Digital Commons Network^™

Extracellular Domain Of Pept1 Interacts With Tm1 To Facilitate Substrate Transport, Jiemin Shen, Miaohui Hu, Xiao Fan, Zhenning Ren, Corinne Portioli, Xiuwen Yan, Mingqiang Rong, Ming Zhou

Faculty, Staff and Students Publications

Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their bioavailability. PepT has twelve transmembrane (TM) helices that fold into an N-terminal domain (NTD, TM1–6) and a C-terminal domain (CTD, TM7–12), and has a large extracellular domain (ECD) between TM9–10. It is well-recognized that peptide transport requires movements of the NTD and CTD, but the role of the ECD in PepT1 remains unclear. Here we report the structure of horse PepT1 encircled in lipid nanodiscs and captured in the inward-open apo …

Insights Into The Speciation Process From Genomic And Phenotypic Analysis Of An Avian Hybrid Zone In Amazonia, Glaucia Christina Del-Rio

LSU Doctoral Dissertations

Understanding the outcome of secondary contact is essential to shed light on the mechanisms governing species formation and maintenance. In Amazonia, closely related bird taxa with limited dispersal abilities are often separated by rivers, which presumably act as dispersal barriers. However, at the headwaters, rivers cease to be dispersal barriers, and this generates opportunities for secondary contact. In my dissertation, I studied genomic mechanisms associated with phenotypic differences, mitochondrial DNA structure, and putative reproductive barriers between two hybridizing Amazonian bird species in the genus Rhegmatorhina, a group of antbirds that find their arthropod prey exclusively by following army-ant swarms. …

Leafing Through Literature: Late Embryogenesis Abundant Proteins Coming Of Age – Achievements And Perspectives, Itzell E. Hernandez-Sanchez, Israel Maruri Lopez, Coral Martinez-Martinez, Brett Janis, Juan Francisco Jimenez Bremont, Alejandra A. Covarrubias, Michael A. Menze, Steffen P. Graether, Anja Thalhammer

Faculty and Staff Scholarship

To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review we recap the current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, …

Cd169 (Siglec-1) As A Robust Human Cell Biomarker Of Toll-Like Receptor 9 Agonist Immunotherapy, Stine Sofie Frank Lende, Marie H. Pahus, Ida Monrad, Rikka Olesen, Anna Mahr, Line K. Vibholm, Lars Østergaard, Ole Schmeltz Søgaard, Anna Halling Folkmar Andersen, Paul Denton, Martin Tolstrup

Biology Faculty Publications

Immunotherapy is a promising therapeutic area in cancer and chronic viral infections. An important component of immunotherapy in these contexts is the activation of innate immunity. Here we investigate the potential for CD169 (Siglec 1) expression on monocytes to serve as a robust biomarker for activation of innate immunity and, particular, as a proxy for IFN-α production. Specifically, we investigated the effects of Toll-like receptor 9 agonism with MGN1703 (lefitolimod) across experimental conditions ex vivo, in humanized mice, and in clinical trial participants. Ex vivo we observed that the percentage of classical monocytes expressing CD169 increased dramatically from …

Coordinating Tiny Limbs And Long Bodies: Geometric Mechanics Of Lizard Terrestrial Swimming, Baxi Chong, Tianyu Wang, Eva Erickson, Philip J. Bergmann, Daniel I. Goldman

Biology

Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body–limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards (Brachymeles and Lerista) and laboratory studies of fully limbed lizards (Uma scoparia and Sceloporus olivaceus) and a snake (Chionactis occipitalis) reveal that body-wave dynamics …

Leaf Development In Medicago Truncatula, Liren Du, Samuel Winright Adkins, Mingli Xu

Faculty Publications

Forage yield is largely dependent on leaf development, during which the number of leaves, leaflets, leaf size, and shape are determined. In this mini-review, we briefly summarize recent studies of leaf development in Medicago truncatula, a model plant for legumes, with a focus on factors that could affect biomass of leaves. These include: floral development and related genes, lateral organ boundary genes, auxin biosynthesis, transportation and signaling genes, and WOX related genes.

