Biology Commons^™

Field-Based Selenium Partitioning Coefficients, Trophic Transfer Factors, And Otolith Time-Series Analyses For A Walleye Community From An Ecotonal Plains Reservoir, Colorado. Iii., Scott J. Herrmann, Del Wayne R. Nimmo, Lynn M. Herrmann-Hoesing, Igor V. Melnykov, Norman M. Halden

Western North American Naturalist

Little is known about partitioning coefficients, tissue bioaccumulation, trophic transfer, and otolith timeseries analyses of selenium (Se) in a fishery dominated by walleye (Sander vitreus) that consume multiple prey species and occur in a Se-rich reservoir. Concentrations of dissolved total Se in Pueblo Reservoir water consistently exceeded the current EPA criterion benchmark for lentic aquatic ecosystems. The major objectives of this study were to analyze Se in diet-borne consumables of a walleye fishery and perform time-series trend tests of 21 walleye sagittae. In contrast to previous reports, we proposed investigating Se partitioning from water to subsequent trophic levels …

A Thesis On Phosphatidylserine As A Key Signaling Moiety During Adipocyte Differentiation, Brady Jeffrey Barron

Arts & Sciences Graduate Student Theses and Dissertations

The adipose tissue is composed of specialized energy storage cells called adipocytes. In white adipose tissue, when committed precursor cells (preadipocytes), receive specific cues, the preadipocytes differentiate into mature adipocytes via an adipogenic gene program promoted by transcription factors such as PPAR. Phosphatidylserine (PS) is a phospholipid asymmetrically maintained on the inner leaflet of the plasma membrane in healthy cells. PS flipping to the outer leaflet is a well-known hallmark of cell death, such as apoptosis. Here, while exploring the interplay between PS exposure and adipose tissue homeostasis, we made a surprising discovery in that non apoptotic PS exposure occurs …

Genetic And Pharmacological Factors Control Aging In Caenorhabditis Elegans., Brian Mcnally Egan

Arts & Sciences Graduate Student Theses and Dissertations

Aging is a time-dependent decline in organismal structure and function that ultimately results in death. Aging occurs in nearly all metazoan organisms, and is a major risk factor for many human diseases including cancer, diabetes, hypertension, heart disease, and Alzheimer’s Disease. The genetic pathways and mechanistic factors that underly the aging process are poorly understood. Control of aging in the nematode C. elegans can be accomplished via modulation of gene activity by genetic knockdown or by the introduction of inhibitory pharmaceutical compounds. While many such interventions have been described in the literature, understanding the underlying mechanisms that control aging remains …

Mitochondrial Transplantation And Transfer: The Promising Method For Diseases, Gökhan Burçi̇n Kubat

Turkish Journal of Biology

Mitochondria are organelles that serve as the powerhouses for cellular bioenergetics in eukaryotic cells. It is responsible for mitochondrial adenosine triphosphate (ATP) generation, cell signaling and activity, calcium balance, cell survival, proliferation, apoptosis, and autophagy. Mitochondrial transplantation is a promising disease therapy that involves the recovery of mitochondrial dysfunction using isolated functioning mitochondria. The objective of the present article is to provide current knowledge on natural mitochondrial transfer processes, in vitro and in vivo applications of mitochondrial transplantation, clinical trials, and challenges associated with mitochondrial transplantation.

Androgen Receptor Contributes To Repairing Dna Damage Induced By Inflammation And Oxidative Stress In Prostate Cancer, Bi̇lge Debeleç Bütüner, Nurşah Ertunç Hasbal, Eli̇f İşel, Dirk Roggenbuck, Kemal Sami̇ Korkmaz

Turkish Journal of Biology

Background: Androgen deprivation therapy remains the first-line therapy option for prostate cancer, mostly resulting in the transition of the disease to a castration-resistant state. The lack of androgen signaling during therapy affects various cellular processes, which sometimes paradoxically contributes to cancer progression. As androgen receptor (AR) signaling is known to contribute to oxidative stress regulation, loss of AR may also affect DNA damage level and the response mechanism in oxidant and inflammatory conditions of the prostate tumor microenvironment. Therefore, this study aimed to investigate the role of AR and AR-regulated tumor suppressor NKX3.1 upon oxidative stress-induced DNA damage response (DDR) …

