Digital Commons Network^™

Please Don’T Break: Best Practices For Digitizing And Archiving Glass Plate Photographs, Ariel Hammond, Noelle Zocco, Alejandra Tomeo, Diego Jimenez

Journal of Western Archives

Glass plate photographs, taken primarily between 1860-1930, were meant to document and preserve imagery, however, these photographs developed directly on glass are increasingly prone to destruction. With recent advances in imaging techniques, metadata, and collections care, the preservation of glass photography has evolved. This paper is a snapshot of the current best practices for preserving, digitizing, and storing glass plate and lantern slide photographs. It also features a case study from the San Diego Natural History Museum Library & Archives, which digitized a collection of 2,000+ glass photographs depicting the earliest images of flora and fauna in San Diego County, …

Draft Genome Assemblies Of Three Klebsiella Grimontii Strains Isolated From Catheterized Urine Samples From The Same Male Participant Over The Course Of 6 Months, Helen Appleberry, Warwick Price, Lorenzo Roque, Evelyn Umana, Alan J. Wolfe, Catherine Putonti, Alex Kula

Biology: Faculty Publications and Other Works

Klebsiella grimontii is a newly identified species within the Klebsiella oxytoca complex. Here, we present the draft genome sequence of three K. grimontii strains that were isolated from catheterized urine samples collected from a participant in a longitudinal study over ~6 months.

Transcriptional Precision In Photoreceptor Development And Diseases - Lessons From The Retinal Transcription Factor Crx, Yiqiao Zheng

Arts & Sciences Graduate Student Theses and Dissertations

Precise gene expression programs are foundational to organism development and homeostasis. Transcription factors play a central role in establishing and maintaining these programs. Large-scale transcriptomic studies have generated parts lists of transcription factors. However, these descriptive works rarely formulate a cohesive model of how these transcription factors work together to support a functional organism. Mutations that affect transcription factor functions can lead to a broad range of human diseases. Therefore, it is crucial to understand the principles that transcription factors achieve spatial, temporal, and quantitative precision in their regulated gene expression programs. I have investigated transcriptional regulation in rod and …

Genetic Diversity Of 1,845 Rhesus Macaques Improves Genetic Variation Interpretation And Identifies Disease Models, Jun Wang, Meng Wang, Ala Moshiri, R Alan Harris, Muthuswamy Raveendran, Tracy Nguyen, Soohyun Kim, Laura Young, Keqing Wang, Roger Wiseman, David H O'Connor, Zach Johnson, Melween Martinez, Michael J Montague, Ken Sayers, Martha Lyke, Eric Vallender, Tim Stout, Yumei Li, Sara M Thomasy, Jeffrey Rogers, Rui Chen

Faculty, Staff and Students Publications

Understanding and treating human diseases require valid animal models. Leveraging the genetic diversity in rhesus macaque populations across eight primate centers in the United States, we conduct targeted-sequencing on 1845 individuals for 374 genes linked to inherited human retinal and neurodevelopmental diseases. We identify over 47,000 single nucleotide variants, a substantial proportion of which are shared with human populations. By combining rhesus and human allele frequencies with established variant prediction methods, we develop a machine learning-based score that outperforms established methods in predicting missense variant pathogenicity. Remarkably, we find a marked number of loss-of-function variants and putative deleterious variants, which …

Sexually Antagonistic Coevolution Of The Male Nuptial Gift And Female Feeding Behaviour In Decorated Crickets, Samuel Burns-Dunn, Tassie Mortys, Clarissa M. House, Christopher Mitchell, Kristin R. Duffield, Bert Foquet, Ben M. Sadd, Scott K. Sakaluk, John Hunt

Faculty Publications – Biological Sciences

The evolution of nuptial gifts has traditionally been considered a harmonious affair, providing benefits to both mating partners. There is growing evidence, however, that receiving a nuptial gift can be actively detrimental to the female. In decorated crickets (Gryllodes sigillatus), males produce a gelatinous spermatophylax that enhances sperm transfer but provides little nutritional benefit and hinders female post-copulatory mate choice. Here, we examine the sexually antagonistic coevolution of the spermatophylax and the female feeding response to this gift in G. sigillatus maintained in experimental populations with either a male-biased or female-biased adult sex ratio. After 25 generations, males …

