Biology Commons^™

Integrating Species Traits Into Species Pools, Marko J. Spasojevic, Christopher P. Catano, Joseph A. Lamanna, Jonathan A. Myers

Biological Sciences Faculty Research and Publications

Despite decades of research on the species‐pool concept and the recent explosion of interest in trait‐based frameworks in ecology and biogeography, surprisingly little is known about how spatial and temporal changes in species‐pool functional diversity (SPFD) influence biodiversity and the processes underlying community assembly. Current trait‐based frameworks focus primarily on community assembly from a static regional species pool, without considering how spatial or temporal variation in SPFD alters the relative importance of deterministic and stochastic assembly processes. Likewise, species‐pool concepts primarily focus on how the number of species in the species pool influences local biodiversity. However, species pools with similar …

Response To Comment On “Plant Diversity Increases With The Strength Of Negative Density Dependence At The Global Scale”, Joseph A. Lamanna, Scott A. Mangan, Alfonso Alonso, Norman A. Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Li-Wan Chang, Iyh-Min Chiang, George B. Chuyong, Keith Clay, Susan Cordell, Stuart J. Davies, Tucker J. Furniss, Christian P. Giardina, I. A.U. Nimal Gunatilleke, C. V. Savitri Gunatilleke, Fangliang He, Robert W. Howe, Stephen P. Hubbell, Chang-Fu Hsieh, Faith M. Inman-Narahari, David Janik, Daniel J. Johnson, David Kenfack, Lisa Korte, Kamil Král, Andrew J. Larson, James A. Lutz, Sean M. Mcmahon, William J. Mcshea, Hervé R. Memiaghe, Anuttara Nathalang, Vojtech Novotny, Perry S. Ong, David A. Orwig, Rebecca Ostertag, Geoffrey G. Parker, Richard P. Phillips, Lawren Sack, I-Fang Sun, J. Sebastián Tello, Duncan W. Thomas, Benjamin L. Turner, Dilys M. Vela Díaz, Tomáš Vrška, George D. Weiblen, Amy Wolf, Sandra Yap, Jonathan A. Myers

Biological Sciences Faculty Research and Publications

Hülsmann and Hartig suggest that ecological mechanisms other than specialized natural enemies or intraspecific competition contribute to our estimates of conspecific negative density dependence (CNDD). To address their concern, we show that our results are not the result of a methodological artifact and present a null-model analysis that demonstrates that our original findings—(i) stronger CNDD at tropical relative to temperate latitudes and (ii) a latitudinal shift in the relationship between CNDD and species abundance—persist even after controlling for other processes that might influence spatial relationships between adults and recruits.

Biotic Filtering In Endophytic Fungal Communities, Kevin Daniel Ricks

Theses and Dissertations

Plants can be colonized by complex communities of endophytic fungi. This thesis presents two studies, both of which investigate biotic filtering in endophytic fungal communities. Chapter 1. Endophytic fungi can be acquired horizontally via propagules produced in the environment such as in plant litters of various species. Given that litters from different plant species harbor distinct endophytic fungal communities and that endophytic fungi may be dispersal-limited, the structure of the endophytic fungal community of a given plant may be determined by proximity to particular inoculum sources. Community assembly may also be affected by biotic filtering by the plant. Therefore, a …

A High-Throughput Screening Assay For Pyruvate Carboxylase, Brittney N. Wyatt, Leggy A. Arnold, Martin St. Maurice

Biological Sciences Faculty Research and Publications

Pyruvate carboxylase (PC) catalyzes the conversion of pyruvate to oxaloacetate (OAA), an important metabolic reaction in a wide range of organisms. Small molecules directed against PC would enable detailed studies on the metabolic role of this enzyme and would have the potential to be developed into pharmacological agents. Currently, specific and potentsmall molecule regulators of PC are unavailable. To assist in efforts to find, develop, and characterize small molecule effectors of PC, a novel fixed-time assay has been developed based on the reaction of OAA with the diazonium salt, Fast Violet B (FVB), which produces a colored adduct with …

Xx/Xy Sex Chromosomes In The South American Dwarf Gecko (Gonatodes Humeralis), Tony Gamble, Erin Mckenna, Wyatt Meyer, Stuart V. Nielsen, Brendan J. Pinto, Daniel P. Scantlebury, Timothy E. Higham