Evaluation Of Silver Nanoparticles Attached To Methylene Blue As An Antimicrobial Agent And Its Cytotoxicity, Somon Hakimov

Masters Theses & Specialist Projects

Antibiotics resistance is considered as one of the greatest public health challenges of our time. In this work, we have synthesized silver nanoparticles (Ag NPs) using pulsed liquid ablation in different medium of growth and later combined with methylene blue (MB) to evaluate its potential as an effective photodynamic therapy agent. Ag NPs were synthesized by pulsed laser ablation technique in Polyvinylpyrrolidone (PVP), citrate, and Polyvinyl alcohol (PVA). The Ag NPs were characterized using transmission electron microscopy (TEM), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Next, Ag NPs were coupled with MB and used to deactivate the Gram-negative bacteria, Escherichia coli …

Analysis Of Hawk Mountain Sanctuary Observation Data From 1976 Through 2021, Dale E. Parson

Computer Science and Information Technology Faculty

The primary objective is to correlate climate change data to changes in raptor observations at the Hawk Mountain Sanctuary in northern Berks County, Pennsylvania. Additional objectives include uncovering trends in climate observations at Hawk Mountain's North Lookout and the Allentown Airport throughout the observation period, and to examine trends in raptor observation properties independent of climate changes.

Nature, Data, And Power: How Hegemonies Shaped This Special Section, A. Kamath, B. Velocci, A. Wesner, N. Chen, Vincent A. Formica, B. Subramaniam, M. Rebolleda-Gómez

Biology Faculty Works

Systems of oppression—racism, colonialism, misogyny, cissexism, ableism, heteronormativity, and more—have long shaped the content and practice of science. But opportunities to reckon with these influences are rarely found within academic science, even though such critiques are well developed in the social sciences and humanities. In this special section, we attempt to bring cross-disciplinary conversations among ecology, evolution, behavior, and genetics on the one hand and critical perspectives from the social sciences and humanities on the other into the pages—and in front of the readers—of a scientific journal. In this introduction to the special section, we recount and reflect on the …

A Haploid Pseudo-Chromosome Genome Assembly For A Keystone Sagebrush Species Of Western North American Rangelands, Anthony E. Melton, Richard S. Beard Jr., Carlos Dave C. Dumaguit, Jennifer S. Forbey, Marie-Anne De Graaff, Peggy Martinez, Stephen J. Novak, Desiree Self, Marcelo Serpe, Sven Buerki

Biology Faculty Publications and Presentations

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km² in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality …

The Effects Of Genotype And Nutrient Conditions On Poplar Growth And Physiology, Bethanie Natalie

Theses - ALL

The United States is currently reliant on other nations for energy and has been unable tomeet goals set for domestic production of 'green' energy such as second generation biofuel. Overcoming these challenges requires examination of transgenic biofuel feedstock plants, specifically in terms of their responses to two nutrient treatments. Here, we investigated the photosynthetic and growth impacts of expressing a hyperthermophilic endoglucanase in planta in a wildtype (WT) Populus alba × grandidentata background under 100% and 15% strength nutrient treatments. This gene was inserted for improvement of the pretreatment process and to limit inputs required during biofuel production. We characterized …

Distribution Of Carrion-Associated Beetles And Their Phoretic Mites Along An Urban-Rural Gradient In Northeast Alabama, Kennedy Norris

Theses

Global insect decline has been linked to urbanization, most notably by habitat fragmentation. These insects perform important ecological functions such as pollination, managing pests, and decomposing carrion to recycle nutrients back into the environment. Despite the importance of nutrient recycling behavior displayed by carrion-associated beetles, little research has been done on them in the southeastern US. Previous studies have found a relationship between urbanization, less favorable environmental conditions, carrion availability, and decreased insect diversity. However, no studies have been conducted in the southeastern United States on the relationship of these beetles to their environment despite having the highest rates of …

Habitat Use Of The Threatened River Redhorse (Moxostoma Carinatum) In The Grand River, Mi, Usa, Nicholas M. Preville, Eric B. Snyder, Dan O'Keefe, Scott Hanshue, Amy Russell, Justin Radecki

