Life Sciences Commons^™

Deep Learning-Enabled Breast Cancer Endocrine Response Determination From H&E Staining Based On Esr1 Signaling Activity, Chun Wai Ng, Kwong-Kwok Wong

Faculty, Staff and Student Publications

Estrogen receptor (ER) positivity by immunohistochemistry has long been a main selection criterium for breast cancer patients to be treated with endocrine therapy. However, ER positivity might not directly correlate with activated ER signaling activity, which is a better predictor for endocrine therapy responsiveness. In this study, we investigated if a deep learning method using whole-slide H&E-stained images could predict ER signaling activity. First, ER signaling activity score was determined using RNAseq data available from each of the 1082 breast cancer samples in the TCGA Pan-Cancer dataset based on the Hallmark Estrogen Response Early gene set from the Molecular Signature …

Microplastics, Macro-Problems: Abundance Of Man-Made Materials In The Waters And Sediments Of Florida State Parks, Luciana M. Banquero, Kate Mclendon, Andres Alatorre, Mackenzie Daniels, Savanna Freeman, Cassidy Starke, Katherine Harris, Sidney J. Busch

The Pegasus Review: UCF Undergraduate Research Journal

Man-made materials (MMM) are pollutants introduced to the environment by human activity. Microplastics (MP) are a type of MMM that threaten living organisms through bioaccumulation. The term MMM also encompasses pollutants produced from natural materials, such as rayon and microfibrillated cellulose, which are used in food packaging. This study aims to determine the extent of MMM pollution within estuaries in two of Florida’s state parks, as well as the effectiveness of using restored vegetation on shorelines to reduce MMM pollution. Tomoka State Park and Gamble Rogers State Park were selected at the request of the Florida Department of Environmental Protection. …

Determining The Extent Of Pioneer Mangrove Acidification On Intertidal Oyster Reefs, Cindy Whitten, Andres Alatorre, Nicole Campbell, Savanna Freeman, Sydney Henderson, Kate Mclendon, Connor Wright, June Davison, Madison Ganci, Katherine Harris

The Pegasus Review: UCF Undergraduate Research Journal

The Indian River Lagoon (IRL) stretches 251 kilometers along Florida’s east coast and is one of the most biodiverse estuaries in North America. Mosquito Lagoon, the northernmost portion of the IRL, is home to mangroves and intertidal oyster reefs that provide numerous ecosystem services. These two habitats are overlapping as climate change drives mangroves poleward. Scientists have documented mangrove expansion and the transition of oyster reef habitat to mangrove islands. Past studies have shown large, adult mangrove stands drive soil acidification. The goal of this study was to understand if stand-alone, or pioneer, Rhizophora mangle (red mangroves) and Avicennia germinans …

Hypothesis And Theory: Do Trees "Release The Tension" In Rainwater? Surface Tension Reduction In Throughfall And Stemflow From Urban Trees, Benjamin J. Noren, Nicholas R. Lewis, Kelly Cristina Tonello, Anna Ilek, John T. Van Stan Ii

Biological, Geological, and Environmental Faculty Publications

Knowledge of the processes and impacts associated with the canopy's partitioning of rainfall into stemflow (water that drains to the base of tree stems) and throughfall (water that drips through gaps and from canopy surfaces) has expanded in recent years. However, the effect of canopy interactions on the fundamental physical properties of rainwater as it travels through the canopy to the soil, particularly surface tension, remains understudied. To discuss specific hypotheses within this context and their relevance to ecohydrological theory, the surface tension of rainwater samples was examined directly. Over a period of 9 months, open rainwater, throughfall and stemflow …

Oregon State Rank Assessment For Klamath Smallscale Sucker (Catostomus Rimiculus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Klamath smallscale sucker (Catostomus rimiculus) using NatureServe methodology, 2023.

