Biotechnology Commons^™

Evaluation Of Semen Characteristics And The Impact Of Storage Time In Dong Tao And Ho Indigenous Chickens, Phan Nhan, Nguyen Thi My Phuong

The Philippine Agricultural Scientist

This study aimed to evaluate the semen quality of 2 indigenous Vietnamese chicken breeds, Dong Tao and Ho, and to assess their reproductive potential for breeding and conservation programs. Semen samples were collected from 10 roosters of each breed and analyzed for macroscopic and microscopic traits. The results indicated that both breeds exhibited semen quality within acceptable physiological ranges. Mean semen volume was 0.47 mL in Dong Tao and 0.48 mL in Ho roosters; pH values were 7.47 and 7.42, respectively. Semen color scores (2.39 vs. 2.35), sperm concentrations (2.11 vs. 1.92 × 109/mL), and mass activity scores (3.79 vs. …

Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu

Dissertations, Theses, and Capstone Projects

This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …

Low-Cost Cutaneous Protoporphyrin Ix (Ppix) Detection (Cpd) Device For Follow-Up Monitoring Of Patients After Photodynamic Therapy, Md Asaduzzaman Rasel

Graduate Masters Theses

Background: Photodynamic Therapy (PDT) utilizes specific wavelengths of light to activate photosensitizing chemical compounds, known as photosensitizers, which induce the generation of cytotoxic reactive oxygen species (ROS) for the targeted destruction of cancer cells. Among various photosensitizers for PDT, Protoporphyrin IX (PpIX) is widely employed in oncology and dermatology due to its natural in situ generation via the metabolic conversion of 5- aminolevulinic acid (ALA), a non-phototoxic prodrug. Systemic administration of ALA after 3-6 hr drug delay leads to peak PpIX accumulation in tissues, facilitating therapeutic and diagnostic applications. However, PpIX can persist in the skin for 24–48 hours post-treatment, …

Antibiogram Development For Neonatal Intensive Care Unit In A Referral Hospital In Sana'a City, Yemen, Mohammed A. Kubas, Massoud K. Rassam, Amaal A. Alsayani

AUIQ Complementary Biological System

Neonates have an immature immune system, making them highly susceptible to infections. Treatment failure in newborns may result from antibiotic resistance, a significant challenge in the management of infectious illnesses worldwide. So the main objective of this research was to develop a newborn-specific antibiogram at the University of Science and Technology hospital (USTH) in Sana’a, Yemen. A retrospective analysis was conducted using microbiological data from the USTH database during the period from January 2021 to March 2022, antibiogram was generated and analyzed using the WHONET application. Gram-positive bacteria were the most frequently isolated pathogens in neonates, followed by gram-negative bacteria. …

Biosorption Of Crystal Violet Onto Fenugreek Seed Powder: Comprehensive Optimization Through Response Surface Methodology And Elucidation Of Dye Uptake Mechanism, Hasan M. Agha, Zaher Mundher Yaseen, Wafaa Raji Alfatlawi, Khansaa Al-Essa, Abdallah Reghioua, Hussein A. Kazem, Lee D. Wilson

AUIQ Complementary Biological System

This work investigates the efficacy of fenugreek seed powder (FSP), an agricultural product, as an economical and sustainable biosorbent for the extraction of crystal violet (CV) dye from aqueous environments. The biosorbent was analyzed using XRD, FTIR, and SEM-EDX, validating its amorphous structure, surface functional groups, and porous shape. Batch biosorption tests were adjusted utilizing a Box–Behnken design (BBD), incorporating three independent variables: FSP dose (0.02–0.1 g/100 mL), pH (4–10), and time (5–60 min). The model exhibited exceptional prediction accuracy (R² = 0.99, CV = 2.12%) and recognized all three variables as statistically significant (p < 0.05). The maximum CV removal attained was 91.8% efficiency at an FSP dose of 0.1 g/100 mL, pH 7, and a time of 60 minutes. FTIR examination indicated changes in the –OH, C=O, and C–O functional groups, signifying their participation in dye interaction, whilst SEM pictures validated dye deposition on the biosorbent surface. The biosorption process was ascribed to electrostatic forces, hydrogen bonding, π–π stacking, and pore filling. These findings underscore FSP as a viable, economical biosorbent for the removal of cationic dyes in wastewater treatment applications.