High Sugar Diet Alters Immune Function And The Gut Microbiome In Juvenile Green Iguanas (Iguana Iguana), Kwanho C. Ki, Erin L. Lewis, Elizabeth Wu, Francis J. Oliaro, Lise M. Aubry, Charles R. Knapp, Karen M. Kapheim, Dale Denardo, Susannah S. French

Biology Faculty Publications

The present work aimed to study whether a high sugar diet can alter immune responses and the gut microbiome in green iguanas. Thirty-six iguanas were split into four treatment groups using a 2x2 design. Iguanas received either a sugar-supplemented diet or a control diet, and either a lipopolysaccharide (LPS) injection or a phosphate-buffered saline (PBS) injection. Iguanas were given their respective diet treatment through the entire study (~3 months) and received a primary immune challenge 1 and 2 months into the experiment. Blood samples and cloacal swabs were taken at various points in the experiment and used to measure changes …

How Will Climate Change-Induced Increases In Wildfire Frequency Affect Soil Microbial Communities?, Bahar Saadaie Jahromi, David Karowe

Waldo Library Student Exhibits

As climate change progresses, wildfires will become more common, increasing their impact on soil microbial ecosystems. This research examines how increased fire frequency affects soil microbial communities and whether effects differ for communities associated with different tree species. Soil samples were collected from under five individuals of four tree species within each of four 1-ha plots that had experienced fire from 24 to 111 years ago. Samples were analyzed for microbial DNA using next generation sequencing techniques in order to explore the influence of fire return interval and tree species on microbial diversity and community structure. Correlations were also examined …

The Influence Of Resource Patch Condition And Size On Social Interactions, Reproductive Behaviors, And Oviposition In A Fungivorous Beetle, Lillian J. Fornoff , '21, C. A. Stahlmann Roeder, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Variation among resource patches can structure spatial patterns of social behavior. Individual preferences and requirements for heterogeneous resources can lead to differences in where behaviors take place and which kinds of individuals interact. In this study we examined whether properties of habitat patches predict presence of and interactions among wild forked fungus beetles (Bolitotherus cornutus). B. cornutus use shelf-like fruiting bodies of wood decaying fungi (brackets) as social arenas, courtship and mating sites, oviposition locations, and food sources. Brackets on a single log vary in size and condition and represent a dynamic resource as individual brackets decay over …

Investigating The Antimicrobial Potential Of Bovine Lactoferrin Against The Neonatal Pathogen, Staphylococcus Capitis, Anna Desmond, Lesley Cotter, Des Field, Fiona O'Halloran

Department of Biological Sciences Publications

Lactoferrin is an antimicrobial glycoprotein that demonstrates a broad-spectrum of activity against a wide variety of clinical pathogens. This study investigated the potential of bovine lactoferrin (bLf) against multidrug resistant Staphylococcus capitis (S. capitis) strains. Growth curve analysis and time-kill curves demonstrated that at 750 µg ml−1 lactoferrin significantly inhibited (50.6%, P < 0.05) the growth of most isolates tested (90%), and this effect was based on a bacteriostatic mechanism. At the same concentration, bLf also significantly inhibited (30%, P < 0.05) biofilm formation in 40% of strains tested. Combinations of bLf with selected antibiotics were assessed for enhanced antimicrobial activity using growth curves. BLf combined with β-lactam antibiotics reduced the growth of S. capitis strains, however, the effects were not significant. BLf displays antimicrobial effects against multidrug resistant S. capitis isolates, but with strain-specific effects.

Ocular Gene Transfer In The Spotlight: Implications Of Newspaper Content For Clinical Communications, Shelly Benjaminy, Tania M. Bubela

Office of the Provost

Background: Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of …

A Timely Death Of The Tapetum Underlies More Floret1 (Mof1) Regulation Of Male Fertility In Rice, Janlo M. Robil

Biology Faculty Publications

No abstract provided.

Scientific Note: An Incursion Of The Widely-Cultivated Katsura (Cercidiphyllum Japonicum, Cercidiphyllaceae) In Pennsylvania, Kayleigh R. Long, Melody P. Sain, Elizabeth H. Williams, Christopher T. Martine

Faculty Journal Articles

Cercidiphyllum japonicum (katsura) is a dioecious tree native to China and Japan. Although imperiled in parts of its natural distribution, the species has become quite common as a cultivated tree in temperate North America. The species is noted as occasionally escaping cultivation in the eastern United States, but few records of established incursions (and the conditions under which they might recruit) exist in the literature. We here report an incursion of C. japonicum in central Pennsylvania, along with notes on seedling recruitment on the Bucknell University campus.

