Digital Commons Network^™

Abundance And Demography Of The Wood Turtle (Glyptemys Insculpta) Across Two River Systems In Michigan’S Lower Peninsula, Marianne Kelso

Masters Theses

Turtles worldwide are declining from habitat loss and fragmentation, predation, and illegal collection, and their slow life histories and sensitivity to environmental change make reliable abundance and demographic data critical for conservation. Wood turtles (Glyptemys insculpta) are declining across much of their range, yet baseline information is lacking in Michigan’s Lower Peninsula. To fill that gap, we performed standardized visual mark–recapture surveys at 27 one-kilometer river reaches in two distinct watershed systems during springs of 2022 and 2023. Using hierarchical N-mixture models with negative binomial mixtures to account for imperfect detection, we estimated site-level latent abundance and evaluated …

Dna Double-Stranded Breaks, A Hallmark Of Aging, Defined At The Nucleotide Resolution, Are Increased And Associated With Transcription In The Cardiac Myocytes In Lmna-Cardiomyopathy, Benjamin Cathcart, Sirisha M Cheedipudi, Leila Rouhi, Zhongming Zhao, Priyatansh Gurha, Ali J Marian

Faculty, Staff and Student Publications

Aims: An intrinsic feature of gene transcription is the formation of DNA superhelices near the transcription bubble, which are resolved upon induction of transient double-stranded breaks (DSBs) by topoisomerases. Unrepaired DSBs are pathogenic as they lead to cell cycle arrest, senescence, inflammation, and organ dysfunction. We posit that DSBs would be more prevalent at the genomic sites that are associated with gene expression. The objectives were to identify and characterize genome-wide DSBs at the nucleotide resolution and determine the association of DSBs with transcription in cardiac myocytes.

Methods and results: We identified the genome-wide DSBs in ∼1 million cardiac myocytes …

Dairy And Food Science Student Newsletter, August 28, 2025, Department Of Dairy And Food Science

Dairy and Food Science Student Newsletter

No abstract provided.

An Antioxidant Approach To Ameliorate The Effects Of Radiation And Chemotherapy On Cognition, Raymond Anan Otoo

Theses and Dissertations

Acute Lymphoblastic Leukemia (ALL) is a hematologic malignancy that primarily affects children and young adults. While advancements in treatment—including chemotherapy and cranial irradiation—have significantly improved 5-year survival rates in children to nearly 90%, radiation-induced cognitive impairment (RICI) remains a persistent and debilitating side effect. The brain, particularly the hippocampus, is highly susceptible to radiation-induced oxidative stress and inflammation. In the treatment of ALL, the combined use of chemotherapy and radiotherapy contributes to a heightened oxidative burden, exacerbating the risk of cognitive dysfunction. Although previous studies have linked radiation exposure to neurocognitive decline, the molecular mechanisms underlying RICI and chemotherapy-induced cognitive …

Adams Contribute To Triple Negative Breast Cancer Via Mtorc1 Pathway: Targeting Adam-Mtor Axis Improves Efficacy, Shuying Liu, Huiqin Chen, Mihai Gagea, Lorenzo Federico, Fan Zhang, Javier Gomez, Kim-Anh Do, William F Symmans, Gabriel N Hortobagyi, Gordon B Mills, Ana M Gonzalez-Angulo, Debasish Tripathy

Faculty, Staff and Student Publications

Breast cancer is the most frequently diagnosed cancer globally and the second leading cause of cancer-related deaths in American women. Triple-negative breast cancer (TNBC) lacks estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Thus, fewer targeting therapies are available for this most aggressive subtype. The A Disintegrin and Metalloproteinase (ADAM) family plays a vital role in cancer pathophysiology. Previous studies focused on single ADAM members. However, none of these have entered into the clinical arena as diagnostics or therapeutics for breast cancer. In this study, we demonstrate the upregulation of a panel of ADAM members in TNBC, …

