Digital Commons Network^™

Performance Of A Fertilizer Sludge Contaminated With Heavy Metals Collected From Two Wastewater Treatment Plants On (Lactuca Sativa), Leila Lila Belkhedim, Yamina Tahri

Makara Journal of Science

The improper management of sewage sludge poses a significant global risk to environmental and public health. In this study, the valorization of sludge as an organic fertilizer for lettuce cultivation was evaluated, offering a sustainable waste-to-resource solution. Sludge from two wastewater treatment plants (Mazouna and El Kerma) were collected between 2019 and 2021. Comprehensive physicochemical analysis was conducted to determine its nutrient value and contaminant levels. In addition, the efficacy and safety of the fertilizer were assessed by measuring lettuce growth and the bioaccumulation of heavy metals in plant tissues. The analyzed sludge, with an organic matter content of 9.91%–83% …

Promiscuous Mutualisms: John Dupré And The Centrality Of Symbiosis In The Living World, Thomas Pradeu

Presidential Fellows Articles and Research

My goal in this chapter is to show that symbiosis, especially symbiotic interactions between ‘macrobes’ (non-microbial organisms) and microbes, is a central topic in John Dupré’s work. This topic is undeniably one of the topics by which Dupré has gained wide recognition among practicing scientists, in addition to his recognition within the philosophical community. I spell out why symbiosis has turned out to be a sort of ideal trope for Dupré, as it encapsulates many of his main personal themes—from promiscuous realism to process ontology. I then show that immunology offers one interesting and complementary entry point into microbial symbiosis …

Humans Rule? Development Of Stewardship Mindsets Among Religious Undergraduates, Jamie Jensen, J Robert Nielson

ScholarsArchive Data

Two cohorts of students enrolled in a non-major introductory biology course were surveyed in 2020 and 2025 using the Revised New Ecological Paradigm (R-NEP) instrument. Open-ended student responses concerning their definition of ‘rule’ as a human prerogative were also analyzed using qualitative coding.

Parental Effects In Fall Webworm, Emma Sellers, Mykaela Tanino-Springsteen, Mayra Vidal, Dhaval Vyas, Gina Wimp, Mariana Abarca, Mattheau Comerford, Shannon Murphy

Data

The environment or experiences of a parent generation can impact the fitness of the next generation, a phenomenon known as parental effects. While a high-quality diet can directly benefit an individual and a low-quality diet can reduce fitness, a parental effect occurs only when there is a transgenerational response to these stimuli that manifests in the individual’s offspring. In dietary generalists, a parental effect could play an important role for offspring performance if the species experiences considerable variation in quality across host plants; positive parental effects may result from host matching between parents and offspring on high-quality host plants, whereas …

An Inf2-Dependent Actin-Mediated Step In Inositol 1,4,5-Trisphosphate Receptor Cluster Formation And Activity, Maite R. Zavala, Amrapali Ghosh, Suresh K. Joseph, Rajarshi Chakrabarti

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Intracellular calcium signaling plays a vital role in regulating various cellular processes including gene regulation, motility, metabolism, and cell death. Inositol 1,4,5-trisphosphate receptors (IP3Rs) on the endoplasmic reticulum (ER) are a major cation channel that regulates stimulus-induced calcium release from the ER. While several molecular players regulate the activity of IP3R, its regulation by actin filaments was uncharacterized. Here, we show that actin filaments polymerized by the specific actin nucleator INF2 facilitate agonist-induced IP3R activity. Our results demonstrate that INF2-mediated actin filaments regulate the formation and/or stability of IP3R clusters on the ER that have been previously shown to be …

Cap1 (Cyclase-Associated Protein 1) Mediates The Camp Regulation Of Adhesion And Proliferation Of Schwann Cells In The Peripheral Nervous System, Jarna Karmoker