Effects Of Vitis Vinifera L. Seed Extract On Short-Term Memory Of Amyloid-Beta-Mediated Neurodegeneration In Transgenic Caenorhabditis Elegans, Elise Patrick

Theses

Alzheimer's disease (AD) is a neurodegenerative condition that is a common cause of dementia and a growing concern worldwide with no effective treatment or cure. Two pathological AD hallmarks include buildup of amyloid beta (Aβ) plaques and neurofibrillary tangles in the brain. Recent attention has turned to exploring natural products and compounds for AD symptom relief and treatment. Vitis vinifera grape seed extract (GSE) contains many beneficial substances. GSE has been tested in several animal models and has shown to improve memory and is even being examined in an AD treatment human clinical trial. In this study, the aim was …

Variation And Adaptation In Guppies And Gambusia, Alan L. Gillen, Anna Collins

Faculty Publications and Presentations

The guppy fish is considered by many to be a symbol of fertility, renewal, and growth. Gambusia are likely relatives of guppies and are known as mosquito fish because they largely prey on mosquito larvae. For a century, they have been used locally and globally in mosquito control. Guppies, Endler’s livebearers, and Gambusia are in the Poeciliidae family and freely interbreed in the wild. They are assumed to be in the same baramin or created kind. Their purpose in creation is often associated with harmony, balance, and abundance. It appears that the Poeciliidae family was designed with an array of …

Seagrass Ecosystem Recovery: Experimental Removal And Synthesis Of Disturbance Studies, Spencer J. Tassone, Carolyn J. Ewers Lewis, Karen J. Mcglathery, Michael L. Pace

Michigan Tech Publications

Net global losses of seagrasses have accelerated efforts to understand recovery from disturbances. Stressors causing disturbances (e.g., storms, heatwaves, boating) vary temporally and spatially within meadows potentially affecting recovery. To test differential recovery, we conducted a removal experiment at sites that differed in thermal stress for a temperate seagrass (Zostera marina). We also synthesized prior studies of seagrass recovery to assess general patterns. Seagrass shoots were removed from 28.3 m2 plots at edge and central sites of a meadow in South Bay, Virginia, USA. We hypothesized faster recovery for edge plots where greater oceanic exchange reduces thermal stress. Contrary to …

Development Of Anti-Fibrotic Agents For Potential Use In Glaucoma Filtration Surgery To Prevent Scar Formation, Nikhala Shree S

Theses and Dissertations

Glaucoma is the second leading cause of blindness with irreversible vision loss. It is marked by the degeneration of retinal ganglion cells, which results in optic nerve head damage. Intraocular pressure (IOP) is a prime risk factor of glaucoma controlled by various treatment regimens i.e., medication, laser, and/ or surgery. It is reported that longterm exposure to anti-glaucoma medications (AGM) may subtle the surgical success rate leading to postoperative fibrosis. Transforming growth factor beta (TGF-β) is a growth factor that plays an important role in the development of glaucoma and promotes fibrosis.

This study is aimed at developing peptides to …

Private Management Of African Protected Areas Improves Wildlife And Tourism Outcomes But With Security Concerns In Conflict Regions, Sean Denny, Gabriel Englander, Patrick Hunnicutt

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Protected areas can conserve wildlife and benefit people when managed effectively. African governments increasingly delegate the management of protected areas to private, nongovernmental organizations, hoping that private organizations’ significant resources and technical capacities actualize protected areas’ potential. Does private sector management improve outcomes compared to a counterfactual of government management? We leverage the transfer of management authority from governments to African Parks (AP)—the largest private manager of protected areas in Africa—to show that private management significantly improves wildlife outcomes via reduced elephant poaching and increased bird abundances. Our results also suggest that AP’s management augments tourism, while the effect on …

Uncovering Over 150 Years Of Herbarium Specimen Data To Examine The Impacts Of Climate Change On Alpine Plant Phenology In The Southern Rocky Mountains, Erin Berkowitz