Ribosomal Protein L8 Regulates The Expression And Splicing Pattern Of Genes Associated With Cancer-Related Pathways, Leilei Xu, Gui Yang, Bin Song, Dong Chen, Akbar. Yunus, Jiangtao Chen, Xiaogang Yang, Zheng Tian

Turkish Journal of Biology

Background/aim: Ribosomal proteins have been shown to perform unique extraribosomal functions in cell apoptosis and other biological processes. Ribosomal protein L8 (RPL8) not only has important nonribosomal regulatory functions but also participates in the oncogenesis and development of tumors. However, the specific biological functions and pathways involved in this process are still unknown. Materials and methods: RPL8 was overexpressed (RPL8-OE) in HeLa cells. MTT assay and flow cytometry were used to detect cell proliferation and apoptosis, respectively. Transcriptome sequencing was performed to analyze the differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs) by RPL8-OE, both of which were …

Gooseberry Anthocyanins Alleviate Insulin Resistance By Regulating Ceramide Metabolism In High Fat Diet Mice, Xian Tang, Jun Gao, Jinpeng Huang, Chenjuan Zhang, Hongwei Liu, Jie Wei

Turkish Journal of Biology

Background/aim: Obesity is the fifth largest risk factor of death in the world. The ceramide produced by obesity is closely related to insulin resistance (IR) caused by obesity. At present, the commercially available weight loss products have large side effects and limited therapeutic effects. Therefore, it is particularly important to find effective natural nontoxic products to treat obesity and explore its possible pathways and mechanisms. Materials and methods: In this paper, a high-fat diet (HFD) mice model was established by intragastric administration of high-fat emulsion to investigate the intervention effect of Gooseberry anthocyanins (GA) on IR in HFD mice. We …

Connection To Nature: A Student Perspective, Jessica Duke, Emily Holt

Biological Sciences Faculty Publications

Connection to nature has been linked to increased physical and mental health and increased performance of sustainable behaviors for individuals more connected to nature. Understanding why humans, especially younger generations, are connected to nature is an important tool for both public and environmental health. Our work used a qualitative, phenomenological study design to examine university biology students' descriptions of others' connection to nature, the frequency with which students predict their own connection to nature, and students' descriptions of the discrepancies between their prediction of their own connection to nature and their score on the Environmental Identity Scale. We found that …

Fortifying Iot Against Crimpling Cyber-Attacks: A Systematic Review, Usman Tariq, Irfan Ahmed, Muhammad Attique Khan, Ali Kashif Bashir

Karbala International Journal of Modern Science

The rapid growth and increasing demand for Internet of Things (IoT) devices in our everyday lives create exciting opportunities for human involvement, data integration, and seamless automation. This fully interconnected ecosystem considerably impacts crucial aspects of our lives, such as transportation, healthcare, energy management, and urban infrastructure. However, alongside the immense benefits, the widespread adoption of IoT also brings a complex web of security threats that can influence society, policy, and infrastructure conditions. IoT devices are particularly vulnerable to security violations, and industrial routines face potentially damaging vulnerabilities. To ensure a trustworthy and robust security framework, it is crucial to …

New Quantum Genetic Algorithm Based On Constrained Quantum Optimization, Mohammed R. Almasaoodi, Abdulbasit M. A. Sabaawi, Sara El Gaily, Sándor Imre

Karbala International Journal of Modern Science

In the past decades, many quantum algorithms have been developed. The main obstacle that prevents the widespread implementation of these algorithms is the small size of the available quantum computer in terms of qubits. Blind Quantum Computation (BQC) holds the promise of handling this issue by delegating computation to quantum remote devices. Here, we introduce a novel Constrained Quantum Genetic Algorithm (CQGA) that selects the optimum extreme (minimum or maximum) value of a constrained goal function (or a vast unsorted database) with very low computational complexity. Since the convergence speed to the optimal solution for the Constrained Classical Genetic Algorithm …

Coexistence Of Specialist And Generalist Species Within Mixed Plastic Derivative-Utilizing Microbial Communities, Laura G. Schaerer, Lindsay I. Putman, Isaac Bigcraft, Emma Byrne, Daniel G. Kulas, Ali Zolghadr, Sulihat Aloba, Rebecca Ong, David Shonnard, Stephen Techtmann

