest challenge to the healthcare system. In order to fight the antibiotic-resistant crises, novel antibiotic-producers must be discovered. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from the soil. Pseudomonas was revealed to produce a zone of inhibition against Bacillus subtilis on LB media. The next step …

Wise Blood: The Principle Of Overcoming In Disease And Immunity (Part 1), Alan L. Gillen, Keoprommony Huy

Faculty Publications and Presentations

The immune system is an intelligently made system designed for interaction with microbes even in a perfect world; it is more than a defense. However, in a post-fall world, it is primarily a body’s defense system. Battle imagery is appropriate for describing the interaction with pathogens and parasites. A person’s blood becomes more potent over time as that person prevails and overcomes pathogens and parasites with its newly formed antibodies in high numbers. Antibodies have the secret locked away to defeat the germ that has invaded. The second infection usually has minimal harm; hence, the “wise” blood is more likely …

The Potential Of Bone Morphogenetic Protein 2 As A Neurotrophic Factor For Parkinson's Disease, Susan R. Goulding, Aideen M. Sullivan, Gerard W. O'Keeffe, Louise M. Collins

Department of Biological Sciences Publications

Parkinson's disease is the second most common neurodegenerative disorder; it affects 1% of the population over the age of 65. The number of people with Parkinson's disease is set to rapidly increase due to changing demographics and there is an unmet clinical need for disease-modifying therapies. The pathological hallmarks of Parkinson's disease are the progressive degeneration of dopaminergic neurons in the substantia nigra and their axons which project to the striatum, and the aggregation of α-synuclein; these result in a range of debilitating motor and non-motor symptoms. The application of neurotrophic factors to protect and potentially regenerate the remaining dopaminergic …

Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

The recent emergence of antibiotic resistance bacterial strains presents a significant challenge and threat to human healthcare. While new methods of treatment such as bacteriophage therapy and combinations of existing antibiotics are being researched, the human population is in dire need of new antibiotics to replace those that are ineffective. This research addresses this need by identifying antibiotic producing bacteria in a soil sample from Davenport, IA. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from soil. Microbiology lab techniques and 16S …

Host Population Genetics And Biogeography Structure The Microbiome Of The Sponge Cliona Delitrix, Cole Easson, Andia Chaves-Fonnegra, Robert W. Thacker, Jose Lopez

Biology Faculty Articles

Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted by the excavating sponge Cliona delitrix. A total of 53 samples, previously used to demarcate the population genetic structure of C. delitrix, were selected from two locations in the Caribbean Sea and …

"When The Enemy Drew Our Attention": Reconsidering Prior Restraint In The Context Of Dual Use Research Of Concern, Caine Caverly

William & Mary Bill of Rights Journal

Through 2016 and 2017, a team led by Canadian virologist David Evans, and funded by an American pharmaceutical company, attempted to synthesize the previously extinct horsepox virus. After just six months and an expenditure of $100,000, the research team was able to successfully construct the virus “using only commercially available information, technology and tools.” In January of 2018, the team went on to publish their information in an American-based journal, PLOS ONE.

The publication was controversial because it included a potential “blueprint” for the synthesis of a genetic strand in the same viral family as the highly lethal, albeit eradicated, …

Top-Down And Bottom-Up Controls On Microeukaryotic Diversity (I.E., Amplicon Analyses Of Sar Lineages) And Function (I.E., Metatranscriptome Analyses) Assessed In Microcosm Experiments, Jean David Grattepanche, Laura A. Katz

Biological Sciences: Faculty Publications

The availability of high-throughput sequencing (HTS) has transformed our understanding of the diversity of microbial eukaryotes (i.e., protists) across diverse habitats. Yet relating this biodiversity to function remains a challenge, particularly in the context of microbial food webs. Here we perform a set of microcosm experiments to evaluate the impact of changing predator and prey concentrations on a marine protist community, focusing on SAR (Stramenopila, Alveolata, and Rhizaria) lineages. We combine an estimate of taxonomic diversity through analysis of SSU-rDNA amplicons with metatranscriptomics, a proxy for function. We assess changes in a community sampled from New England waters with varying …

Investigating The Relationship Between Corticosterone And Glucose In A Reptile, Lorin A. Neuman-Lee, Spencer B. Hudson, Alison C. Webb, Susannah S. French