Peer Reviewed Publications

The resilience of aquatic ecosystems hinges on our ability to protect the native species that reside within them. The river redhorse (Moxostoma carinatum) is one such example and populations have become low enough to warrant a threatened status by the State of Michigan. An insufficient understanding of the species’ habitat use outside of its spawning season hinders the ability of fisheries managers to implement appropriate habitat protection and restoration measures. To enhance our understanding of river redhorse habitat use, we implanted 15 individuals with radio transmitters during the spring spawning run and tracked their locations over the course …

Demographic Expansions And The Emergence Of Host Specialization In Genetically Distinct Ecotypes Of The Tick-Transmitted Bacterium Anaplasma Phagocytophilum, Matthew L. Aardema, Nina V. Bates, Qiana E. Archer, Friederike D.Von Loewenich

Department of Biology Faculty Scholarship and Creative Works

In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (Ne) has tracked changes in the population of its …

Illuminating Protist Diversity In Pitcher Plants And Bromeliad Tanks, Robin S. Sleith, Laura A. Katz

Biological Sciences: Faculty Publications

Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and …

What Are Mycorrhizal Traits?, V. Bala Chaudhary, E. Penelope Holland, Suw Charman-Anderson, Aidee Guzman, Lukas Bell-Dereske, Tanya E. Cheeke, Adriana Corrales, Jessica Duchicela, Cameron Egan, Pushpa G. Soti

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

Highlights

• Applying trait-based approaches to ecological research on mycorrhizal symbioses broadens ecological inferences, but there is no single unified framework to unite disparate language, terminology, and methods across the many multidisciplinary scientists studying mycorrhizas.
• We propose an inclusive framework for trait-based mycorrhizal ecology aimed to stimulate scientists around the world to collect and use more mycorrhizal trait data, particularly in understudied areas. This would widen our understanding regarding the ecological role of mycorrhizal symbioses at individual, species, community, and ecosystem scales.
• Analyzing how mycorrhizal symbioses fit within existing trait definitions highlights significant theoretical and empirical knowledge gaps, novel questions, and …

Evolution Of Sex Chromosomes In Geckos (Reptilia: Gekkota), Shannon Elizabeth Keating

Dissertations (1934 -)

Sex chromosomes control sex determination in many plants and animals, playing a vital role in a species’ evolution. Current models of sex chromosome evolution have been formulated by studying clades with stable, morphologically distinct (heteromorphic) sex chromosomes, such as mammals and birds. However, many taxa have morphologically indistinguishable (homomorphic) sex chromosomes, including many fish, amphibians, and reptiles. The knowledge gained from these understudied systems may provide new insights into the overarching paradigms of sex chromosome evolution. Thus, the historical focus on stable, heteromorphic sex chromosomes and failure to consider homomorphic sex chromosomes or systems with frequent turnovers may mean the …

Embryology Of The Gekkota: Insights Into The Evolution An Development Of Morphological Diversity, Aaron Harp Griffing

Dissertations (1934 -)

Understanding the patterns and processes which result in morphological diversity is a central goal of evolutionary developmental biology or evo-devo. This diversity encompasses morphologies which have evolved numerous, independent times within a clade (evolutionary convergence) and others which have evolved only once within a clade (i.e. evolutionary novelty). Though many of these diverse morphologies exhibit functional capabilities and are intertwined with the ecology and diversification of the evolutionary lineage in question, their origins are largely unknown. Robust phylogenic analysis, genomic information, and detailed developmental data are critical lines of evidence to explain the evolutionary and ontogenetic origins of morphological novelty …

Implications Of The Actin Cytoskeleton On The Multi-Step Process Of [ Psi+] Prion Formation, Jane E. Dorweiler, Douglas R. Lyke, Nathan P. Lemoine, Sam Guereca, Hannah E. Buchholz, Emily R. Legan, Claire M. Radtke, Anita L. Manogaran