Psammocora Stellata Distribution At Devil's Crown, Floreana Island, Galápagos Islands, Ecuador, María José Guarderas Sevilla

All HCAS Student Capstones, Theses, and Dissertations

In the Galápagos Archipelago, the free-living nodular coral Psammocora stellata is a common species that does not form reef structures. However, it is a key component of the ecosystem by increasing habitat complexity and, consequently, species diversity. This species experienced a drastic decline in Devil’s Crown channel, Floreana Island, where it disappeared after the 1982-83 El Niño-Southern Oscillation, presumably by displacement of unattached colonies by strong surface waves and currents. This assemblage has now recovered to pre-impact levels. A combination of underwater photoquadrats from 2007 and 2009 and recent (2023) orthomosaics were used to determine changes in coral densities and …

Mitochondrial Gtp Metabolism Controls Reproductive Aging In C. Elegans, Yi-Tang Lee, Marzia Savini, Tao Chen, Yang, Jin, Qian Zhao, Lang Ding, Shihong Max Gao, Jessica N. Sowa, Jue D. Wang, Meng C. Wang

Biology Faculty Publications

Healthy mitochondria are critical for reproduction. During aging, both reproductive fitness and mitochondrial homeostasis decline. Mitochondrial metabolism and dynamics are key factors in supporting mitochondrial homeostasis. However, how they are coupled to control reproductive health remains unclear. We report that mitochondrial GTP (mtGTP) metabolism acts through mitochondrial dynamics factors to regulate reproductive aging. We discovered that germline-only inactivation of GTP-but not ATP-specific succinyl-CoA synthetase (SCS) promotes reproductive longevity in Caenorhabditis elegans. We further identified an age-associated increase in mitochondrial clustering surrounding oocyte nuclei, which is attenuated by GTP-specific SCS inactivation. Germline-only induction of mitochondrial fission factors sufficiently promotes mitochondrial dispersion …

Jun Upregulation Drives Aberrant Transposable Element Mobilization, Associated Innate Immune Response, And Impaired Neurogenesis In Alzheimer’S Disease, Chiara Scopa, Samantha Barnada, Maria Cicardi, Mo Singer, Davide Trotti, Marco Trizzino

Farber Institute for Neuroscience Faculty Papers

Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death …

Oregon State Rank Assessment For Jenny Creek Sucker (Catostomus Rimiculus Pop. 1), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Jenny Creek sucker (Catostomus rimiculus pop. 1) using NatureServe methodology, 2023.

Organ-Specific Characteristics Govern The Relationship Between Histone Code Dynamics And Transcriptional Reprogramming During Nitrogen Response In Tomato, Russell Julian, Ryan M. Patrick, Ying Li

Purdue University Libraries Open Access Publishing Fund

Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same …

Phi-1, An Endogenous Inhibitor Protein For Protein Phosphatase-1 And A Pan-Cancer Marker, Regulates Raf-1 Proteostasis, Jason Kirkbride, Garbo Nilsson, Jee In Kim, Kosuke Takeya, Yoshinori Tanaka, Hiroshi Tokumitsu, Futoshi Suizu, Masumi Eto

Kimmel Cancer Center Faculty Papers

Raf-1, a multifunctional kinase, regulates various cellular processes, including cell proliferation, apoptosis, and migration, by phosphorylating MAPK/ERK kinase and interacting with specific kinases. Cellular Raf-1 activity is intricately regulated through pathways involving the binding of regulatory proteins, direct phosphorylation, and the ubiquitin-proteasome axis. In this study, we demonstrate that PHI-1, an endogenous inhibitor of protein phosphatase-1 (PP1), plays a pivotal role in modulating Raf-1 proteostasis within cells. Knocking down endogenous PHI-1 in HEK293 cells using siRNA resulted in increased cell proliferation and reduced apoptosis. This heightened cell proliferation was accompanied by a 15-fold increase in ERK1/2 phosphorylation. Importantly, the observed …

