Biotechnology Commons^™

Study Of Primer Efficiency And Relative Genetic Band Abundance In Different Genotypes, Mundher Kh. Jabbar

Karbala International Journal of Modern Science

This experiment was aimed to find some indicators related to primers and genetic variations. Six bread wheat genotypes were selected as the dataset. The RAPD marker technique was used with oligonucleotide primers as marker of study. The goal was to identify factors used for the relationship between primers and their ability to elicit DNA fragments through different genotypes, as well as the relative genetic band abundance among genotypes. After the designed factors, key findings emerged: in relative primer amplification rate, C1 genotype exhibited a higher relative primer amplification rate (RPAR) of fragments from OP-H01 but did not differ from OP-V19 …

Ddrr Acts As A Dna Damage-Induced Cell Division Inhibitor In Acinetobacter Baumannii, Christian P. Lowe, Deborah Cook, Lily Hoard, Mckinnley Martin, Janelle M. Hare

Acinetobacter baumannii DNA Damage Database

An article titled, "DdrR acts as a DNA damage-induced cell division inhibitor in Acinetobacter baumannii" published in the Journal of Bacteriology on September 9, 2026.

Data Curation And Integration For Cancer Cell Line Pharmacogenomics Analysis, Meric Kinali

Graduate Masters Theses

Cancer cell lines are essential resources for connecting genomic and molecular features with drug response and identifying biomarkers. Therefore, large-scale cancer cell line resources have been growing, but this introduces challenges such as data standardization, consistent annotation, matching identifiers, cross-database integration, and a reproducible computational framework. CellMiner Cross Database (CellMinerCDB) integrates pharmacogenomic datasets from multiple resources and provides a standardized analysis of cell lines across datasets. This thesis examines cancer cell line cross-databases and their importance in pharmacogenomics, with a particular focus on CellMinerCDB. As part of this work, I developed an R package for the gCSI (Genentech Cell Line …

The Role Of Seed Mix Characteristics And Soil Amendments During Post-Agricultural Prairie Restoration, Valerie N. Thurston, Michaela J. Woods, Madelaine Gregory, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Introduction: Prairie restoration on degraded lands may be influenced by seed mix characteristics, including species richness and legume establishment. Soil amendments may facilitate restoration; however, the practical usefulness of techniques such as applications of whole soil and leaf mulch remains relatively unclear.

Objectives: We assessed whether increasing species richness and legume content in seed mixes enhances prairie restoration success and examined how soil amendments interact with seed mix composition to influence cover, species richness, diversity, and legume establishment.

Methods: We conducted a field experiment on a 12-ha post-agricultural site in Ohio, U.S.A. Twenty 50 × 50 m plots received one …

Differential Effects Of Thiamine, Bap, And Thidiazuron Combinations On Shoot Multiplication And Phenolic-Flavonoid Accumulation In Pineapple In Vitro Cultures, Dinda Septia Rachman, Erni Suminar, Anne Nuraini, Fiky Yulianto Wicaksono, Suseno Amien, Syariful Mubarok, Hermanto

Jurnal Kultivasi

The demand for high-quality pineapple (Ananas comosus (L.) Merr.) planting materials continues to increase, while conventional propagation methods are limited in multiplication rate, uniformity, and production efficiency. In vitro culture offers an alternative approach for rapid and large-scale seedling production. However, information on the effects of thiamine and cytokinin combinations on both shoot multiplication and phenolic-flavonoid accumulation in pineapple in vitro remains limited. This study evaluated ten defined combinations of thiamine and cytokinin for shoot multiplication and total phenolic-flavonoid contents of pineapple explants. The experiment employed a completely randomized design with 10 treatment combinations of thiamine (0.1 and 0.4 mg/L), …

Phytochemical Analysis And Safety Assessment Of Watercress Nasturtium Officinale: Antioxidant Capacity, Heavy Metal Profiling, And Toxicity Using Brine Shrimp Model, Qurrota A’Yunin, Chamini Kasun Hemachandra, Muhaimin Rifa’I, Yoga Dwi Jatmiko, Maftuch Maftuch, Rizky Fadilla Agustin Rangkuti, Cucun Herlina, Zulfa Mahdiatur Rasyida, Moh Dliyauddin