Biological Sciences Faculty Research and Publications

Yeast prions are self-perpetuating misfolded proteins that are infectious. In yeast, [PSI⁺] is the prion form of the Sup35 protein. While the study of [PSI⁺] has revealed important cellular mechanisms that contribute to prion propagation, the underlying cellular factors that influence prion formation are not well understood. Prion formation has been described as a multi-step process involving both the initial nucleation and growth of aggregates, followed by the subsequent transmission of prion particles to daughter cells. Prior evidence suggests that actin plays a role in this multi-step process, but actin’s precise role is unclear. Here, we …

Transcriptome Assembly And Characterization Of Chemoreceptors For Corn Rootworms, Bailee Egan

School of Biological Sciences: Dissertations, Theses, and Student Research

The western corn rootworm (Diabrotica virgifera virgifera LeConte) is the most important insect pest of corn in the United States Corn Belt, costing the agricultural industry over two billion dollars per year. As current management practices have been losing their effectiveness, new targets for corn rootworm control need to be explored. In this thesis, we focused on identifying rootworm chemoreceptors, which can be considered for potential targets for management. Transcriptomes from seven life stages were assembled for the western corn rootworm as well as two other related corn rootworm species, the northern corn rootworm (D. barberi) …

Mechanisms Of Connectivity In Neuronal Development, Janay Vacharasin

Theses and Dissertations

The development of neuronal connectivity requires the careful orchestration of multiple cellular processes including the control of neuronal arborization and synapse formation or function. Defects in these processes during neuronal development will give rise to disorders of neuronal connectivity like autism. In the present work, we examine the genetic and epigenetic mechanisms that build the neuronal wiring of the developing brain. We use human stem cell-derived neurons to study neuronal arborization and function focusing on genetic and environmental risk factors of neurodevelopmental disorders that include autism and intellectual disability. Specifically, we focused on the contribution of the endomembrane, chromatin, and …

In Vivo And In Vitro Investigations Of Mammalian Stem Cell Development: Neurogenesis And Pituitary Progenitors, Allison Culver

Theses and Dissertations

Human development is tightly regulated by complex mechanisms to pattern the early embryo and form specialized tissues. Understanding this regulation is of fundamental importance and can help further understand disease pathologies. Because it is difficult to observe the processes of interest, researchers must rely on the use of model systems. Our research goal is to combine both animal models and in vitro stem cell cultures to address key questions about the mechanisms of development for both the pituitary gland and brain. It is estimated that there are 290-455 cases per million of congenital hypopituitarism. In addition, autism spectrum disorder (ASD) …

Molecular And Morphological Investigations Of Grouper (Serranidae) Biodiversity In Saudi Arabia, Mohammad Saeed Al Jazza Alqahtani

Theses and Dissertations

Chapter 1: The seas surrounding the Arabian Peninsula, which represent the northernmost portion of the Indian Ocean, are considered to have the highest aquatic biodiversity among the worlds marine regions. Seas that surround the Arabian Peninsula include the Red Sea, the Gulf of Aden, the Arabian Sea, the Gulf of Oman, and the Arabian Gulf. In aggregate, this area harbors a large number of endemic and more widespread marine species, including fishes, echinoderms, and corals.

There are unique challenges involved in grouper species identification in the Arabian region including ‘familiar’ Arabic species designations that are not standardized in the Arabic …

A Rationally Designed Synthetic Antimicrobial Peptide Against Pseudomonas-Associated Corneal Keratitis: Structure-Function Correlation, Sk Abdul Mohid, Prerana Sharma, Amani Alghalayini, Tripti Saini, Debarun Datta, Mark D. P. Willcox, Haydar Ali, Sreyan Raha, Achintya Singha, Nirakar Sahoo

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

Contact lens wearers are at an increased risk of developing Pseudomonas-associated corneal keratitis, which can lead to a host of serious ocular complications. Despite the use of topical antibiotics, ocular infections remain a major clinical problem, and a strategy to avoid Pseudomonas-associated microbial keratitis is urgently required. The hybrid peptide VR18 (VARGWGRKCPLFGKNKSR) was designed to have enhanced antimicrobial properties in the fight against Pseudomonas-induced microbial keratitis, including contact lens-related keratitis. In this paper, VR18's modes of action against Pseudomonas membranes were shown by live cell Raman spectroscopy, live cell NMR, live-cell fluorescence microscopy and measures taken using sparsely tethered bilayer …