Biological Sciences Faculty Research and Publications

Sex-specific genetic markers identified using restriction site-associated DNA sequencing, or RADseq, permits the recognition of a species’ sex chromosome system in cases where standard cytogenetic methods fail. Thus, species with male-specific RAD markers have an XX/XY sex chromosome system (male heterogamety) while species with female-specific RAD markers have a ZZ/ZW sex chromosome (female heterogamety). Here, we use RADseq data from 5 male and 5 female South American dwarf geckos (Gonatodes humeralis) to identify an XX/XY sex chromosome system. This is the first confidently known sex chromosome system in a Gonatodes species. We used a low-coverage de novo G. …

Potential Mechanisms For Nns-Induced Metabolic Deviances: Satiety Hormone Secretion And Alterations In The Gut Microbiota, Kyle J. Decker

DePaul Discoveries

Rising rates of obesity and type 2 diabetes have prompted the usage and recommendation of nonnutritive sweeteners (NNS) as harmless sugar substitutes in attempts to decrease caloric intake. Contrary to the common belief that NNS remain physiologically inert post-consumption, evidence highlights their ability to alter metabolic processes via interactions in the gastrointestinal tract. An extensive review was conducted on the potential NNS-induced metabolic deviances by way of two non-mutually exclusive mechanisms. One possible mechanism involves their ability (or inability) to induce the secretion of GLP-1, a hormone produced in the gut that promotes satiety and accelerates glucose-dependent insulin secretion by …

Direct And Indirect Controls On Bee Community Composition, Caroline Marie Devan

Dissertations

Bees are important pollinators, critical for the continued survival of plants in both natural and agricultural ecosystems. Diverse bee communities have been shown to increase richness in plant communities and plant reproduction depends upon bee community richness. Yet there is growing concern that pollinators, especially bees, are declining globally. This dissertation focuses on evaluating the mechanisms responsible for bee community composition in order to promote bee conservation in natural systems and their restoration in human-dominated urban and agricultural landscapes.

Bee populations are impacted directly by three things: floral resources, nesting resources and risk, primarily from natural enemies. Bees are indirectly …

The Y-Screen Assay: Validation And Evaluation Of Subsequent Str Success, Kassandra Luyando

Student Theses

There are hundreds of untested sexual assault kits in police custody. As of 2017, New York State passed a law stating that all untested kits must be turned over to forensic laboratories to be tested, causing backlogs at laboratories to increase. The Y-Screen assay is a DNA extraction protocol which utilizes NaOH to rapidly lyse epithelial and sperm cells, and the Quantifiler Trio DNA quantification kit to detect the presence or absence of male DNA prior to standard sample processing. The Y-Screen assay is a commercial product used in this research to test a defined set of validation samples with …

A Biodegradable Piezoelectric Composite Scaffold Containing Zinc Oxide For Cartilage Repair Applications, Ateka Mohd Arabi Khader

Dissertations

Osteoarthritis (OA) affects 27 million adults in the United States. OA causes degeneration of articular cartilage and subchondral bone. Articular cartilage has limited ability to regenerate and repair. Bone and cartilage tissues have known piezoelectric properties, which means they can generate electrical activity in response to mechanical deformation. Using a biomimetic approach, zinc oxide (ZnO), which has known piezoelectric properties, is fabricated into a flexible three-dimensional fibrous scaffold by embedding ZnO nanoparticles into slow degrading polycaprolactone (PCL). Zinc ions can be released from the fibrous scaffold over time, which also may be beneficial for cell function since zinc has well-known …

Investigating The Effects Of Trans-Spinal Direct Current Stimulation On The Expression Of Nkcc1 In Mice, Pasindu Weliwaththage

Student Theses

Trans-spinal direct current stimulation (tsDCS) is a non-invasive powerful tool demonstrated to positively affect behavior and motor function. tsDCS is a neuromodulatory technique capable of altering spinal and cortical excitability and even regain motor function after complete motor paralysis (Cortes et at, 2017). tsDCS causes immediate and long-term effects in spinal excitability (Ahmed, 2011, 2013; Ahmed and Wieraszko, 2012; Cogiamanian et al., 2011, 2012). Studies have been conducted on both healthy and injured subjects. The ultimate goal is to ameliorate the devastating effects of Spinal Cord Injury. Though researchers have been successful in improving motor function, the molecular basis of …

Population Genetics And Bumble Bee Conservation: Saving Species By Thinking Small, Cady Greenslit

Lawrence University Honors Projects

Pollinators have experienced a severe decline over the last few decades, and this includes bumble bee populations (g. Bombus). Bumble bees are important native pollinators, and here I investigate the health of local populations with molecular tools. The field of conservation genetics has created useful methodology for investigating the health and informing management strategies of threatened populations. This work investigates and describes the applications of population genetics, which uses span across the board. These applications are then brought back into the context of bumble bee conservation, and how they fit into the experimental plan I originally designed. I designed …