In Silico Investigation Of The Anticancer Activity Of Natural Isoquinoline Alkaloids Targeting The Monoamine Oxidase A Enzyme, Reham A. Al-Anssari, Anwar H. Ali, Ola Adel Al-Saad, Shaker A.N. Al-Jadaan

AUIQ Complementary Biological System

Monoamine oxidase A (MAO-A) has recently been identified as a candidate for cancer therapy due to its roles in tumor development and growth. Conventional approaches for the discovery of MAO-A inhibitors are both costly and time-consuming. The objective of this work was to apply in silico methods to predict natural isoquinoline alkaloids capable of acting as potent MAO-A inhibitors, and to establish this class of compounds as potential sources of a cost-effective anticancer therapy. Twenty-one natural isoquinoline alkaloids were subjected to a multistep computer-aided drug discovery protocol. The compounds were initially screened for pharmacokinetic (ADME), toxicity, and drug-likeliness properties by …

Enhanced Meropenem Activity And Stability Following Load In Polyvinyl Alcohol Nanofiber Scaffolds With Sitagliptin As Quorum Sensing Inhibitor On Pseudomonas Aeruginosa, Samar A. Salim, Abdelrhman Mohsen, Mohamed Emara, Taghrid Elmahdy

Nanotechnology Research Centre

Background The increasing resistance of bacteria to conventional antibiotics poses a significant health challenge. Innovative strategies, such as combining antibiotics with agents like quorum sensing inhibitors (QSIs), have been developed to combat this issue. QSIs enhance antibiotic efficacy without inhibiting bacterial growth, minimizing the risk of resistance. Aims Evaluate the combined effect of Sitagliptin (STG) as a QSI with Meropenem (MER), fabricate drug-loaded Polyvinyl Alcohol (PVA) nanofibers, and investigate their antimicrobial activity against standard Pseudomonas aeruginosa (PAO1) and carbapenem-resistant P. aeruginosa (CRPA). Methods The combinatorial effect was assessed using a checkerboard assay. PVA/STG, PVA/MER, and PVA/STG/ MER nanofibers were fabricated …

Biogenic Calcite Precipitation For Coastal Sand Stabilization: A Synergistic Approach Using Marine Bacteria And Natural Fibers, Aparna Gs

Theses and Dissertations

Coastal erosion, driven by natural forces such as waves, tides, winds, and currents and further intensified by anthropogenic activities like urbanization, climate change, and coastal infrastructure development, poses a significant threat to shoreline stability. Conventional erosion control methods, including jetties, embankments, and artificial reefs, often face limitations in sustainability and effectiveness. In this context, microbially induced calcite precipitation (MICP) has emerged as a promising ecofriendly solution for ground stabilization.

The present study investigates the potential of an indigenous ureolytic marine bacterium, Bacillus sp. N₉, isolated from the coastal sediments of Nagapattinam, Tamil Nadu, for coastal sand stabilization. The strain was …

Genomic Surveillance Of Indian Klebsiella Pneumoniae And Exploration Of Resistance Inhibitors, Abhirami Ks Ms

Theses and Dissertations

Klebsiella pneumoniae is an important ESKAPE pathogen that causes life threatening infections. The strains exhibiting multidrug-resistance (MDR) and hypervirulence are the priority pathogens for which immediate treatment and dissemination prevention strategies are required. To address this, genome profiling was performed to understand the AMR patterns, role of episomes, phages, virulence determinants and its association with sequence types.

The study includes 267 publicly available Indian K. pneumoniae genomes over a period of ten years and four sequenced isolates. Whole genome analysis revealed the widespread presence of diverse β-lactamase genes, with β-lactam resistance being predominant. Genes such as blaCTX-M-15, blaTEM-1B and blaOXA-232 …

Agricultural Biotechnology In The Courts: Judicial Opinions And Commentary, Drew L. Kershen

Faculty Articles

Seven jurisdictions from around the world have issued judicial opinions that address fundamental issues about the governance and regulatory systems of agricultural biotechnology. This article summarizes these legal proceedings and describes their impact upon agricultural biotechnology. The article then provides a commentary and critique of the legal proceedings and resulting judicial opinions.