Student Theses and Dissertations

The peripheral nervous system relays signals between the central nervous system and the rest of the body, and peripheral nerve injuries and neuropathies can cause permanent neurological deficits. Schwann cells (SCs) are glial cells that myelinate neurons, which is essential for neuronal function and nerve repair. CAP1 (Cyclase-Associated Protein 1) is best characterized as an actin-regulating protein, while it also regulates other cellular processes, including matrix adhesion, migration, and proliferation. We discovered that cAMP-induced CAP1 dephosphorylation regulates relevant cell functions. While cAMP is also important for SC function and myelination, the underlying mechanisms remain largely unknown. We silenced CAP1 in …

Assessing The Effectiveness Of Wetland Reserve Easements As Habitat For Birds In The Mississippi Alluvial Valley Of Eastern Arkansas, Colin K. Dobson

Student Theses and Dissertations

Globally, wetland habitats suffered major declines during the 20th century. In the 1990s, the United States government created the Wetland Reserve Program (later consolidated into the Agricultural Conservation Easement Program), to combat the loss of wetlands. Despite success in attracting landowners, minimal monitoring of properties enrolled into the program (easements) has occurred. In this study, we monitored avian communities at easements, compared avian diversity at easements to agriculture and bottomland forests, and quantified microhabitat, site-specific, and surrounding landscape features at easements. We also studied the demographic rates of an indicator species of bottomland forests, the Prothonotary Warbler (Protonotaria citrea) at …

Small Rna Sequencing Identifies Tsrna-05020 As A Potential Regulator Of Cervical Cancer Progression, Cheng Peng, Cong Liang, Jie Liu, Yunlu Liu, Ping Liu

Turkish Journal of Biology

Background/aim: Cervical cancer (CC) is a malignant gynecologic tumor. Small RNAs derived from tRNA (tsRNAs) have been reported to play regulatory roles in tumor progression and suppression. However, the functional role of tsRNAs in CC remains largely unclear.

Materials and methods: Small RNA sequencing was performed on normal, cervical intraepithelial neoplasia (CIN), and CC clinical cell samples to identify differentially expressed tsRNAs (DEtsRNAs). qRT-PCR was used to validate the selected DEtsRNAs. The effects of tsRNA-05020 on HeLa cell proliferation, apoptosis, and epithelial-to-mesenchymal transition were assessed.

Results: Compared with the normal group, 215 tsRNAs were significantly differentially expressed in CIN tissues, …

An In Vitro Mechanistic Study Of Cholinergic-Associated Mechanisms Relevant To Masld In Hepg2 Cells, Gamze Sönmez, Müslüm Gök, Suat Sari, Ebru Bodur

Turkish Journal of Biology

Background/aim: Polyunsaturated fatty acids (PUFAs) and the hepatic cholinergic axis are critical regulators of lipid metabolism and inflammatory signaling; however, their time-dependent interplay in hepatocytes remains incompletely understood. Clarifying how n-6 and n-3 PUFAs interact with cholinergic pathways may provide mechanistic insight into metabolic dysfunction-associated steatotic liver disease (MASLD).

Materials and methods: HepG2 cells were used to examine the combined effects of butyrylcholinesterase (BChE) overexpression and PUFA exposure. Cells were treated with linoleic acid (LA; n-6) or α-linolenic acid (α-LA; n-3) for 24 or 48 h. Gene expression analyses were performed to assess pathways involved in de novo lipogenesis, β-oxidation, …

Context-Dependent Regulation Of Six1 By Ets1 Within Emt-Associated Transcriptional Networks, İrem Yalim Camci

Turkish Journal of Biology

Background/aim: Epithelial-mesenchymal transition (EMT) is a fundamental process driving tumor plasticity, metastasis, and therapy resistance. Although E26 transformation-specific transcription factor 1 (ETS1) and Sine oculis homeobox homolog 1 (SIX1) are individually implicated in EMT-related transcriptional programs, the regulatory interplay and functional coordination of these proteins across tumor states remain unclear. Hence, this study aimed to investigate the mechanistic and clinical behavior of the ETS1–SIX1 axis, with a focus on hepatocellular carcinoma (HCC) and aggressive endothelial-like cancer phenotypes.