Rna Sequencing-Based Transcriptome Analysis Of Liver In Laying Hens Supplemented With Dietary Probiotic Bacillus Species And Prebiotic Yeast (Saccharomyces Cerevisiae) Cell Walls, Ala E. Abudabos, Zafar M. Hakami, Ali R. Al Sulaiman, Riyadh S. Aljumaah, Valentino Palombo, Mashael R. Aljumaah, Mariasilvia D’Andrea, Abdulrahman S. Alharthi, Rashed A. Alhotan

Food and Animal Sciences Faculty Research

To investigate the impacts of dietary Bacillus-based probiotics and yeast-derived prebiotics on the hepatic transcriptome profile, 500 Hisex White laying hens were randomly allotted into five dietary treatments from 37 to 52 weeks of age: control; control + Bacillus subtilis; control + Bacillus subtilis and Bacillus licheniformis; control + Bacillus coagulans; and control + Saccharomyces cerevisiae yeast cell wall. Transcriptome analysis revealed a substantial number of differentially expressed genes exclusively between the control and prebiotic groups, identifying 2221 genes (FDR ≤ 0.05), with 980 genes upregulated (log2 fold change 0.69 to 24.62) and 1241 downregulated (log2 fold change −0.74 to …

Fragments Of A Crusader-Period Chancel Screen From ‘Akko, The Knights’ Hotel Site, Vardit R. Shotten-Hallel

'Atiqot

The phrase ‘where [or: when] least expected’ is rarely used in archaeology. In fact, when excavating a cesspit, the opposite is often true. Cesspits are precisely where archaeologists expect to uncover hoards of household artifacts, like pottery and glass, or sometimes valuables, dislocated sculptures and even skeletons. In this regard, the excavation at the Knights’ Hotel site in ‘Akko is no exception. Four richly decorated marble fragments were found in a cesspit, integrated in the shaft’s wall as part of repair work. A stylistic analysis, and consideration of the historical context of their deposition, revealed an unexpected possibility regarding their …

The Metal Finds From ‘Akko, The Knights’ Hotel Site, Joppe Gosker

'Atiqot

The 2007 excavation at the Knights Hotel Site yielded about 170 metal finds, mostly iron or copper alloy, though silver and gilded items were also found. Some objects associated with warfare may have been linked to the final battle of ‘Akko in 1291 CE, but most of the finds relate to daily life, encompassing activities such as horse keeping, dress, foodways, medicine and construction. The dominance of Eastern-type arrowheads indicates that local traditions were sometimes adopted, certainly for the arrows if not the bows. Concerning dress accessories, the overall impression is of European traditions. It seems that the Franks preferred …

Crusader-Period Ceramics From The Knights’ Hotel Site, ‘Akko, Edna J. Stern, Nohar Shahar

'Atiqot

The Crusader-period ceramic assemblage unearthed in the Knights’ Hotel site in ‘Akko contains a large variety of daily wares. The assemblage consists of local and imported wares from various regions, some of which were identified through petrographic analysis. The imported wares indicate trade connections with Mediterranean port cities, and the petrographic analysis identified a new group of vessels from Egypt’s northern Nile region. The article outlines the pottery typology and quantification, and presents the ceramic distribution within the excavated urban area. The findings indicate changes in land use, as some residential and commercial areas were converted into dumps and cesspits. …

Daily Life And Industry In Crusader ‘Akko: The Knights’ Hotel Site, Danny Syon

'Atiqot

This report details the second season of excavations at the Knights’ Hotel site, carried out in 2007, covering three areas (A–C) not excavated in the first season (1995). The excavations revealed domestic and public(?) architecture dating from the thirteenth century CE. The architectural features are mostly similar to the ones exposed in the first season and include an abundance of water and sanitary installations: cisterns, wells and cesspits. The mixed character of this neighborhood of the capital of the Crusader kingdom of Jerusalem, and the daily life of its residents is highlighted by the wealth of pottery and glass vessels …

Remains Of Two Iron Age Iib–C(?) Updraft Pottery Kilns At The Foot Of Tel Gamma (Tell Jemma), Davida Eisenberg-Degen, Ilana Peters, Svetlana Talis, Yael Abadi-Reiss, Emily Bischoff Bruintjes, Yotam Asscher