Advancing Single-Molecule Nanopore Sensing: From Protein Conformation And Metal Binding To Dna Transport Via Hybrid Nanostructures, Matthew J. Odonohue

Multidisciplinary Studies Theses and Dissertations

This dissertation presents the development and application of solid-state and hybrid nanopore platforms for single-molecule analysis of biomolecular interactions. First, a silicon nitride nanopore was employed to characterize the conformational states of the transferrin receptor (TfR), enabling discrimination between its monomeric and dimeric forms, as well as from its ligand, human serum transferrin (hSTf), despite their similar molecular weights. In a separate study, the same nanopore configuration was used to track the real-time binding of titanium ions to transferrin, demonstrating single-molecule sensitivity to metal-induced conformational changes. A hybrid microtubule–solid-state nanopore (MT–SSN) was then engineered, repurposing microtubules as electrostatically anchored conduits …

Volumetric Imaging Of Cellular Dynamics Using Light-Sheet Microscopy: From Subcellular Structures To Whole Organisms, Md Nasful Huda Prince

Optical Science and Engineering ETDs

Advancing biomedical imaging requires platforms that combine high-resolution, speed, and stability across biological scales. This dissertation presents three innovations designed to address limitations of conventional light-sheet and oblique plane imaging. First, we introduce Reflected Inline Detection in Epi-Oblique Plane Microscopy (RIDE-OPM), a compact and drift-resistant system that eliminates a tertiary detection path while maintaining alignment flexibility, enabling robust long-term live imaging. Second, we present a high-speed Axially Swept Light-Sheet Microscopy (ASLM) platform for cleared tissues, using dual foci and synchronized sweeping to achieve isotropic sub-micron resolution at up to 40 frames-per-second, a fourfold improvement over standard ASLM. Integrated with a …

Applying Transcriptomics For Technology Development And Conservation In North American Marine Organisms, Cory Von Eiff

Dissertations

RNA biology is a rapidly expanding field, with many avenues of discovery among marine organisms. In this study, we analyze both mollusks and sawfish. First, we perform an evaluation of sRNA biogenesis pathways throughout Mollusca, with emphasis on the easter oyster, Crassostrea virginica. Understanding these molecules prescribes RNAi-based gene silencing approaches, benefiting genetic investigation and biotechnology. Similar to other animal groups, mollusks have conserved microRNAs (miRNAs), with some shared with ecdysozoans and deuterostomes; however, there is no evidence of an endogenous small interfering RNA (siRNA) pathway. These results suggest that long double-stranded RNA (dsRNA)-based RNAi is not appropriate for gene …

Modeling U.S. Corn Production Archetypes In The Agricultural Policy/Environmental Extender Model To Generate Life Cycle Assessment Inventory Data, Brandon Taylor

Graduate Theses and Dissertations

Corn (Zea mays) is an important crop grown across the US for many uses such as grain for animal feed, bio-ethanol production, food products, and industrial products. Corn is produced in almost every state in the US, but most corn production is concentrated in the Corn Belt Region including Iowa, Illinois, Ohio, Indiana, Minnesota, and Nebraska. Although technologies and production practices are improving corn production efficiency primarily through increased yields (improved land use), corn production at this scale greatly impacts the environment through emissions from fertilizer and pesticide runoff and leaching, soil degradation due to improper field practices, as well …

Reframing Sleep Diagnostics: A Structured Clinical Guide To Polysomnography Evaluation, Elvie Zulka Kautzia Rachmawati, Mikhael Yosia

AUIQ Complementary Biological System

Polysomnography (PSG) remains the gold standard for evaluating sleep-disordered breathing (SDB) and related conditions, yet its clinical potential is often limited by overreliance on the apnea-hypopnea index (AHI) and similar summary metrics. This narrative review offers a structured, physiology-informed approach to PSG interpretation that integrates sleep architecture, arousal burden, respiratory event morphology, oxygenation patterns, and CO₂ trends. Recognizing phenotypic patterns-such as REM-related and positional OSA-through sleep stage and positional stratification is essential for directing targeted therapy. We outline common interpretive pitfalls, including automated scoring errors, overlooked signal artifacts, and the first night effect, emphasizing the need for careful manual …

Transformative Role Of Laser Technology In Ophthalmology And Dermatology: A Mini Review Of Precision Applications In Modern Medicine, Haider Hameed, Maryam Aqeel, Hussein Rafid, Rasha Sabah, Mustafa Fadhel, Zahraa Hameed, Muqtada Khalawi, Zahraa Sarmed, Ail Ahmed, Ayat Abd Albari, Lina M. Shaker