Michigan Tech Publications

BACKGROUND Plastic-degrading microbial isolates offer great potential to degrade, transform, and upcycle plastic waste. Tandem chemical and biological processing of plastic wastes has been shown to substantially increase the rates of plastic degradation however, the focus of this work has been almost entirely on microbial isolates (either bioengineered or naturally occurring). We propose that a microbial community has even greater potential for plastic upcycling. A microbial community has greater metabolic diversity to process mixed plastic waste streams and has built-in functional redundancy for optimal resilience. RESULTS Here, we used two plastic-derivative degrading communities as a model system to investigate the …

Temperature And Predators As Interactive Drivers Of Community Properties, John P. Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …

Temperature And Predators As Interactive Drivers Of Community Properties, John Delong, Kyle E. Coblentz, Stella F. Uiterwaal, Chika Akwani, Miranda E. Salsbery

School of Biological Sciences: Faculty Publications

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and …

Burrowing Owl Skull, Nicolas M. Caracuel, Hannah Lesko, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Multivariate Adaptive Shrinkage Improves Cross-Population Transcriptome Prediction And Association Studies In Underrepresented Populations, Daniel Araujo, Chris Nguyen, Xiaowei Hu, Anna V. Mikhaylova, Christopher R. Gignoux, Kristin Ardlie, Kent D. Taylor, Peter Durda, Yongmei Liu, George Papanicolaou, Michael H. Cho, Stephen S. Rich, Jerome I. Rotter, Nhlbi Topmed Consortium, Hae Kyung Im, Ani Manichaikul, Heather Wheeler

Biology: Faculty Publications and Other Works

Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized that methods that leverage shared regulatory effects across different conditions, in this case, across different populations, may improve cross-population transcriptome prediction. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWASs) using different methods (elastic net, joint-tissue imputation [JTI], matrix expression quantitative trait loci [Matrix eQTL], multivariate adaptive shrinkage in R [MASHR], and transcriptome-integrated genetic association resource [TIGAR]) and tested their out-of-sample transcriptome prediction accuracy …

Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation And Progression, Janine M. Deblasi

USF Tampa Graduate Theses and Dissertations

NRF2 is a redox-responsive transcription factor the directs the antioxidant program and several critical metabolic processes. Mutations in NRF2 or its negative regulator KEAP1 occur in up to one third of non-small cell lung cancers (NSCLCs) and are often associated with resistance to therapy and poor outcomes. In the present studies, murine alleles of the Keap1 and Nrf2 mutations found in human NSCLC were developed and I comprehensively investigated their impact on tumor initiation and progression. I observed that chronic Nrf2 stabilization by Keap1 loss-of-function or Nrf2 activating mutation was not sufficient to cause lung tumor initiation, even when p53 …

Insights Into The Molecular Roles Of Foxr2 In The Pathology Of Primary Pediatric Brain Tumors, Rajendra Gharbaran

Publications and Research

Forkhead box gene R2 (FOXR2) belongs to the family of FOX genes which codes for highly conserved transcription factors (TFs) with critical roles in biological processes ranging from development to organogenesis to metabolic and immune regulation to cellular homeostasis. A number of FOX genes are associated with cancer development and progression and poor prognosis. A growing body of evidence suggests that FOXR2 is an oncogene. Studies suggested important roles for FOXR2 in cancer cell growth, metastasis, and drug resistance. Recent studies showed that FOXR2 is overexpressed by a subset of newly identified entities of embryonal tumors. This review discusses the …

Recent Advances In Crispr/Cas9-Assisted Gene Therapy, Apeksha Srivastava, Shikha Chauhan, Vishal Ahuja

Karbala International Journal of Modern Science

CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats) is an exponentially growing tool with wide-spread applications in therapeutics like gene modifications that focus on altering the hereditary material to repair or eliminate any defective gene-causing diseases like cancer, AIDS (Acquired immunodeficiency syndrome), etc. It also includes the identification of the target sequence with the help of sgRNA followed by the substitution of a malfunction-ing gene with a normal version. It offers high efficiency, specificity, and post-gene-editing efficacy, but have also some off-target impressions, and immunogenic effects. The contribution of CRISPR/Cas9 has already been proved primarily in in-vitro studies using animal germ …

Optical, Structural, And Electrochemical Properties Of P3ht:Y6 Photoactive Layer For Organic Photovoltaics, Hassan Tarikhum B., Furqan Almyahi, Basil Ali