'Atiqot

An excavation southwest of Tel Gamma exposed two Iron Age II updraft pottery kilns and a refuse pit. The eastern kiln was only partially preserved; its fill contained workshop debris and storage-jar wasters. The better-preserved western kiln retained an almost intact, elongated combustion chamber with two sets of mud-brick flues and evidence of periodic upkeep. An activity layer was identified between and around the kilns, from which a mixed Iron IIA–C ceramic assemblage and a few stone artifacts were collected. The stone artifacts likely served in fine grinding and burnishing. In the refuse pit, potsherds, vitrified bricks, animal bones and …

A Middle Bronze Iia Pottery Production Site On The Northern Bank Of NaḥAl Soreq, Near Yavne-Yam, Lily Singer-Avitz, Yossi Levy, Etan Ayalon

'Atiqot

A Middle Bronze Age IIA pottery production site was uncovered on the northern bank of Naḥal Soreq, near Yavne-Yam. Excavations revealed installations, including pits, an oven, a stone pavement and a two-story pottery kiln. The discovery of a potter’s wheel and petrographic analysis confirm local ceramic production using nearby ḥamra and kurkar materials. Stone anchors found on-site suggest the transport of vessels via small boats along the stream, connecting the site with nearby settlements such as Nabi Rubin and Yavne-Yam.

The Faunal Assemblage From Nahal Rimmonim, An Intermediate And Middle Bronze Age Site In The Jezreel Valley, Zohar Turgeman-Yaffe

'Atiqot

The rural site of Naḥal Rimmonim yielded 421 identifiable animal bones that originated in well-stratified loci from five strata dating to the Intermediate and Middle Bronze Ages. The site’s economy seems to have been independent, or production-based, with residents providing most of their own needs while also trading with other groups. The economy was based on animal husbandry, with some hunting, mostly of gazelles, alongside the production of secondary products, such as milk, wool and labor, with a preference for wool. Pigs were the most common species in all domestic levels, including a unique pig burial. The faunal assemblage from …

Nahal Rimmonim: An Intermediate–Middle Bronze Age Village And Pottery Workshop In The Jezreel Valley, Karen Covello-Paran, Yotam Tepper

'Atiqot

The excavations at Naḥal Rimmonim exposed a stratified rural settlement spanning the Intermediate and Middle Bronze Age III. Stratified remains—including domestic structures, installations, a pottery workshop and burials—demonstrate diachronic shifts in site function and organization. The Intermediate Bronze Age strata exhibit substantial domestic activity with evidence of localized adaptation to marshy conditions. In the Middle Bronze Age I–II phases, a specialized potters’ workshop and later domestic structures highlight evolving intrasite spatial planning and craft production, likely tied to economic interactions with nearby Tel Megiddo. Elite tombs with prestige goods from the Middle Bronze Age III, signal socioeconomic ties to urban …

Secondary Use Of Textiles For Wick Production In Light Of The Finds From The Intermediate Bronze Age Cemetery At Newe Efrayim, Naama Sukenik, Yonah Maor, Yaniv Agmon, Yossi Elisha, Gilad Itach

'Atiqot

Three Intermediate Bronze Age wicks discovered in the Newe Efrayim cemetery constitute some of the earliest known archaeological evidence of wick use, an essential object for lighting, yet lacking distinctive features, as it was intended to be burned, making it a rare find. The exceptional preservation of the wicks sheds light on both preservation issues and the technological aspects of wick production in antiquity. The wicks were made from textiles, indicating the maximal reuse of a valuable raw material after it had served its original purpose. These finds offer evidence of material recycling in the ancient world. It is likely …

Researching Chalcolithic Ivories From The Southern Levant: Craft Items For Ritual, Prestige And Exchange, Harel Shochat, Liora Kolska Horwitz, Avishay Levi-Hevroni, Martin D. Pasternak, Pablo Betzer, Daniel Varga, Yael Abadi-Reiss, Olga Negnevitsky, Ilan Naor, Ianir Milevski