Off-Target Based Drug Repurposing Using Systems Pharmacology, Brent M. Kuenzi

USF Tampa Graduate Theses and Dissertations

The goal of this study was to identify novel drug repurposing opportunities in cancer by utilizing the off-target profiles of clinically relevant kinase inhibitors. This was based on the observation that the global target profiles of compounds are largely ignored and that many compounds have activity that cannot be explained by their cognate target alone. Additionally, by utilizing clinically relevant compounds, any results would hold a high potential for eventual clinical implementation. We utilized a systems pharmacology approach utilizing cell viability-based drug screening to identify compounds with beneficial off-target activity and then using chemical and phosphoproteomics in order to elucidate …

Synthesis And Preliminary Antimicrobial Analysis Of Isatin- Ferrocene And Isatin-Ferrocenyl Chalcone Conjugates, Amandeep Singh, Grant Fong, Jenny Liu, Yun-Hsuan Wu, Kevin Chang, William Park, Jihwan Kim, Christina Tam, Luisa W. Cheng, Kirkwood M. Land, Vipan Kumar

College of the Pacific Faculty Articles

In this study, we outline the synthesis of isatin-ferrocenyl chalcone and 1H-1,2,3-triazole-tethered isatin-ferrocene conjugates along with their antimicrobial evaluation against the human mucosal pathogen Trichomonas vaginalis. The introduction of a triazole ring among the synthesized conjugates improved the activity profiles with most of the compounds in the library, exhibiting 100% growth inhibition in a preliminary susceptibility screen at 100 μM. IC50 determination of the most potent compounds in the set revealed an inhibitory range between 2 and 13 μM. Normal flora microbiome are unaffected by these compounds, suggesting that these may be new chemical scaffolds for the discovery of new …

Mapping Out Head Country: Expression Of Daf-19c In The Head Neurons Of C. Elegans, Hanwenheng (Billy) Liu

Lawrence University Honors Projects

C. elegans has been used as a model system for studies of nervous system development and function for over 50 years due to its relative simplicity and strong similarity to other animals. One of such similarities is the presence of an RFX transcription factor, which is responsible for controlling gene expression in a handful of important organs, including the brain. RFX proteins are a family of highly evolutionarily conserved proteins that usually function by binding to a specific region (called the X-box) in the promoter of their target genes. A single RFX-coding gene has been found in C. elegans, …

Interplay Of Transcription Factor E And Spt4/5 During Transcription Initiation In Pyrococcus Furiosus, Kimberly Kay Sheffield

Dissertations and Theses

Transcription, the first step in gene expression, is a highly regulated process which relies on a multi-protein complex to occur. Among these proteins are transcription factors, including initiation and elongation factors, which play differing roles in early and late stages of transcription. The mechanisms of transition from transcription initiation to elongation are not well understood in archaea, nor are the structures of the transcription factors involved. For transcription to occur in vitro, transcription factors TATA binding protein (TBP) and Transcription Factor B (TFB) are sufficient to allow RNA polymerase (RNAP) to synthesize RNA from template DNA. Another factor, Transcription …

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Jennifer Cox, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Biology: Faculty Publications and Other Works

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Bioinformatics Faculty Publications

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

Sensitive High-Frequency Hearing In Earless And Partially Eared Harlequin Frogs (Atelopus), Molly C. Womack, Jakob Christensen-Dalsgaard, Luis A. Coloma, Kim L. Hoke

Biology Faculty Publications

Harlequin frogs, genus Atelopus, communicate at high frequencies despite most species lacking a complete tympanic middle ear that facilitates high-frequency hearing in most anurans and other tetrapods. Here, we tested whether Atelopus are better at sensing high-frequency acoustic sound compared with other eared and earless species in the Bufonidae family, determined whether middle ear variation within Atelopus affects hearing sensitivity and tested potential hearing mechanisms in Atelopus. We determined that at high frequencies (2000‚Äì4000‚ÄÖHz), Atelopus are 10‚Äì34‚ÄÖdB more sensitive than other earless bufonids but are relatively insensitive to mid-range frequencies (900‚Äì1500‚ÄÖHz) compared with eared bufonids. Hearing among Atelopus species is …

Identification Of Raw As A Regulator Of Glial Development, Diana Luong, Luselena Perez, Jennifer Mierisch