Biology Faculty Publications

The glucocorticoid hormone corticosterone (CORT) has classically been used in ecophysiological studies as a proxy for stress and energy mobilization, but rarely are CORT and the energy metabolites themselves concurrently measured. To examine CORT's role in mobilizing glucose in a wild reptile, we conducted two studies. The first study measured natural baseline and stress-induced blood-borne CORT and glucose levels in snakes during spring emergence and again when snakes return to the denning sites in autumn. The second study manipulated the hypothalamic–pituitary–adrenal (HPA) axis in male snakes in the autumn by taking a baseline blood sample, then subjecting individuals to one …

An Artificial Habitat Increases The Reproductive Fitness Of A Range-Shifting Species Within A Newly Colonized Ecosystem, Zachary J. Cannizzo, Susan Q. Lang, Bryan Benitez-Nelson, Blaine D. Griffen

Faculty Publications

When a range-shifting species colonizes an ecosystem it has not previously inhabited, it may experience suboptimal conditions that challenge its continued persistence and expansion. Some impacts may be partially mitigated by artificial habitat analogues: artificial habitats that more closely resemble a species' historic ecosystem than the surrounding habitat. If conditions provided by such habitats increase reproductive success, they could be vital to the expansion and persistence of range-shifting species. We investigated the reproduction of the mangrove tree crab Aratus pisonii in its historic mangrove habitat, the suboptimal colonized salt marsh ecosystem, and on docks within the marsh, an artificial mangrove …

Statistical Analysis Of Nutrient Loads From The Mississippi-Atchafalaya River Basin (Marb) To The Gulf Of Mexico, Phyllis Okwan, Yi Zhen, Huan Feng, Shinjae Yoo, Murty S. Kambhampati, Abreione Walker, Shayne Boykin, Joe Omojola, Noel Blackburn

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

This study investigated the annual and seasonal variations in nutrient loads (NO₂⁻ + NO₃⁻ and orthophosphate) delivered to the Gulf of Mexico from the Mississippi-Atchafalaya River Basin (MARB) and examined the water quality variations. The results indicate that (1) annually, the mean NO₂⁻ + NO₃⁻ and orthophosphate loads showed a steady increase during 1996–1999, a persistent level during 2000–2007, and a moderate increase during 2008–2016; (2) seasonally, NO₂⁻ + NO₃⁻ and orthophosphate in MARB in spring and summer were higher than those in autumn and winter. Analysis of …

Microrna-298 Reduces Levels Of Human Amyloid-Β Precursor Protein (App), Β-Site App-Converting Enzyme 1 (Bace1) And Specific Tau Protein Moieties, Nipun Chopra, Ruizhi Wang, Et Al.

Biology Faculty publications

Alzheimer’s disease (AD) is the most common age-related form of dementia, associated with deposition of intracellular neuronal tangles consisting primarily of hyperphosphorylated microtubule-associated protein tau (p-tau) and extracellular plaques primarily comprising amyloid- β (Aβ) peptide. The p-tau tangle unit is a posttranslational modification of normal tau protein. Aβ is a neurotoxic peptide excised from the amyloid-β precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) and the γ-secretase complex. MicroRNAs (miRNAs) are short, single-stranded RNAs that modulate protein expression as part of the RNA-induced silencing complex (RISC). We identified miR-298 as a repressor of APP, BACE1, and the two primary …

Proteasome Inhibition Rapidly Exacerbates Photoinhibition And Impedes Recovery During High Light Stress In Chlamydomonas Reinhardtii, Felipe Mendoza, Carson Berry, Laura Prestigiacomo, Doug Van Hoewyk

Biology

Background: Proteasomes remove regulatory proteins in eukaryotic cells, and control a variety of plant processes. Proteasomes are localized to the cytosol and nuclear, but their role in plant biology has recently been extended to chloroplasts, where it regulates TOC complex. This is turn controls the import of nuclear-encoded chloroplastic proteins, which remodels the chloroplast proteome and facilitates proper developmental transitions. Proteasomal regulation of the TOC complex also alleviates stressors that generate reactive oxygen species. These recent advances motivated us to determine if proteasome inhibition rapidly alters photosynthetic processes stemming from photoinhibition induced by high light. Results: The short-term effects of …

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 …