Methyltransferase Mystery: Epigenetic Mechanisms Induced By Food Limitation In Daphnia Pule, Trenton C. Agrelius

Theses and Dissertations

Daphnia are ecologically important organisms that have been well studied in the context of evolution, ecology, ecotoxicity, and genomics. Daphnia have strong maternal effects in which the environment experienced by the mother can alter offspring disease resistance, life history traits, and morphology, as well as gene expression and methylation for multiple generations. Coupled with their ability to reduce genetic differences via parthenogenesis, Daphnia are an ideal system for epigenetic studies involving the transmission of maternal effects. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food …

Scientist's Warning On Climate Change And Insects, Jeffrey A. Harvey, Kévin Tougeron, Rieta Gols, Robin Heinen, Mariana Abarca, Et Al

Biological Sciences: Faculty Publications

Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human-mediate threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insects—central components of many ecosystems—for which climate change has pervasive effects from individuals to communities. In this contribution to the scientists’ warning series, we summarize the effect …

Differentiation And Temperature Adaptation Of Pampus Echinogaster Based On Genome-Wide Snps, Yuan Li, Fangrui Lou, Shigang Liu, Hai Li, Jiali Xiang, Binbin Shan, Longshan Lin, Xuan Zhuang

Biological Sciences Faculty Publications and Presentations

Climate change and overfishing have led to the degradation of the quality and stock of Pampus echinogaster. Exploring the genetic structure and local adaptive evolutionary mechanisms of P. echinogaster is crucial for the management of this species. This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the population size of the …

Emergence Activity At Hibernacula Differs Among Four Bat Species Affected By White-Nose Syndrome, Reilly T. Jackson, Emma V. Wilcox, John M. Zobel, Riley F. Bernard

Biological Sciences Faculty Publications and Presentations

Prior to the introduction of white-nose syndrome (WNS) to North America, temperate bats were thought to remain within hibernacula throughout most of the winter. However, recent research has shown that bats in the southeastern United States emerge regularly from hibernation and are active on the landscape, regardless of their WNS status. The relationship between winter activity and susceptibility to WNS has yet to be explored but warrants attention, as it may enable managers to implement targeted management for WNS-affected species. We investigated this relationship by implanting 1346 passive integrated transponder (PIT) tags in four species that vary in their susceptibility …

Regulation Of The Heat Shock Response Via Lysine Acetyltransferase Cbp-1 And In Neurodegenerative Disease In Caenorhabditis Elegans, Lindsey N. Barrett

USF Tampa Graduate Theses and Dissertations

The decline of proteostasis is a hallmark of aging that is, in part, affected by the dysregulation of the heat shock response (HSR), a highly conserved cellular response to proteotoxic stress in the cell. The heat shock transcription factor HSF-1 is well-studied as a key regulator of proteostasis, but mechanisms that could be used to modulate HSF-1 function to enhance proteostasis during aging are largely unknown. In this study, we examined lysine acetyltransferase regulation of the HSR and HSF-1 in C. elegans. We performed an RNA interference screen of lysine acetyltransferases and examined mRNA expression of the heat-shock inducible gene …

Spatial Analysis Of Drug Absorption, Distribution, Metabolism, And Toxicology Using Mass Spectrometry Imaging, Michelle L Spruill, Mirjana Maletic-Savatic, Howard Martin, Feng Li, Xinli Liu

Faculty, Staff and Students Publications

Mass spectrometry imaging (MSI) is emerging as a powerful analytical tool for detection, quantification, and simultaneous spatial molecular imaging of endogenous and exogenous molecules via in situ mass spectrometry analysis of thin tissue sections without the requirement of chemical labeling. The MSI generates chemically specific and spatially resolved ion distribution information for administered drugs and metabolites, which allows numerous applications for studies involving various stages of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). MSI-based pharmacokinetic imaging analysis provides a histological context and cellular environment regarding dynamic drug distribution and metabolism processes, and facilitates the understanding of the spatial pharmacokinetics …