Diaryl Oxazoles As Cleavable Linkers For Drug Discovery Platforms, Elizabeth Taggart

Honors Theses

Within the field of medicine and pharmacology, discovering small molecule or biologic based molecules with therapeutic potential is a difficult task. Current methods involve individually screening hundreds of compounds on a potential target biomolecule, and recent technologies have explored peptide encoded libraries (PELs) as a means of making this screening process more high-throughput. These libraries produce a large number of small molecule drug candidates each conjugated to a unique peptide fragment, functioning as a barcode. Analysis of PELs requires the capture of hit small molecules and the subsequent release of their peptide tags; however, current approaches are limited in their …

Two New Phreatic Snails (Mollusca, Caenogastropoda, Cochliopidae) From The Edwards And Edwards-Trinity Aquifers, Texas, Kathryn E. Perez, Yamileth Guerrero, Roel Castañeda, Peter H. Diaz, Randy Gibson, Benjamin F. Schwartz, Benjamin T. Hutchins

School of Integrative Biological & Chemical Sciences Faculty Publications

The Edwards and Edwards-Trinity Aquifers of Texas have diverse stygofauna, including fifteen species of snails found in phreatic and hyporheic habitats. These species have the hallmarks of adaptation to subterranean environments including extremely small body size and the loss of pigmentation and eyes. Here we use an integrative taxonomic approach, using shell, radula, and anatomical features as well as mitochondrial and nuclear DNA data, to circumscribe a new genus and two new cavesnail species from Central Texas. Vitropyrgus lillianae gen. et sp. nov. is described from Comal Springs (Comal County) and Fessenden Springs (Kerr County) and distinguished by a glassy, …

Evaluating The Effectiveness Of The Internal Transcribed Sequences (Its) As Dna Barcodes To Estimate Fungal Diversity, Jailisa Linares

All HCAS Student Capstones, Theses, and Dissertations

Universal phylogenetic markers such as the nuclear ribosomal internal transcribed sequences (ITS), specifically ITS1 and ITS2, are routinely used to estimate fungal diversity in environmental samples. However, numerous studies report differences in the performance and efficacy of ITS1 and ITS2 in documenting fungal diversity. To better understand the implications of using ITS1 versus ITS2, a comprehensive representation of the diverse fungal taxa was necessary to conduct a meta-analysis of their use across multiple fungal taxa. In order to address this, a thorough literature review was conducted to compare and contrast the use of ITS1 and ITS2 as effective DNA barcodes. …

Two New Phreatic Snails (Mollusca, Caenogastropoda, Cochliopidae) From The Edwards And Edwards-Trinity Aquifers, Texas, Kathryn E. Perez, Yamileth Guerrero, Roel Castañeda, Peter H. Diaz, Randy Gibson, Benjamin F. Schwartz, Benjamin T. Hutchins

School of Integrative Biological & Chemical Sciences Faculty Publications

The Edwards and Edwards-Trinity Aquifers of Texas have diverse stygofauna, including fifteen species of snails found in phreatic and hyporheic habitats. These species have the hallmarks of adaptation to subterranean environments including extremely small body size and the loss of pigmentation and eyes. Here we use an integrative taxonomic approach, using shell, radula, and anatomical features as well as mitochondrial and nuclear DNA data, to circumscribe a new genus and two new cavesnail species from Central Texas. Vitropyrgus lillianae gen. et sp. nov. is described from Comal Springs (Comal County) and Fessenden Springs (Kerr County) and distinguished by a glassy, …

Structural Basis Of Gating In Msl Channels, Jingying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

All living organisms experience exogenous and endogenous mechanical stress that are fundamental to their growth, survival, and development. A prominent strategy to manage these stresses and ensure efficient physiological responses is through mechanosensitive (MS) ion channels by transforming mechanical forces into electrochemical signaling. However, given their structural diversity and the inherent challenges of applying membrane tension during structural study, how MS channels sense mechanical force and transit into different functional states remain unclear. MSL channels in plants, members of the mechanosensitive ion channel of small conductance (MscS) superfamily, provide a compelling avenue for studying the structural basis for gating of …