Museum Studies Theses

Due to generalized botanical collecting practices, herbarium specimens provide important long term data dating back hundreds of years. The historical data preserved in herbaria can be used to study biological responses to climate change, such as changes in plant phenology, across various habitats including understudied alpine ecosystems. This study will use historical data from over one hundred years of plant collecting, along with updated collecting and community science efforts, to investigate how climate change is influencing alpine plant phenology in the Southern Rocky Mountains. These records will be analyzed alongside historical climate data to explore phenological sensitivities to climate change, …

Elucidation Of Potential Antimicrobial Properties Of Chalcones, Caleb Howell

Theses

The rise of antibiotic-resistant bacteria is a growing concern for the medical and biological community. Increased use of antibiotics has led to increased development of bacterial tolerances. This phenomenon, driven by the principles of evolution, has been exacerbated by the improper antibiotic use of these antibiotics. Often, individuals stop taking antibiotics once symptoms subside, mistakenly believing the infection is cured. This practice allows bacteria or fungi to develop resistance.

These antibiotics have been developed from secondary metabolites. While we have many effective antibiotics we are facing new threats. Chalcones are being looked at for their potential in addressing this issue. …

The Role Of Obesity In The Development Of Disordered Breathing, Sarah N. Framnes-Deboer

Master's Theses (2009 -)

Obesity is a complex disease that is defined by an excess amount of body fat. Obesity can have physical, neurological, and endocrine effects and detrimental effects on health. Some obese co-morbid conditions, such as type 2 diabetes have known mechanisms, while others, such as sleep disordered breathing do not. Moreover, there are common respiratory diseases associated with obesity, such as obstructive sleep apnea and obesity hypoventilation syndrome. Furthermore, individuals with obesity or obstructive sleep apnea have a blunted hypercapnic ventilatory response (HCVR) (120), which is indicative of impaired chemosensitivity, as HCVR is a measure of how well an individual responds …

Natural Variation In Yeast Reveals Multiple Paths For Acquiring Higher Stress Resistance, Amanda N. Scholes, Tara N. Stuecker, Stephanie E. Hood, Cader J. Locke, Carson L. Stacy, Qingyang Zhang, Jeffrey A. Lewis

Biological Sciences Faculty Publications and Presentations

Background

Organisms frequently experience environmental stresses that occur in predictable patterns and combinations. For wild Saccharomyces cerevisiae yeast growing in natural environments, cells may experience high osmotic stress when they first enter broken fruit, followed by high ethanol levels during fermentation, and then finally high levels of oxidative stress resulting from respiration of ethanol. Yeast have adapted to these patterns by evolving sophisticated “cross protection” mechanisms, where mild ‘primary’ doses of one stress can enhance tolerance to severe doses of a different ‘secondary’ stress. For example, in many yeast strains, mild osmotic or mild ethanol stresses cross protect against severe …

Osteopathic Manipulative Therapy: An Effective Alternative To Common Pharmacological Treatments For Low Back Pain, Nicole Shirman

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Osteopathic manipulative therapy (OMT) is a promising non-pharmacological treatment for low back pain, but its efficacy and mechanisms have been debated. This literature review provides a comprehensive assessment of OMT’s therapeutic effects and potential mechanisms for the treatment of low back pain. Multiple randomized trials demonstrate OMT provides statistically and clinically meaningful reductions in pain intensity and disability compared to sham treatments or standard care, particularly among patients with higher baseline symptom severity. Subgroup analyses reveal older age and absence of depression enhance OMT response rates. OMT appears safe and well-tolerated, with high patient satisfaction and reduced analgesic requirements versus …

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

A Careful Examination Of The Parameters Impacting The Study Of Plant/Bacteria Interactions, Caroline Victoria Royals

Theses and Dissertations

Our laboratory has been studying how different Caulobacter strains impact Arabidopsis plant growth. While reading papers published by other laboratories, I noticed inconsistencies in the methods used by different plant/bacteria interaction studies. For example, a variety of different variables have been used for defining a bacterium as Plant Growth Promoting (PGP). To establish a baseline, I conducted longitudinal studies that examined the impact of bacteria on all phases of a plant’s life. I found that individual Caulobacter wild type strains impact different aspects of plant growth. In addition, I continuously encountered problems with within and between pot variation in plant …

Evidence Of Lactobacillus Strains Shared Between The Female Urinary And Vaginal Microbiota, Haley Atkins, Baani Sabharwal, Leah Boger, Natalie Stegman, Alexander Kula, Alan J. Wolfe, Swarnali Banerjee, Catherine Putonti

