Biology Commons^™

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

(R2167) Global Stability Of Seirs Model With Single Dose Vaccination In Varying Population, Govind Jha, Prabhat Mandal, Sarita Jha

Applications and Applied Mathematics: An International Journal (AAM)

Understanding the evolution of infectious diseases within a dynamic population is essential for formulating effective public health strategies. This work introduces an enhanced SEIRS epidemic model that incorporates demographic variation and a single-dose vaccination strategy, supporting that immunity can be reduced over time. The model reflects diseases in which individuals may return to the susceptible state after recovery. Extending prior reduced three-dimensional models, this study develops a complete four-dimensional SEIRS framework, thereby increasing the model’s applicability to real-world scenarios. The inclusion of the full system presents greater analytical challenges. To overcome this, we extend the second additive compound matrix and …

(R2124) Impact Of Delay And Awareness On Hiv/Aids Epidemic Model, Debashis Biswas

Applications and Applied Mathematics: An International Journal (AAM)

A delayed HIV/AIDS epidemic model with awareness has been taken here. Essentially, it is mentioned that the disease spreads among the population only through contact (horizontal transmission). The equilibrium points of both the proposed models are investigated, and their stability is discussed. Both models have two types of equilibria, namely the disease-free and the disease positive. The basic reproductive number of both models has been calculated by using the next generation matrix technique. In this paper, the main motivation is to find a way to decrease the disease transmission. Also discussed the impact of delay and awareness on the HIV/AIDS …

Investigating The Role Of Cellular Senescence On Vestibular Dysfunction In Repetitive Mild Traumatic Brain Injury, Michael Volyanyuk

Dissertations

Vestibular dysfunction is a prevalent and persistent consequence of mild traumatic brain injury (mTBI). Clinical reports reveal that women experience vestibular deficits more frequently than men following mTBI. Despite the high prevalence and debilitating nature of vestibular symptoms, preclinical literature evaluating mTBI-associated vestibular impairments is limited. Emerging evidence demonstrates that cellular senescence is involved in the pathological molecular sequela of mTBI. It has been shown that senescence contributes to cognitive deficits following repetitive mTBI (rmTBI); however, its role in rmTBI-associated vestibular dysfunction remains unexplored. This body of work investigated the role of cellular senescence on rmTBI-induced vestibular dysfunction in both …

Molecular Identification Of Cryptococcus Albidus Isolated From A Gingivitis Infection In A Male From Karbala City, Iraq, Maysaa Taqi Al-Khazali, Zahraa Raheem Murshidy, Sarah Kadhim Al-Rahimy, Sura Abd Ali Kadhim Mohammed, Dhuha Ali Hussein

Karbala International Journal of Modern Science

The current study presents a case of gingivitis caused by Cryptococcus albidus in a 35-year-old male from the city of Karbala in Iraq. This fungal species was identified via morphology, microscopy, additionally to the VITEK system. C. albidus was further confirmed using the polymerase chain reaction (PCR) technique by amplifying the 18S rRNA gene as a universal primer and sequencing. Sequences analysis revealed that this strain of C. albidus had not been previously documented in the NCBI database. Hence, the newly obtained sequences were submitted to the GenBank repository and assigned the accession number OQ975882.1, marking the first report of …

History And Distribution Of The Dark Ibises (Glossy Ibis Plegadis Falcinellus And White-Faced Ibis P. Chihi) In Arkansas, R. Tumlison, P. D. Rodriguez

Journal of the Arkansas Academy of Science

The Glossy Ibis (Plegadis falcinellus) and White-faced Ibis (P. chihi) sometimes are reported simply as Dark Ibises due to difficulty in identifying them when mature characters are not clearly visible. We evaluated reports verified on citizen science websites to examine the origins and distributions of these migratory species in Arkansas. The Glossy Ibis was first documented in Arkansas in 1956, has been reported in 21 of our 75 counties, and is found more commonly in eastern Arkansas. The White-faced Ibis was first reported in Arkansas in 1971, has been reported in 41 of our 75 counties, …