Hnf4Α Isoforms Regulate The Circadian Balance Between Carbohydrate And Lipid Metabolism In The Liver, Jonathan R Deans, Poonamjot Deol, Nina Titova, Sarah H Radi, Linh M Vuong, Jane R Evans, Songqin Pan, Johannes Fahrmann, Jun Yang, Bruce D Hammock, Oliver Fiehn, Baharan Fekry, Kristin Eckel-Mahan, Frances M Sladek

Faculty, Staff and Student Publications

Hepatocyte Nuclear Factor 4α (HNF4α), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2) which drive the expression of different isoforms. P1-HNF4α is the major isoform in the adult liver while P2-HNF4α is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2-HNF4α is indeed expressed in the normal adult liver at Zeitgeber time (ZT)9 and ZT21. Using exon swap mice that express only P2-HNF4α we show that this isoform orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions, including with different clock proteins at different …

Lakota Ethnobotany For South Dakota Middle School Students, Mikayla .Janis, Michael. A. Little Eagle, Madhav P. Nepal

iLEARN Teaching Resources

In this engaging lesson, students use mobile apps to identify local plant species in their school yards, along nature trails, or in any designated areas on the reservation. They will document the common names and morphological characteristics of the identified plants, explore native names, and uses, as well as the roles of plants in biogeochemical cycles. This immersive experience not only deepens students’ interest in science but also allows them to understand the bigger role of plants in the natural balance, enhancing their appreciation of the deeper connections between the Lakota culture and plant species.

The Influence Of Body Mass Index On Ready-To-Wear Clothing Preferences Of Young African-American Female Consumers, Jung-Im Seo, Vadel Shivers

Faculty Publications

Although consumers’ body shapes are various, the sizes of bust, waist, and hips of ready-to-wear (RTW) are fairly standardized in the apparel manufactures’ sizing charts, leading to clothing fit issues for many consumers. Body Mass Index (BMI) is an important factor that has an impact on body image perception, but there is little research on the influence of the obesity prevalence on RTW clothing preferences. The purposes of this study are to examine the correlation between African-American women’s obesity prevalence represented by BMI and RTW clothing preferences such as store preference and clothing benefit sought as well as clothing fitting …

Modeling A Parkinson’S Disease Like State In Zebrafish Larvae Utilizing 6-Hydroxydopamine, Adrian Romero

Biology Theses

Parkinson's’ disease (PD) is a neurodegenerative disorder characterized by the loss of midbrain dopaminergic (mDA) neurons that currently has no cure. It is primarily characterized in patients by motor symptoms that include but are not limited to: tremor at rest, rigidity, akinesia, and postural instability affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to induce a Parkinson’s disease-like state in several animal models; however, assessment of 6-OHDA use in zebrafish demonstrated a lack of consensus on method and utility. We determined an optimized protocol utilizing 6-OHDA to produce a PD-like …

Activity Patterns Of The Endangered Amargosa Vole (Microtus Californicus Scripensis), Austin N. Roy, Anna D. Rivera Roy, Deana L. Clifford, Janet E. Foley

School of Earth, Environmental, & Marine Sciences Faculty Publications

Examining the activity patterns of wildlife is an important aspect of understanding the ecology of a species and may be especially important for species of conservation concern. We used remotely triggered cameras to describe the daily and seasonal activity patterns and examine ecological factors that influence the activity of the Amargosa Vole (Microtus californicus scirpensis), a California endemic listed federally and by the state as Endangered, and is a marsh habitatspecialist in the Mojave Desert. We found that vole activity was greatest during crepuscular periods, followed by nocturnal and diurnal periods. We saw strong seasonal effects, with the highest activity …