Materials and methods: ETS1–SIX1 expression patterns were analyzed using real‐time quantitative polymerase chain reaction in HCCderived cell lines and the endothelial-like SK-HEP-1 cell …

Retinoic Acid-Loaded Nanoparticles Enhance Macrophage-Mediated Control Of Leishmania Infantum, Zeynep İşlek, Merve Gündoğdu, Zeynep Di̇la Yüksel

Turkish Journal of Biology

Background/aim: Visceral leishmaniasis, primarily caused by Leishmania infantum, remains a major global health challenge due to limitations in current chemotherapeutic options, including toxicity and emerging drug resistance. Host-directed therapeutic approaches are increasingly recognized as promising alternatives. All-trans retinoic acid (ATRA) is an immunomodulatory molecule with host-dependent effects on macrophage function; however, its therapeutic use is hindered by instability and poor solubility. Solid lipid nanoparticles (SLNs) offer a controlled and biocompatible delivery platform capable of enhancing intracellular drug accumulation.

Materials and methods: ATRA-loaded SLNs were prepared and characterized for size, polydispersity index, zeta potential, and morphology. Their antileishmanial activity was evaluated …

Characterization Of Poly-Β-Hydroxybutyrate And Its Biosynthesis In Priestia Endophytica Ucm B-5715, Alina Kharchuk, Maksym Kharchuk, Maksym Kharkhota, Sergiy Rogalsky, Oksana Tarasyuk, Oleksandr Kisten, Anastasiia Hubina, Illya Kapats, Liliia Avdieieva

Turkish Journal of Biology

Background/aim: Polyhydroxyalkanoates (PHAs) are biodegradable biopolymers with promising applications in biotechnology and medicine; however, the diversity of their biosynthesis within the genus Priestia remains poorly characterized. Although Priestia species have been recognized as potential PHA producers, the detailed genomic architecture and physicochemical properties of the polymers synthesized by these bacteria, particularly in the type strain, remain poorly understood. This study aimed to characterize the poly-β-hydroxybutyrate (PHB) produced by Priestia endophytica UCM B-5715 and to investigate the PHB biosynthetic genes across related strains.

Materials and methods: PHB granules were visualized and measured using fluorescence microscopy, transmission electron microscopy, and scanning electron …

Nutrient Uptake Of Two Microalgae From Culture Medium Under Nickel Treatment, Di̇lara Erdaği, Büşranur Şeker, Celal Caner, Gi̇zem Çeti̇n, Hüseyi̇n Altundağ, Hati̇ce Tunca

Turkish Journal of Biology

Background/aim: Phycoremediation is essential for purifying wastewater of heavy metals to ensure a sustainable environment, as these components can be detrimental to organisms upon entering the food chain. Among heavy metals, nickel is vital at low concentrations due to its presence in the active sites of many metalloenzymes in algae. However, at high concentrations, it disrupts the functioning of many metabolic reactions. This study examines the effects of nickel treatment on the uptake of macro- and micronutrients in medium by algae via ion exchange pathways or in competition with other metals. The study aims to determine the effects of nickel …

Contribution Of Phosphorylation To Hp1a Function, James Walts

ETDs from 2020-2029

Heterochromatin Protein 1 (HP1) family members are highly conserved, non-histone chromosomal proteins essential for heterochromatin formation and transcriptional regulation. In Drosophila melanogaster, HP1a functions both as a transcriptional repressor and activator, as well as other functions, and undergoes post-translational modifications, including phosphorylation. The functional consequences of HP1a phosphorylation remain largely unexplored. This thesis investigates the role of phosphorylation at serines 89/90/91 (S899091) of HP1a by generating two mutant alleles: a phospho-mimic (SE) and a phospho-block (SA). Both alleles produce stable mRNA transcripts; however, Western blot analysis revealed reduced protein accumulation relative to wildtype HP1a. Homozygous phospho-block animals are embryonic lethal …