Biology: Faculty Publications and Other Works

Glial cells perform numerous functions to support neuron development and function, including axon wrapping, formation of the blood brain barrier, and enhancement of synaptic transmission. We have identified a novel gene, raw, which functions in glia of the central and peripheral nervous systems in Drosophila. Reducing Raw levels in glia results in morphological defects in the brain and ventral nerve cord, as well as defects in neuron function, as revealed by decreased locomotion in crawling assays. Examination of the number of glia along peripheral nerves reveals a reduction in glial number upon raw knockdown. The reduced number of …

Genomewide Evaluation Of Cis-Elements And Cognate Transcription Factors In Nicotiana Attenuata Predicts 27 Unique Transcription Factor-Binding Site Pairs, Ashton Omdahl

Undergraduate Honors Theses

Nicotiana attenuata has been widely studied for its ecological plant-herbivore relationships and response to environmental stress. The jasmonate signaling pathway regulated by jasmonate ZIM-domiain (JAZ) repressor proteins that modulate defense response levels has been of particular focus in this research. While our understanding of the genes associated with defense response and their regulation continues to expand, the transcriptional regulation of these genes is largely uncharacterized. In an effort to provide insight into these relationships, we performed genomewide analysis of transcript level data in order to predict transcription factors (TFs), their respective binding sites (TFBS), and the genes they regulate. We …

Determining The Relationship Between Aging And Oxidative Stress In A Drosophila Melanogaster P38 Kb Framework, Aleksandra J. Majewski

Theses and Dissertations

Aging is inevitable for all organisms and can be characterized by degeneration of tissue, adecrease in motor function, and impaired stress response. In humans, it is often accompanied by an increased propensity for age related diseases. While all adults experience biological aging (senescence) not all adults experience age-associated disease. Thus, we claim these are not normal prospects of aging. Although the implications of aging are well understood, the molecular underpinnings for these processes remain elusive. As advances in medical science have been successful at prolonging lifespan, they concurrently extend the amount of time spend in diseased states. If we wish …

Phenotypic Plasticity In Light-Induced Flavonoids Varies Among Tissues In Silene Littorea (Caryophyllaceae), José Carlos Del Valle, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Plants respond to environmental stimuli in a diversity of ways including the production of secondary metabolites. Biosynthesis of plant phenolics, including flavonoids, is frequently activated in response to a variety of abiotic and biotic stressors (e.g. extreme temperatures, high radiation, pathogens, etc.). This induced reaction is typically assumed to be a plastic response, but the components attributable to plasticity vs genetic variance in these components are poorly understood. Here, we investigate the variation in flavonoid production (anthocyanins and flavones) in petals and in photosynthetic tissues (calyces, leaves and stems) of Silene littorea. We performed a common garden experiment with …

Perinatal Pb2+ Exposure Alters The Expression Of Genes Related To The Neurodevelopmental Gaba-Shift In Postnatal Rats, Lorenz Simon Neuwirth, Greg R. Phillips, Abdeslem El Idrissi

Publications and Research

Background: Lead (Pb2+) is an environmental neurotoxicant that disrupts neurodevelopment, communication, and organization through competition with Ca2+ signaling. How perinatal Pb2+ exposure affects Ca2+-related gene regulation remains unclear. However, Ca2+ activates the L-Type voltage sensitive calcium channel β-3 subunit (Ca-β3), which autoregulates neuronal excitability and plays a role in the GABA-shift from excitatory-toinhibitory neurotransmission.

Method: A total of eight females (n = 4 Control and n = 4 Perinatal) and four males (n = 2 Control and n = 2 Perinatal) rats were used as breeders to serve as Dams and Sires. The Dam’s litters each ranged from N = …

Studies On Inositol Polyphosphate-Mediated Cell Death Process In Dictyostelium Discoideum And Its Sensitivity To Single-Walled Carbon Nanotubes, Qudes Ali Al-Anbaky

Theses and Dissertations

Inositol polyphosphates (InsPs) are naturally occurring compounds that are widely distributed in both plant and animal cells. They regulate a variety of cellular processes including programmed cell death or apoptosis. Apoptosis maintains tissue homeostasis in higher organisms. Among inositol polyphosphates, inositolhexakisphosphate was found to be the most potent inducer of apoptosis in mammalian cells, however, the mechanism of apoptosis particularly mediated by InsPs is not well understood in simple eukaryotes such as Dictyostelium discoideum, despite InsPs having been well studied in this model organism. MTT (3-(4, 5-Dimethylthiazol-2-yl)-2, 5-Diphenyltetrazolium Bromide, LDH, and trypan blue assays were used to investigate the cytotoxic …