Cytogenetic Profile In Monoclonal Gammopathy Of Undetermined Significance, Smoldering And Symptomatic Multiple Myeloma: A Study Of 1087 Patients With Highly Purified Plasma Cells, Guilin Tang, Yilin Wu, Pei Lin, Gokce A Toruner, Shimin Hu, Shaoying Li, Muzaffar H Qazilbash, Robert Z Orlowski, Christine Ye, Jie Xu, Karen A Nahmod, L Jeffrey Medeiros, Zhenya Tang

Faculty, Staff and Student Publications

The aim of this study was to examine the cytogenetic profiles of plasma cell neoplasms (PCNs) at various disease stages, encompassing 1087 patients with monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), newly diagnosed multiple myeloma (NDMM), and refractory/relapsed multiple myeloma (RRMM). Fluorescence in situ hybridization (FISH) analyses were conducted on highly purified plasma cell samples, revealing that 96% of patients exhibited at least one cytogenetic abnormality. The genomic complexity escalated from MGUS to SMM and further to NDMM and RRMM, largely driven by 1q gain, del(17p), MYC-rearrangement (MYC-R), del(1p), and tetraploidy. Elevated frequencies of …

Nitrogen Fertilization And Harvest Management Improve Forage And Crude Protein Content In Crabgrass, B. C. Pedreira, I. T. M. D. Barros, J. I. Yasuoka, D. Helwig, J. K. Farney, G. F. Sassenrath

IGC Proceedings (1977-2023)

Crabgrass (Digitaria spp.) is an annual summer grass that can provide high-quality forage, but optimal management strategies are unclear. Our objective was to compare the yield and quality of crabgrass (Mojo and Quick-N-Big) under different nitrogen rates and harvest management. The experimental design was a randomized complete block with five treatments and three replications for each crabgrass variety, totaling fifteen experimental units for both Mojo and Quick-N-Big, in adjacent sites. Treatments were nitrogen rates (0, 100, and 200 lb N/acre) and harvest management (cut once or twice per year) for two growing seasons (2020 and 2021). Total forage accumulation …

Chemical Composition And Microbial Diversity Of The Silage Of Forage Peanut Harvested At Two Regrowth Ages And Treated With Microbial Inoculants, A. J. S. Macêdo, O. G. Pereira, V. P. Da Silva, A. J. Dos Anjos, W. Alves, H. R. O. Santos, K. G. Ribeiro

IGC Proceedings (1977-2023)

The objective of this study was to evaluate the chemical composition and microbial diversity of the silage of forage peanut harvested at 40 and 80 days of regrowth and treated with microbial inoculants. The inoculants evaluated were commercial inoculant (CI) Sil-All 4×4 (Lallemand®, Brazil); the AV14.17, Lactiplantibacillus pentosus strain (ISO) isolated from alfalfa silage; and control (CTRL), without inoculant. A total of 500 g of forage was ensiled in nylon-polyethylene bags (25.40 × 35.56 cm). After 60 days of fermentation, the bags were opened and silages were analyzed for dry matter (DM), mineral matter (MM), organic matter (OM), crude protein …

Evapotranspiration Of Rewetted And Drained Fen Soils With Grass – Long Term Lysimeter Studies, M. Pesch, J. Hoysagk, F. Eulenstein, A. Behrendt

IGC Proceedings (1977-2023)

In the context of reducing greenhouse gas (GHG) emissions to combat climate change, rewetting of peatlands is of particular importance. High groundwater levels covering organic matter in the soil prevent its oxidation to CO₂. The amount of water needed to allow the rewetting of peatlands can be determined in lysimeter studies.