'Atiqot

The Late Chalcolithic period in the Southern Levant, mainly the Ghassulian culture (mid-fifth–mid-fourth millennia BCE), heralded a new and unique trajectory in craft specialization, with ivory objects, including figurines, tools and vessels, among the outstanding ones. Hippopotamus and elephant ivory, probably of varied geographic provenience, were the raw materials employed. This paper presents two recently excavated ivory caches from the Late Chalcolithic sites of Ḥorbat Raqiq and Yavne (East), and reviews Chalcolithic ivories from this region. Additionally, a systematic microscopic analysis to determine the taxonomic identification of raw material and typological classification of each artifact is presented, offering novel perspectives …

Data For Recreation Effects On Soil Carbon, Biocrust, Soil Stability, And Invasives In Indian Creek, Bears Ears National Monument, Elisabeth M. Currit, Tara B. Bishop, April Hulet, Nathan Allen Currit, Teresa Gomez, Nathan T. Thompson, Shannon Lambson, Heidi Jean Wilding Mann, Evan Miller, Erin Jones, Alexandra Olson, Katherine A. Anselmi, Meredith Murdock, Ella Reid, Kirsten Steele, Indy Lawrence, Neil Hansen

ScholarsArchive Data

This data is about how different types of recreation impact different soil and vegetation properties related to soil carbon in Indian Creek, Bears Ears National Monument. The data was collected from May 2023 to October 2023. It contains plant functional group cover, biocrust cover and type, soil stability, and compaction data for each individual site. There are 5-7 of each site type: camping, foot trails, and motorized offroading trails, and undisturbed sites, with a total of 30 sites. It also contains the code used to analyze the raw data and the figures created.

Suppression Of Cardiac Allograft Vasculopathy By A Macrophage Efferocytosis Receptor, Sahil Shah, Aparnaa Ananthakrishnan, Matthew Deberge, Kristofor Glinton, Rebecca T L Jones, Mallory Filipp, Ivana Shen, Joey Lockhart, Connor W Lantz, Edward B Thorp

Faculty, Staff and Student Publications

Cardiac allograft vasculopathy remains a major cause of late morbidity following heart transplantation. While accumulating evidence implicates innate macrophages in the inflammatory progression of CAV, the underlying mechanisms remain incompletely understood. In murine models of CAV, we identified proteolytic cleavage of MERTK, a key anti-inflammatory receptor on macrophages, as a contributing factor to CAV progression. In a model of CAV, MERTK deficiency accelerated allograft rejection and increased intimal leukocyte infiltration. In contrast, mice expressing a genetically cleavage-resistant form of MERTK (MertkCR/CR) exhibited prolonged graft survival, reduced intimal thickening, diminished immune cell infiltration, and decreased circulating effector T cells. …

The Role Of Recruited Adipose Stromal Cells And Their Fibroblastic Differentiation In Cancer, Lingyi Cai, Mikhail G Kolonin, Dimitris Anastassiou

Faculty, Staff and Student Publications

Adipose stromal cells (ASCs) are perivascular mesenchymal progenitors of adipose tissue. In cancer patients, ASCs can mobilize and migrate to the tumor, where they subsequently play an important role in cancer progression. This biological process involves the conversion of recruited ASCs into cancer-associated fibroblasts (CAFs). ASC-derived CAFs influence the tumor microenvironment through extracellular matrix remodeling, vascularization, and immunomodulation. These and other processes mediated by secreted paracrine factors also affect gene expression in carcinoma cells to promote the epithelial-mesenchymal transition (EMT), metabolic adaptation, survival, and invasiveness of cancer cells. ASC-derived CAFs can enhance tumor aggressiveness, accounting in part for the link …

Artificial Intelligence In Ocular Transcriptomics: Applications Of Unsupervised And Supervised Learning, Catherine Lalman, Yimin Yang, Janice L. Walker