Karbala International Journal of Modern Science

Recently, organic photovoltaics (OPV) have emerged as a promising technology for environmentally friendly energy production. Achieving high performance in OPV requires the discovery of novel compounds. This article aims to study the optical, structural, electrochemical, and electrical properties of a P3HT:Y6 blend. The UV-visible spectra of the blend provided insight into how composition affects the optoelectronic properties of OPV devices. The optimised P3HT:Y6 ratio (0.6:1) resulted in the largest redshift and the highest absorption intensity. Raman and X-ray diffraction tests showed low aggregation and low crystallinity of the polymer P3HT as Y6 content increased. In the OPV devices, the best …

Estimation Of Water Quality Of Dikhu River Of Nagaland Through A Combination Of Water Quality Index And Principal Component Analysis Techniques., Lanuyanger Longchar, Wati Temjen, Khikeya Semy, Wati Lemla

Karbala International Journal of Modern Science

Monitoring the physico-chemical attributes of water is essential for determining water quality. The present study explores the effect of various anthropogenic factors on the quality of Dikhu River, Nagaland. Water samples from three sampling stations were compared against three standards: Indian Council of Medical Research, Bureau of Indian Standards, and World Health Organization. Although all parameters were within the permissible limits, the Water Quality Index categorized all sites during the rainy season as "poor quality", highlighting anthropogenic impacts. A principal component analysis created a Minimum Data Set (MDS) explaining 100%, 93.27%, and 96.26% of the total variance for the three …

Potentially Adaptive Significance Of Genome Size Diversity Across Ecological Gradients And Seed Size In Ivesia (Rosaceae), Israel T. Borokini, Shaun R. Broderick, Zhi Gao, Joshua M. Hallas, James A. Birchler, Mary M. Peacock

Western North American Naturalist

Variation in genome size across taxa has been explained using neutral and nonadaptive theories; however, genome size variation among taxonomic groups can also be shaped by natural selection if it correlates with functional traits. This study investigated the potential adaptive significance of genome size in Ivesia, a radiating genus distributed in the western North American desert ecosystems. We estimated the genome size of 34 taxa (including 31 Ivesia taxa, 2 Potentilla taxa, and 1 Horkelia taxon) using flow cytometric methods. For each taxon, leaf samples were collected from 6 individuals in 1 location each; intraspecific genome size variation was …

Investigating The Influence Of Assessment Question Framing On Undergraduate Biology Student Preference And Affect, Jeremy L. Hsu, Noelle Clark, Kate Hill, Melissa Rowland-Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nearly all undergraduate biology courses rely on quizzes and exams. Despite their prevalence, very little work has been done to explore how the framing of assessment questions may influence student performance and affect. Here, we conduct a quasi-random experimental study where students in different sections of the same course were given isomorphic questions that varied in their framing of experimental scenarios. One section was provided a description using the self-referential term “you”, placing the student in the experiment; another section received the same scenario that used classmate names; while a third section's scenario integrated counterstereotypical scientist names. Our results demonstrate …

Quantification Of Amu River Riverbank Erosion In Balkh Province Of Afghanistan During 2004–2020, Abdul Basir Mahmoodzada, Divyesh Varade, Sawahiko Shimada, Hiromu Okazawa, Shafiqullah Aryan, Gulbuddin Gulab, Abd El Zaher M.A. Mustafa, Humaira Rizwana, Yogesh Ahlawat, Hosam O. Elansary

Michigan Tech Publications

In this study, we propose quantifying the Amu River riverbank erosion with the modelled river discharge in Kaldar District, Balkh Province of Afghanistan from 2004 to 2020. We propose a framework synergizing multi-source information for modelling the erosion area based on three components: (1) river discharge, (2) river width, and (3) erosion area. The total river discharge for the watershed shared by Afghanistan and Tajikistan was modelled using hydrological parameters from the European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis v5 (ERA5) data through multivariate linear regression with ground station data. The river width was determined manually using the Normalized …

Understanding Endangered Sawfish Through The Growth And Structure Of Their Rostral Teeth, Linh Truong, Gabe Gambleton, Jens Hegg