The evapotranspiration in fens depends essentially on the groundwater table, the vegetation (transpirational active biomass) and the saturation deficit of the atmosphere. After rewetting, these factors can lead to an evapotranspiration of 1000 l m^-2 a^-1 and even 2000 l m^-2 a^-1 in …

Industrial Hemp Forage Potential, Swarup Podder, John H. Fike, B. Wilson

IGC Proceedings (1977-2023)

Hemp (Cannabis sativa L.) has been a valuable species for humans throughout history due to its adaptability and diverse uses. Farmers are interested in hemp as a forage and feedstuff due to its unique nutritional properties and fast summer production. Moreover, the presence of cannabinoids in leaf and bud tissues may provide pharmacological benefits to animal health, productivity, and product quality under different regulatory frameworks. This study examined two hemp cultivars, Grandi and Joey, solely as forage crops, and samples were taken at different growth stages in Blacksburg, VA, USA, in 2021. The highest biomass production of 1.41 tons per …

Differential Responses Of Yield And Shoot Traits Of Five Tropical Grasses To N And Distance To Trees In Silvopastoral Systems, L. S. Pontes, Emilio A. Laca

IGC Proceedings (1977-2023)

Light intensity and nitrogen (N) availability are important factors influencing the growth of C₄ forage species. Trade-offs may occur in the adaptive responses of species to shading and N inputs, and functional shoot traits can help to explain the consequences of these responses for species performance. Our objective was to gain understanding of the mechanisms between traits of five C₄ perennial grasses determining above-ground dry matter yield (DMY) when both resources, light and N, vary. Forage grasses were grown in six shading conditions (full sunlight vs. five positions between Eucalyptus dunnii rows) with two N levels (0 vs. …

Clovers Around The World: A Symposium In Memory And Honor Of Dr. Norman L. Taylor, Kenneth H. Quesenberry, D. Boone, B. M. Irish

IGC Proceedings (1977-2023)

Trifolium is arguably the largest and most diverse genera of herbaceous forage legumes (Zohary and Heller, 1984). Dr. Norman L. Taylor, Professor Emeritus, Department of Plant and Soil Science, University of Kentucky, deceased, was a pioneer and champion of collection and preservation of Trifolium species throughout his 57-year career. Dr. Taylor was a native of northern Kentucky, born near where this Conference is being held.

Estimating The Carrying Capacity For Habitat Of Urial Wild Sheep (Ovis Orientalis) In Tandoureh National Park, Iran, M. Rahimian, F. Tabatabaei Yazdi, Mansour Mesdaghi

IGC Proceedings (1977-2023)

In an attempt to estimate forage production and carrying capacity of wild ungulates in Tandoureh National Park of Iran, the Babanestan grassland was selected, as the typical habitat of about 200 Urial wild sheep. In order to estimate the carrying capacity of this habitat for foraging of Urial wild sheep, this habitat with an area of 132 hectares was classified as low flat (LF), high flat (HF), north aspect (NA), and south aspect (SA). Then, to estimate forage production, clipping method of comparative yield was used. In each land form, standing crop yield of five reference plots of 1-^{m2 …}

Development Of Novel Interspecific Fertile Cytotype (4x) Of Pennisetum Glaucum X Pennisetum Purpureum Utilizing Modified Ploidy Coupled With Embryo Rescue Technique, Maneet Rana, N. Kumar, R. Gajghate, S. Kumar, R. Kaldate, Kamini Gautam, R. P. Sah, R. Verma, H. A. Bhargavi, R. P. Saini, S. Ahmed, P. Kaushal, A. K. Roy, A. Chandra

IGC Proceedings (1977-2023)

Interspecific hybrids of genus Pennisetum (P. glaucum x P. purpureum) is the one of the most popular manmade hybrid. It combines the unique features of both P. glaucum (Pearl millet; Bajra) and P. purpureum (Napier; Elephant grass) species, which makes it more resilient to harsh environments with superior fodder quality. Due to ploidy level variation among the parents, these hybrids are sterile and propagated vegetatively only. To overcome this, attempts were made in the present study by exploring the feasibility of novel tetraploid pearl millet (2n=4x=28; Tetra 1; INGR 09047) developed at IGFRI, as a female parent in …