History And Distribution Of Great-Tailed Grackles (Quiscalus Mexicanus) In Arkansas, R. Tumlison, V. Andersen

Journal of the Arkansas Academy of Science

Great-tailed Grackles (Quiscalus mexicanus) were reported first in southwestern Arkansas in 1969, were nesting there in 1977, and established a resident population by 1980. Nesting was reported in far northwestern Arkansas in 1986. Presently, the species is known from 44 of Arkansas’s 75 counties, those mostly in the western and central counties. Most individuals appear to be migratory, with most reports occurring in April and May. However, breeding and now resident populations have been reported in the southwestern, northwestern, and central counties, particularly in urban areas. Birds are very commonly reported to forage at fast-food establishments and truck …

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% …

House Sparrow Invasion Success Across Ecological, Immunological, And Molecular Scales, Kailey Marie Mccain

USF Tampa Graduate Theses and Dissertations

Biological invasions offer natural experiments for studying how organisms cope with ecological novelty. Although invasion success is often attributed to enemy release, introduced organisms do not enter enemy-free environments. Instead, they enter heterogeneous landscapes in which some familiar enemies are absent, others remain, and entirely novel enemies may be encountered. The question, then, is how invaders (hereafter non-natives) are poised to respond to these threats? This dissertation examines whether successful invasions in house sparrows (Passer domesticus) is associated with shifts in pathogen exposure, immune dynamics in blood, gut physiology, and gene co-expression network structure.

Chapter 1 is at the population/ecological …

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.

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 …

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 …

Reproductive Trends Of Male Atlantic Spotted Dolphins (Stenella Frontalis) Following Two Hurricanes In The Bahamas, Tara Southerland Pedersen

USF Tampa Graduate Theses and Dissertations

Marine mammals are impacted by hurricanes that may influence reproductive success and genetic diversity. Understanding how populations respond to demographic change is increasingly important as extreme weather events become more frequent. A population of Atlantic spotted dolphins (Stenella frontalis) on Little Bahama Bank in the Bahamas has been observed continuously since 1985. In 2004, two hurricanes struck the region within one month, resulting in the loss of approximately 36% of the population. Population declines can alter the operational sex ratio (OSR), social structure, and encounter rates among potential mates, potentially influencing patterns of reproductive success. Previous molecular studies showed that …

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 …

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 …

House Sparrows Reveal Hidden Reservoirs Of Antimicrobial Resistance, Nathan Dowling

USF Tampa Graduate Theses and Dissertations

Antimicrobial resistance (AMR) is a growing global health threat, yet surveillance for antimicrobial resistance genes (ARGs) remains concentrated in clinical and livestock systems, leaving environmental and wildlife reservoirs comparatively understudied. The objective of this study was to evaluate whether one synanthropic bird species integrates landscape-level antimicrobial resistance pressures across socioeconomic gradients and to identify the predictors most strongly associated with cross-national variation in ARG prevalence. We examined ARG occurrence in the globally distributed house sparrow (Passer domesticus), sampling 205 individuals across eight countries spanning large gradients in economic development, antimicrobial use, and governance structure. Using targeted molecular screening of gastrointestinal …

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 …

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 …

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 …

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%, …

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 …

Assessment Of Artificial Oyster Reef Health Based On Water Quality, Oyster Recruitment, And Perkinsosis Infection In Tampa Bay, Christian J. Goldman

USF Tampa Graduate Theses and Dissertations

Providing nursey habitat, regulating nutrients, stabilizing shorelines, increasing biological diversity, improving water quality, and creating three-dimensional environments are some of the ecosystem services of oyster reefs. Oyster reefs are threatened by overharvesting, changes in water quality, pollution, and disease. The Eastern oyster, Crassostrea virginica, is the primary oyster species along Florida’s Gulf coast. This study aimed to evaluate the relationship between multiple parameters on artificial reefs and how they influence the health of these reefs. Here, young (less than five years old) artificial oyster reefs were monitored for one year across three sites in Tampa Bay, FL: Lassing Park (LAS), …