CURCI Student Research

Sawfish are an endangered ray with a toothy rostrum containing a large number of teeth. Largetooth sawfish are a critically endangered species worldwide. Little is known about their life history or behavior, and natural populations are too low to easily track them. Preserved rostra are more accessible to study. Measurements of the rostrum teeth and rostrum length were taken which may indicate a subspecies or sexual dimorphism in the sample. 120 sawfish rostra from the Brazil sample were quantified using ImageJ to compare rostrum size to fish age and length. Sawfish rostral teeth have repeated tubule structures within them that …

Unveiling Novel Avenues In Mtor-Targeted Therapeutics: Advancements In Glioblastoma Treatment, Shilpi Singh, Debashis Barik, Karl Lawrie, Iteeshree Mohapatra, Sujata Prasad, Afsar R. Naqvi, Amar Singh, Gatikrushna Singh

Biology Student Work

The mTOR signaling pathway plays a pivotal and intricate role in the pathogenesis of glioblastoma, driving tumorigenesis and proliferation. Mutations or deletions in the PTEN gene constitutively activate the mTOR pathway by expressing growth factors EGF and PDGF, which activate their respective receptor pathways (e.g., EGFR and PDGFR). The convergence of signaling pathways, such as the PI3K-AKT pathway, intensifies the effect of mTOR activity. The inhibition of mTOR has the potential to disrupt diverse oncogenic processes and improve patient outcomes. However, the complexity of the mTOR signaling, off-target effects, cytotoxicity, suboptimal pharmacokinetics, and drug resistance of the mTOR inhibitors pose …

Characterizing The Effects Of Benzyl-Amino Alcohol On Cell Growth, Viability, And Migration, Ryan Miller, Jeff Hansen, Sarah Mordan-Mccombs

Annual Student Research Poster Session

The research we are performing investigates a new compound classified as benzyl-amino alcohol and begins a new endeavor into the effects of this class of compound. This compound would work well in chemotherapies because affecting healthy cells can lead to a patient’s health decline.

Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, University Of Connecticut, University Of The Sunshine Coast, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

1. Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.
2. We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established 40 seedling plot-pairs, with one plot excluding LTH-mammals and …

Avoidance Behavior Ecotoxicity Testing Of Oppia Nitens In Conventional Microplastic And Bioplastic Spiked Soils., Catarina Zabot Pasini, Kaija Carr, Nina Shaffer, Philips Akinwole

Annual Student Research Poster Session

Environment and Climate Change Canada recently completed a standardized protocol of ecotoxicity testing for Oppia nitens, a soil oribatid mite that performs crucial functions to support ecosystem services. Consequently, O. nitens is now recommended among the class of soil invertebrates for ecotoxicity testing, however, its applicability is limited by the paucity of data on its avoidance behavior to contaminants in soils. In this study, we examined the avoidance behavior of O. nitens to three different conventional microplastics (polyvinyl chloride/PVC, polyethylene/PE, polystyrene/PS) and two bioplastics (poly vinyl alcohol/PVA and sodium polyacrylate/NaPa) at five different concentrations following standardized guidelines. PVC and PE …

Stressed, But Doing Fine. An Investigation Of Apocynum Cannabinum Patches And Individuals, Lauren Kyburz, Lily Monnett, Quincie Simmons, Dana Dudle

Annual Student Research Poster Session

Apocynum cannabinum (hemp dogbane) is a native Indiana plant that is abundant in the DePauw University Nature Park’s quarry, a heterogeneous site that contains stretches of dry, rocky terrain in addition to many temporary ponds. In 2023, I mapped the distribution of A. cannabinum in the quarry to see if its habitats are associated with elevation and/or the presence of temporary ponds. I also conducted a study of diurnal pollinator visitation, and an examination of damage caused by the dogbane saucrobotys moth (Saucrobotys futilalis).

Modeling Light For Platanus Occidentalis (American Sycamore) Trees In The Depauw Quarry, Grace Lucchesi, Beth Wilkerson, Quincie Simmons, Dana Dudle

Annual Student Research Poster Session

Platanus Occidentalis, characterized by shedding bark and ball-shaped seed pods, is native to much of the mid-southeastern US, and is commonly used as an ornamental tree. Individuals growing in the quarry of DePauw’s Nature Park are often small, discolored, or even dying. We used devices to measure the UV and Photosynthetically Active Radiation present at the locations of 70 random trees. We then used known sun path equations and GIS to start to develop a way to estimate the maximum amount of time a plant experiences full sun in different locations in the quarry relative to the quarry walls.