Invasive African Fig Flies (Zaprionus Indianus) Have Reduced Cold Acclimation Ability Compared To Cosmopolitan Drosophilid Species, Mia Hollekim, Lucy Smith, Priscilla A. Erickson

Biology Faculty Publications

Zaprionus indianus, an invasive species of fruit fly originating from Africa, has successfully inhabited eastern North America but is thought to be seasonally limited by cold temperatures. We compared the cold acclimation abilities of Z. indianus to six drosophilid species. Each species’ survival at -5°C was tested following acclimation periods at 10°C, 15°C, and 25°C. We found that Z. indianus had a similar baseline cold tolerance to other cosmopolitan species and acclimated following treatment at 15°C. Overall, cold acclimation in Z. indianus was better than tropical species but weaker than some cosmopolitan species, suggesting cold may restrict Z. indianus …

Ai-Based Metacognitive Tutoring And Its Role In Enhancing Higher-Order Thinking Skills In Biology Learning: A Conceptual And Correlational Study, Ririn Mardiana Saputri, Sekar Juang Adilia Pantarei, Widi Purwianingsih

Jurnal Pendidikan Sains

Higher-order thinking skills (HOTS) are essential competencies in biology learning, yet many students continue to struggle with engaging in analytical, evaluative, and reflective thinking processes during science instruction. This study examines the role of AI-based metacognitive tutoring in supporting the development of HOTS in biology education. Employing a conceptual and correlational research design, this study integrates theoretical analysis with empirical correlational data collected from 85 senior high school students in Lombok, Indonesia. Metacognitive awareness was measured using the Metacognitive Awareness Inventory (MAI), while higher-order thinking skills were assessed using a validated biology HOTS instrument. The findings indicate a strong positive …

The Effect Of Project-Based Learning Model On Entrepreneurship (Pjbl-E) With A Deep Learning Approach On Students' Problem-Solving And Cognitive Skills, Ricce Oktasari, Irwandi Irwandi, Siti Darwa Suryani

Jurnal Pendidikan Sains

This study aims to examine the effect of the Entrepreneurship-based Project Based Learning (PjBL-E) model integrated with a pedagogical Deep Learning approach on students’ problem-solving skills and cognitive learning outcomes in biology learning. The novelty of this study lies in the integration of entrepreneurship values and pedagogical deep learning principles into Project Based Learning to create contextual and meaningful learning experiences. Entrepreneurship integration encourages students to develop innovative products, identify real-world problems, and apply biological concepts in practical and socio-economic contexts. Meanwhile, the pedagogical Deep Learning approach promotes reflective thinking, conceptual understanding, critical analysis, and the ability to connect theory …

The Effect Of Discovery Learning Model On Students’ Critical Thinking Skills In Biology Learning At Sman 1 Dampelas, Umiyatul Rahma, Mursito S. Bialangi, Amalia Buntu, Fatma Dhafir, Raya Agni, Gamar B. N Shamdas

Jurnal Pendidikan Sains

Critical thinking skills are essential in biology learning; however, many classroom practices remain teacher-centered, limiting students’ opportunities to engage in higher-order thinking processes. Although previous studies have reported the potential of Discovery Learning to enhance critical thinking, evidence regarding its effectiveness in secondary biology education remains limited, particularly in the context of Indonesian high schools. Therefore, this study aimed to examine the effect of the Discovery Learning model on students’ critical thinking skills in biology learning at SMAN 1 Dampelas. A quasi-experimental study employing a nonequivalent control group design was conducted with 48 Grade XI science students, consisting of 24 …

Student Worksheets Based On The Local Wisdom Of Besilek Serawai For Sixth-Grade Elementary Science Learning, Mice Agustin, Tomi Hidayat, Irwandi Irwandi