AUIQ Complementary Biological System

Laser technology has significantly transformed healthcare and biological sciences by Laser devices are offered precision, efficiency, and Multiple simple solutions in various medical fields and research domains. In ophthalmology, lasers play a pivotal role in vision correction, retinal imaging, and therapeutic applications, such as femtosecond laser-assisted LASIK and two-photon fluorescence scanning laser ophthalmoscopy. Dermatology has also benefited from CO₂, Nd:YAG, excimer, and Q-switched lasers, which are widely used for pigmentation disorders, tattoo removal, and skin rejuvenation. Moreover, Low-Level Laser Therapy (LLLT) enhances wound healing and tissue regeneration, while intense pulsed light (IPL) and diode lasers improve hair removal …

The Influence Of Myocardin Effector Genes On The Tgf-Beta Smad3 Signaling Pathway In Human Pleural Mesothelial Cells, Hema Chandra Hrushi Dusharla

Biotechnology Theses

Pleural Fibrosis (PF) involves excessive extracellular matrix (ECM) deposition, mainly by myofibroblasts, leading to pleural thickening and impaired lung function. Pleural mesothelial cells (PMCs) contribute via mesothelial and mesenchymal transition (MesoMT), triggered by cytokines like TGF-β. Our lab identified Myocardin (MyoCD), a transcriptional co-activator of cardiac and smooth muscle, is a master regulator of pleural fibrosis through interactions with serum response factor (SRF) and Smad2/3 transcription factors which initiate fibrosis signaling. RNA sequencing and qPCR analysis revealed that silencing MyoCD decreased the expression of CTNNB1, MDFI, and Tspan2. MDFI emerged as a potent candidate, as this gene affecting the expression …

The High Burden Of Depression, Anxiety, And Stress Among University Students In Southern Iraq: A Cross-Sectional Study, Hassan Al-Karagoly, Zahraa Al-Attar, Hjar Al-Asadi, Sajad Al-Lahibi, Russul Al-Fartousi, Teeba Al-Jadry, Menatallah Bali, Baneen Al-Hasnawi, Hanan Al-Aboudi, Zainab Al-Fadliu, Ali Al-Mosawi, Zahraa Al-Aboudi, Qassim Al-Rubaie, Mohsin Al-Samawi, Abdulsalam Halboup

AUIQ Complementary Biological System

University students often face significant academic, social, and environmental pressures, making them particularly vulnerable to psychological distress. Despite this, there is limited evidence regarding the prevalence and associated factors of mental health problems among university students in Iraq. Therefore, this study aimed to assess the prevalence and severity of depression, anxiety, and stress in this population and to examine their associations with sociodemographic characteristics, insomnia, internet use, and physical activity. A cross-sectional study was conducted among Iraqi university students using a structured questionnaire, including the DASS-21, Insomnia Severity Index, and Internet Addiction Test. Descriptive and inferential statistics were used to …

Knowledge Of Hiv Transmission And Prevention Among University Students In Pakistan: A Cross-Sectional Study, Muhammad Saleem, Sajid Masood, Shahid Hussain

Journal of Bioresource Management

HIV/AIDS remains a significant public health problem internationally, with young adults being especially at risk because of behavioral and knowledge deficits. In Pakistan, cultural inhibitions and suboptimal health education are the main reasons for limited awareness, particularly among university students. This study had the objectives of determining the knowledge level about HIV transmission and prevention among undergraduate students in Kohsar University Murree (KUM) and to investigate correlations with salient demographic variables. A cross-sectional survey was carried out among 510 students aged 18-27 years through a pre-validated, standardized questionnaire with 12 knowledge-based items. Descriptive statistics and Chi-square tests were utilized to …

Phylogenetic Analysis Of Ftsz In Wolbachia: Implications For Host Specificity, Anwar Rovik, Ayu Rahayu

Makara Journal of Science

Wolbachia are the most prevalent and successful endosymbiont in invertebrates and are categorized into 21 supergroups based on genetic phylogeny. The filamenting temperature-sensitive Z (FtsZ) protein is essential for bacterial cell division and is hypothesized to play a role in Wolbachia's control of host reproduction. However, despite FtsZ's importance, little is known about its diversity and function within Wolbachia. This study investigated the variability of the FtsZ-encoding gene among Wolbachia strains and their hosts. FtsZ gene sequences were retrieved from the National Center for Biotechnology Information database, and representative sequences were randomly selected from each host species and analyzed …