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Transcriptomic profiling is a powerful tool for dissecting the cellular and molecular complexity of ocular tissues, providing insights into retinal development, corneal disease, macular degeneration, and glaucoma. With the expansion of microarray, bulk RNA sequencing (RNA-seq), and single-cell RNA-seq technologies, artificial intelligence (AI) has emerged as a key strategy for analyzing high-dimensional gene expression data. This review synthesizes AI-enabled transcriptomic studies in ophthalmology from 2019 to 2025, highlighting how supervised and unsupervised machine learning (ML) methods have advanced biomarker discovery, cell type classification, and eye development and ocular disease modeling. Here, we discuss unsupervised techniques, such as principal component analysis …

Effects Of Cryoprotective And Mitochondrial Stabilizing Agents On Vitrified Bovine Oocytes, Allison Hoang

LSU Master's Theses

Oocyte vitrification success is highly dependent on cryoprotectant agent (CPA) choice as well as possible additives that could help preserve mitochondrial membrane potential (mMP), reactive oxygen species (ROS) production, and calcium homeostasis within the cell. It is a delicate balance between levels needed for proper oocyte function and activation and levels needed to induce apoptotic pathways. The results of oocyte cryopreservation determine the eventual oocyte viability and subsequent fertilization and embryo development.

In this study potential permeating cryoprotectant combinations were explored such as ethylene glycol (EG) and propylene glycol (PG) or EG in combination with dimethyl sulfoxide (DMSO). Also, the …

Cathartocytosis: Jettisoning Of Cellular Material During Reprogramming Of Differentiated Cells, Jeffrey W Brown, Xiaobo Lin, Gabriel Anthony Nicolazzi, Xuemei Liu, Thanh Nguyen, Megan D Radyk, Joseph Burclaff, Jason C Mills

Faculty, Staff and Students Publications

Injury causes differentiated cells to undergo massive reprogramming to become proliferative and repair tissue via paligenosis. Gastric chief cells use paligenosis to reprogram into progenitor-like spasmolytic-polypeptide-expressing metaplasia (SPEM) cells. Stage 1 of paligenosis is the downscaling of mature cell architecture via a process involving lysosomes. Here, we notice that sulfated glycoproteins are not only digested during paligenosis but also excreted into the gland. Various genetic and pharmacological approaches show that endoplasmic reticulum membranes and secretory granule cargo are also excreted and that the process proceeds in parallel with but is mechanistically independent of autophagy. Three-dimensional light and electron microscopy demonstrated …

Identification, Abundance, And Behavior Of North American Bobcat (Lynx Rufus) Along Road Mitigation Structures Designed For Endangered Species In South Texas, Victoria Hanley, Kevin W. Ryer, Md. Saydur Rahman, John H. Young Jr., Richard J. Kline

School of Integrative Biological & Chemical Sciences Faculty Publications

Endangered species are increasingly used as the target species in implementing and constructing new wildlife crossing structures (WCS). Highways in South Texas fragment the landscape and result in high road mortality for endangered species such as ocelots (Leopardus pardalis, a medium-sized spotted wild cat). In response, the Texas Department of Transportation constructed nine WCS on Farm-to-Market 106 (FM 106), a road which bisects Laguna Atascosa National Wildlife Refuge in Cameron County, Texas. With ocelots being rare and elusive, bobcats (Lynx rufus) are often used as a surrogate species to study felid behavior at road mitigation structures …

A Mini Review On Rodent Models Of Autism Spectrum Disorder (Asd), Rachel Zeller

Research from the Berry Summer Thesis Institute, 2025

Autism spectrum disorder (ASD) is a neurodevelopmental disorder typically diagnosed at a young age. ASD symptoms include deficits in social behavior, repetitive and restrictive behaviors, anxiety, as well as alterations in sensory gating and sensitivity, learning, memory, and attention performance. Since ASD emerges from a combination of genetic and environmental factors, clinical treatment of these conditions presents with challenges. Being able to model behavioral and neurobiological aspects of this disorder at the preclinical level using rodents allows for further investigation of the pathophysiological basis of this disorder. This mini review will focus on selected genetic and pharmacological rodent models of …