Jurnal Pendidikan Sains

This study aims to develop a Student Worksheet (Lembar Kerja Peserta Didik [LKPD]) based on the local wisdom of Besilek Serawai for sixth-grade elementary science education and to evaluate its validity. The study employed the ADDIE development model, consisting of five stages: Analyze, Design, Develop, Implement, and Evaluate. The developed LKPD integrates Besilek Serawai, a traditional martial art of the Seluma community, with the concept of the human locomotor system in science instruction. The worksheet was validated by two subject-matter experts and two media experts. Material validation yielded an average score of 4.26, equivalent to a validity percentage of 85.2%, …

Influence Of Smoking On Mlh1 Gene Polymorphism: Insights Into Colorectal Cancer Incidence, Ali Mohammed Al-Abedi, Rand Muhammed Abdul-Hussein Al-Husseini

Al-Bahir

Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. The MutL Homolog 1 (MLH1) gene plays a critical role in DNA mismatch repair (MMR). Evidence suggests cigarette smoking increases CRC risk, potentially interacting with genetic factors.

Materials and Methods: This case-control study involved 50 Iraqi CRC patients and 50 age- and gender-matched healthy controls. The PCR-RFLP technique was employed for genotyping the -93G/A (rs1800734) polymorphism. Statistical analysis included Chi-square, Fisher's Exact Test, and logistic regression adjusted for confounders. Hardy-Weinberg Equilibrium (HWE) was assessed in controls.

Results: The frequency of the rs1800734 variant was significantly higher in CRC …

Evaluating The Efficacy Of Green-Method-Prepared Zinc Oxide Nanoparticles On Gene Expression Of Efflux Pumps In Klebsiella Pneumoniae Bacteria Isolated From Women With Gestational Diabetes, Wissam Qadry Mutaab, Rana J. Shaker

Al-Bahir

Vaginitis is one of the most common women's health problems, and its severity increases in pregnant women with gestational diabetes due to higher susceptibility to infection and increased rates of antibiotic resistance. The research problem: The increasing prevalence of multidrug-resistant isolates of Klebsiella pneumoniae and its association with AcrAB-TolC ejaculation pumps limits treatment efficacy, while the effect of green-method nanoparticles on gene expression of these pumps remains unclear. This paper aimed to detect the acrA and acrB genes in K. pneumoniae isolates and evaluate the effect of zinc oxide nanoparticles prepared with garlic and rosemary extracts on their gene expression. …

The Helminthic Status Of Selected Tanzanian Subterranean Rodents, The Root-Rats (Spalacidae: Tachyoryctes Splendens) And Emini Silvery Mole-Rats (Bathyergidae: Heliophobius Argenteocinereus Emini), Jestina V. Katandukila

Tanzania Journal of Science

Root-rats (Tachyoryctes splendens) and emini silvery mole-rats (Heliophobius argenteocinereus emini) are common subterranean rodents that are essential component of the ecosystem. They serve as prey for small to medium-sized carnivores and birds of prey but their role as hosts to parasites is limited. The present study, explored the Gastrointestinal Tract (GIT) contents of 40 rodents (20 T. splendens and 20 H. a. emini, respectively) to acquire information on parasites diversity of these mammals. The GIT contents from subterranean rodents in a sex ratio of 1:1 were examined under a compound microscope to isolate helminths. The isolated helminths belonged to the …

Meningioma Detection From Mri: A Comparative Study Of Deep Learning Models, A. H. Doha, Sandi Jennifer, Fatima Alabdaly

AUIQ Complementary Biological System

This study compares several deep learning models including DenseNet20, CNN, ResNet50, VGG19, EfficientNet-B3, MobileNetV2, NASNetMobile, Xception to automatically classify brain meningiomas from MRI scans. A public dataset was used to evaluate the proposed model. All models were trained, validated, and tested on this dataset. Because meningiomas are common and manual reads, the goal is to speed and standardize diagnosis. Our main contribution is pairing a high-accuracy classifier with deep learning models. Among all models, DenseNet201 performed best, reaching 0.991% accuracy and reliably separating tumorous from non-tumorous MRIs. Future work will expand the dataset and incorporate stronger segmentation to further boost …