Biology: Faculty Publications and Other Works

Lactobacillus species are common inhabitants of the ‘healthy’ female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the …

Draft Genome Sequences For A Staphylococcus Aureus And A Staphylococcus Haemolyticus Isolate From Nasal Swab Samples From Healthy Females, Sandra Jablonska, Hannah Brown, Helen Appleberry, Catherine Putonti, Alex Kula

Biology: Faculty Publications and Other Works

Staphylococcus aureus and Staphylococcus haemolyticus are common members of the human microbiota, but they are also opportunistic pathogens. To identify antibiotic resistance in healthy individuals, we present the genome sequences of S. aureus 139 N-1 and S. haemolyticus 173 N-3, both isolated from nasal swab samples from asymptomatic female participants.

Accessory Eyes And Dynamic Color Change In Palaemon Vulgaris, Nicholas Raymond Steichmann

Theses and Dissertations

Eyes are physiologically costly organs to produce and maintain, making the development of secondary eyes intriguing. Caridean shrimp possess reflecting superposition primary eyes, but some species across fourteen families possess an additional pair of eyes called accessory eyes along the dorso-posterior margin of the primary eyes. Secondary eyes are found in lizards, lampreys, and insects, where they often function as illumination detectors. Some shrimps may use accessory eyes to signal endocrine organs in their eyestalks to alter the pigmentation of their carapace providing better camouflage through disruptive coloration. To investigate the role of accessory eyes in dynamic color change we …

Time-Restricted Feeding Reveals A Role For Neural Respiratory Clocks In Optimizing Daily Ventilatory-Metabolic Coupling In Mice, Aaron A. Jones, Gabriella M. Marino, Deanna M. Arble

Biological Sciences Faculty Research and Publications

The master circadian clock, located in the suprachiasmatic nuclei (SCN), organizes the daily rhythm in minute ventilation (V̇e). However, the extent that the daily rhythm in V̇e is secondary to SCN-imposed O2 and CO2 cycles (i.e., metabolic rate) or driven by other clock mechanisms remains unknown. Here, we experimentally shifted metabolic rate using time-restricted feeding (without affecting light-induced synchronization of the SCN) to determine the influence of metabolic rate in orchestrating the daily V̇e rhythm. Mice eating predominantly at night exhibited robust daily rhythms in O2 consumption (V̇o2), CO2 production (V̇co2), and V̇e with similar peak times (approximately ZT18) that …

Isolation Of Naegleria Lustrarea N. Sp. (Excavata, Discoba, Heterolobosea) From The Feces Of Ambystoma Annulatum (Ringed Salamander) In Northwest Arkansas, Brian M. Becker, Idan Banson, James M. Walker, Anant Deshwal, Matthew W. Brown, Jeffrey D. Silberman

Biological Sciences Faculty Publications and Presentations

The salamander, Ambystoma annulatum, is considered a “species of special concern” in the state of Arkansas, USA, due to its limited geographic range, specialized habitat requirements and low population size. Although metazoan parasites have been documented in this salamander species, neither its native protists nor microbiome have yet been evaluated. This is likely due to the elusive nature and under-sampling of the animal. Here, we initiate the cataloguing of microbial associates with the identification of a new heterlobosean species, Naegleria lustrarea n. sp. (Excavata, Discoba, Heterolobosea), isolated from feces of an adult A. annulatum.

Subspecialty Choices Among Medicine-Pediatrics Graduates: Results From A Four-Year National Program Director Survey, Anoop Agrawal, Daniel Wells, Michael Kisielewski, Savita Misra, Benjamin Doolittle

Faculty, Staff and Students Publications

Background and objectives Dual-trained medicine-pediatrics physicians (med-peds) play an important role in the healthcare ecosystem. Little is known about the subspecialty choices of med-peds residency graduates. This study aims to characterize the subspecialty choices of med-peds residency graduates. Methods The Medicine-Pediatrics Program Directors Association (MPPDA) administers an annual survey to the program directors of all med-peds residency programs accredited by the Accreditation Council for Graduate Medical Education (ACGME). This project represents aggregate survey data from 2020-2023. Results The number of program directors responding to the survey ranged from 80.8% (63/78) to 85.7% (66/77; mean response rate: 82.8%). About 465 of …