Evaluating The Environmental Determinants Of Tadpole Mouthpart Deformities, Nicholas J. Canfield

Research from the Berry Summer Thesis Institute, 2025

Amphibians are among the most threatened group of animals on the planet, with over 40% of living species facing an extinction risk. These organisms are highly sensitive to environmental change due to their highly permeable skin and complex life cycle that exposes them to stressors in both aquatic and terrestrial ecosystems. Amphibian populations that are closely monitored can serve as valuable bioindicators of environmental health because they typically respond rapidly to habitat degradation, decreased water quality, and changes in climate. Tadpoles in particular may act as a “canary in a coal mine” for aquatic ecosystems because they easily develop anatomical …

A Comparison Of Diving Behavior Of Goose-Beaked And Dense-Beaked Whales From Tagging Studies In Multiple Ocean Basins, Jay Barlow, Robin W. Baird, Janelle Badger, Gregory S. Schorr, Erin A. Falcone, Shannon N. Coates, Peter L. Tyack, Andrew J. Read, Leigh S. Hickmott, John W. Durban, Diane Claridge, Natacha Aguilar De Soto, Daniel Miranda Gonzalez, Fleur Visser, Machiel G. Oudejans, Stacy L. De Ruiter, David A. Sweeney, Brenda K. Rone, Stephanie L. Watwood

University Faculty Publications and Creative Works

Studies of cetacean diving behavior in multiple locations in different ocean basins allow for an assessment of variability within and among populations. We examine foraging dive behaviors of goose-beaked whales (Ziphius cavirostris) and dense-beaked whales (Mesoplodon densirostris) using data from 132 tagged whales in seven locations in the Pacific and Atlantic Oceans and the Mediterranean Sea. Acoustic recording tags are used to identify foraging dives by the presence of echolocation. For other tag types, foraging dives are identified based on maximum dive depth. Five parameters are used to characterize foraging dives: maximum dive depth, foraging dive duration, dive cycle duration, …

Advancing Rfid Systems: From Head Orientation To Robotic Localization Using Passive Tags, Guilherme Ricardo Mendes Da Silva Barreto De Figueiredo

Doctoral Dissertations

No abstract provided.

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Host, Microbiome, And Parasite: How Apicomplexan Microorganisms Interact With Gut Microbiota, Senia Bu, Andrew T. Ozga

Mako: NSU Undergraduate Student Journal

The gut microbiome, a complex ecosystem of microorganisms residing in the human gastrointestinal tract, plays a crucial role in maintaining overall health. It functions in immune system regulation, digestion, and protection against pathogens. Apicomplexan parasites, such as Toxoplasma gondii, Plasmodium spp., and Cryptosporidium spp., are major pathogens that can significantly disrupt the gut microbiota, leading to alterations in microbial composition and function. This review explores the bidirectional interactions between Apicomplexan parasites and the gut microbiome, focusing on how these parasites influence microbial diversity, immune responses, and host metabolism. It examines the mechanisms by which infection-induced inflammation, altered …

Monitoring The Developmental Stages Of Calendula Officinalis L. Nutrients Efficacy Under Hot Weather Mitigation Through Nutrients In Haripur, Pakistan, Waseem Ahmed, Rafia Azmat, Shah Masaud Khan, Abdul Qayyum, Waseem Hassan, Adnan Noor Shah, Muhammad Hadi Abbas, Fatima M. Abbas, Tahani A.Y. Asseri, Ahmet Hakan Ürüşan

Turkish Journal of Agriculture and Forestry

This study examines the effect of different doses of N and P fertilizer on Calendula officinalis L. (marigold) during the hot weather in summer (May–July) in Pakistan. The aim was to determine whether fertilization can help minimize the impacts of climate change. During the summer peak seasons (May, June, and July), the trial was conducted in potted plants with different N and P application levels to monitor the quality and quantity of C. officinalis. The results showed that the interactive effects (N × P) gave higher values for plant height, number of leaves, fresh weight, leaf length, and number of …