Elucidating The Function Of Yedk In Response To Dna Damage, Hank Munro

University Honors Theses

Apurinic/Apyrimidinic (AP) sites are one of the most prevalent forms of DNA damage. These lesions arise spontaneously or during base excision repair of modified DNA bases and are potentially mutagenic in both mammalian and bacterial cells. 5-hydroxymethylcytosine binding, ES cell specific (HMCES), a protein found in eukaryotic cells, has been shown to form a stable DNA-protein crosslink with AP sites in single stranded DNA and to reduce the number of AP sites occurring either spontaneously or after alkylative DNA damage, resulting in increased genome stability. YedK, the Escherichia coli ortholog of HMCES exhibits some of the same biochemical properties as …

The Neuroprotective Effect Of Cdc42 Inhibition In The G93a Mutant Hsod1 Mouse Model Of Als, Andrea Koly

Undergraduate Theses, Capstones, and Recitals

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease characterized by the selective loss of upper and lower motor neurons, leading to muscle weakness, neuromuscular junction (NMJ) degeneration, paralysis, and eventual death due to respiratory failure. Despite extensive research, effective disease-modifying therapies remain limited, underscoring the need to identify novel molecular targets involved in ALS pathogenesis. Dysregulation of Rho family GTPases has been implicated in neurodegeneration, with Rac and Rho exerting opposing effects on neuronal survival; however, the role of the closely related GTPase Cdc42 remains poorly understood in ALS. In this study, the therapeutic potential of inhibiting …

Differential Roles Of Moesin And Vasp In Β-Catenin-Associated Networks During Zebrafish Heart Regeneration, Allen Rutman

Undergraduate Theses, Capstones, and Recitals

With cardiovascular disease remaining as the leading cause of mortality worldwide, it is largely due to the limited regenerative capacity of the human heart. However, zebrafish (Danio rerio) can fully regenerate cardiac tissue following injury, providing a valuable model for studying the mechanisms of heart repair. To investigate these mechanisms, we used proteomics methods in the past. Proximity labeling is a technique that identifies proteins based on their physical proximity to a protein of interest. It can be applied in organisms and in living cells (Roux et al., 2012; Cho et al., 2020). We used proximity labeling to characterize protein …

An Extension To A. Goldshtein, Et Al, 2025, Manish Rami

Communication Sciences & Disorders Faculty Publications

This note extends the findings reported in “Onboard recordings reveal how bats maneuver under severe acoustic interference” available at:

Goldshtein, Aya, et al. “Onboard Recordings Reveal How Bats Maneuver under Severe Acoustic Interference.” Proceedings of the National Academy of Sciences, vol. 122, no. 14, Apr. 2025, p. e2407810122. pnas.org (Atypon), https://doi.org/10.1073/pnas.2407810122.

Beyond The Best Fit: Fitting Sir-Style Models To Data While Prioritizing Biological Meaning, Meredith L. Greer

CODEE Journal

Many students find comfort in mathematics because math classes have been a place where they can find the “right answer” to exercises. Modeling courses typically emphasize more nuance, teaching students to try modeling approaches, compare back with real-world mechanisms and data, and then refine their models, in an ongoing cycle. One topic, however, can cause students to quickly revert into “right answer” mode: fitting a model to data. Phrases such as best fit and minimize the distance suggest there is one optimal solution that can be determined by an algorithm, and these algorithms typically have no relationship to the biology …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

1 Billion Birds Lost: Mechanisms Of Window Collisions And Possible Mitigation Strategies At Lawrence University, Shoshana Schmit

Lawrence University Honors Projects

Windows are currently the largest killer of birds on the planet, with an estimated 1 billion birds dying from collisions annually. If birds that hit windows do not die on impact, they may either die elsewhere shortly afterwards, resulting in the number of carcasses at collision sites being a conservative estimate of the actual number of fatalities. During the day, proximity to foraging sites and reflectivity play crucial roles in the danger of windows, and during the night, artificial illumination emitting from windows disorients and inhibits navigational cues. To explore this topic on campus, I documented bird collisions at Lawrence …