Lanthanide-Doped Ceria Nanoparticles As Backside Coaters To Improve Silicon Solar Cell Efficiency, Ali Hajjiah, Effat Samir, Nader Shehata, Mohamed Salah

Biology Faculty Publications

This paper introduces lanthanide-doped ceria nanoparticles as silicon solar cell back-side coaters, showing their influence on the solar cell efficiency. Ceria nanoparticles can be synthesized to have formed oxygen vacancies (O-vacancies), which are associated with converting cerium ions from the Ce⁴⁺ state ions to the Ce³⁺ ones. These O-vacancies follow the rule of improving silicon solar cell conductivity through a hopping mechanism. Besides, under near-ultra violet (near-UV) excitation, the reduced trivalent cerium Ce³⁺ ions are directly responsible for down converting the un-absorbed UV wavelengths to a resultant green photo-luminescence emission at ~520 nm, which is absorbed through …

Rab10: The Future Of Alzheimer’S Disease, Keni Reid, Dr. John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is a brain disorder caused by an irreversible degeneration of nerve cells. It is developed in response to a growth of proteins, tau tangles or amyloid plaques, which disrupt communication between neurons in the brain. Because the nerve cells no longer function, they die. It is estimated that as many as 5.1 million Americans may have Alzheimer’s disease and about one to four family members act as caregivers for each individual with Alzheimer’s disease. Many lives are affected by Alzheimer’s which has driven further and extensive research for solutions. However, despite much effort, the genetics of Alzheimer’s remains …

Terrestrial Laser Scanning To Detect Liana Impact On Forest Structure, Sruthi M. Krishna Moorthy, Kim Calders, Manfredo Di Porcia E Brugnera, Hans Verbeeck, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Tropical forests are currently experiencing large-scale structural changes, including an increase in liana abundance and biomass. Higher liana abundance results in reduced tree growth and increased tree mortality, possibly playing an important role in the global carbon cycle. Despite the large amount of data currently available on lianas, there are not many quantitative studies on the influence of lianas on the vertical structure of the forest. We study the potential of terrestrial laser scanning (TLS) in detecting and quantifying changes in forest structure after liana cutting using a small scale removal experiment in two plots (removal plot and non-manipulated control …

Fungal Endophytes In A Seed-Free Host: New Species That Demonstrate Unique Community Dynamics, Brett Steven Younginger

Dissertations and Theses

Fungal endophytes are highly diverse, cryptic plant endosymbionts that form asymptomatic infections within host tissue. They represent a large fraction of the millions of undescribed fungal taxa on our planet with some demonstrating mutualistic benefits to their hosts including herbivore and pathogen defense and abiotic stress tolerance. Other endophytes are latent saprotrophs or pathogens, awaiting host plant senescence to begin alternative stages of their life cycles. Most, however, are likely plant commensals with no observable benefits to their hosts while under study. Yet, when considering the context-dependence that may determine plant resistance to pathogen attack, the consortium of endophytes present …

The Truncated Bell: An Enigmatic But Pervasive Elevational Diversity Pattern In Middle American Ants, John T. Longino, Michael G. Branstetter

All PIRU Publications

Studies on elevation gradients in Panama and Costa Rica have shown that leaf-litter ants exhibit a mid-elevation peak in diversity. This diversity pattern has been observed in other groups and regions, but uncertainty remains as to just how pervasive it is and what might explain it. Here we examine the robustness of the mid-elevation peak in ant diversity across the entire Middle American corridor, from Veracruz, Mexico, to Costa Rica. We sampled 56 sites distributed throughout Middle America. All were in closed-canopy evergreen wet forest, spanning 11° latitude, from near sea level to 2600 m elevation. Ants were extracted from …

Balancing Urban Biodiversity Needs And Resident Preferences For Vacant Lot Management, Christine C. Rega-Brodsky, Charles H. Nilon, Paige S. Warren

Faculty Submissions

Urban vacant lots are often a contentious feature in cities, seen as overgrown, messy eyesores that plague neighborhoods. We propose a shift in this perception to locations of urban potential, because vacant lots may serve as informal greenspaces that maximize urban biodiversity while satisfying residents’ preferences for their design and use. Our goal was to assess what kind of vacant lots are ecologically valuable by assessing their biotic contents and residents’ preferences within a variety of settings. We surveyed 150 vacant lots throughout Baltimore, Maryland for their plant and bird communities, classified the lot’s setting within the urban matrix, and …