Karbala International Journal of Modern Science

Medicinal plants have attracted growing attention as sources of natural bioactive compounds for sustainable aquaculture and health. This study evaluated the phytochemical composition, antioxidant activity, heavy metal profile, and acute toxicity of watercress (Nasturtium officinale W.T. Aiton) methanol extract using maceration, qualitative and quantitative (TPC, TFC, antioxidant DPPH) phytochemical assay, XRF, and BSLA. Phytochemical screening of plant extracts showed the existence of flavonoids, alkaloids, phenols, tannins, triterpenoids, and saponins, but not steroidal. The TPC and TFC were 20.6 mg GAE/g and 10.8 mg QE/g, respectively. The extract displayed significant antioxidant activity (IC₅₀ = 64.78 µg/mL in DPPH assay). …

Electroceuticals In Neuromodulation: Mechanisms, Clinical Applications, And Future Directions, Albashir Tahir, Nura Bello

AUIQ Complementary Biological System

Electroceuticals have emerged as an innovative therapeutic approach that employs targeted electrical stimulation to modulate neural circuits and restore physiological balance. Unlike conventional pharmacological treatments, which act through systemic biochemical pathways, electroceuticals enable precise spatial and temporal control of neural activity. The rapid proliferation of electroceutical devices across clinical and investigational settings, combined with accelerating advances in artificial intelligence, closed-loop engineering, and bioelectronic interface design, has generated an urgent need for rigorous, critically appraised synthesis to guide evidence-based clinical adoption and inform future research priorities. This review addresses the rapidly expanding field of bioelectronic medicine by providing a critical synthesis …

In Vivo Expression Profiling Of Listeria Monocytogenes Internalins (Inlf, Inlp, Inlj) And Their Corresponding Host Receptors (Vim, Afdn, Muc2) Using A Rabbit Ligated Intestinal Loop Model, Nawar Al-Janabi, Nadhim Mushtaq Hashim Al-Bderee, Zahraa M. Madania, Mohanad Jawad Kadhim

Karbala International Journal of Modern Science

Listeria monocytogenes is a Gram-positive pathogen that causes severe infections, particularly in immunocompromised individuals. Internalin genes are important virulence factors that facilitate the bacterium's invasion of host cells. This research aimed to quantify in vivo expression of selected internalin genes (inlF, inlP, and inlJ) and their corresponding host receptors (VIM, AFDN, and MUC2) during L. monocytogenes infection. To achieve this aim, a rabbit ligated intestinal loop model was constructed comprising two intestinal loops. The first loop was injected with 1 mL of L. monocytogenes (1 × 10⁷ CFU/mL), while the second loop was injected with 1 mL of PBS as …

Effectiveness Of Organic Amendments In Enriching Nitrogen In Compost Produced From Organic Fractions Of Market Waste Generated In Dar Es Salaam, Tanzania, Amani Bilula, Ally Mahadhy, Anthony Manoni Mshandete, Amelia Kivaisi

Tanzania Journal of Science

Low nitrogen (N) content remains a key limitation of compost derived from urban organic waste. This study evaluated the effectiveness of selected plant-based organic amendments in enhancing nitrogen content and improving compost quality. Four plant- based organic amendments, Leucaena leucocephala (BN01), Commelina benghalensis (BN02), Morus alba (BN03), and Helianthus annuus (sunflower) cake (BN04), were incorporated into market waste compost at ratios of 1:0.06:0.04, 1:0.06:0.25, and 1:0.06:0.5 (organic waste: sawdust: amendment). Composting was conducted using a 4 × 3 factorial design with three replicates per treatment (n = 36). Temperature, moisture, and pH were monitored throughout the composting period. Total nitrogen, …

Advances In Gene Editing Strategies For Viral Disease Resistance In Pigs: Knock-Out, Knock-In, And Overexpression Approaches, Zhao Namula, Takeshige Otoi, Aya Nakai, Megumi Nagahara, Maki Hirata, Fuminori Tanihara

The Thai Journal of Veterinary Medicine

Highly contagious viral pathogens—such as porcine reproductive and respiratory syndrome, classical swine fever, and African swine fever—continue to pose serious threats to the swine industry and cause major global economic losses. Conventional disease control approaches, such as vaccination and biosecurity, are limited by viral heterogeneity and immune escape mechanisms. Gene editing technologies, most notably the CRISPR/Cas9 system, offer an innovative means of introducing innate viral disease resistance or resilience in pigs. The continuous improvement of these tools can provide a sustainable strategy to enhance animal welfare and global food security and reduce reliance on traditional control measures. This review provides …

First Photographic Record Of A Pale-Colored Wild Boar (Sus Scrofa) Consistent With Leucism In The Zagros Mountains, Iraqi Kurdistan, Bahez F. Ali, Hana A. Raza, Nabaz Horeni

AUIQ Complementary Biological System

Pigmentation anomalies in wild mammals are rare and poorly documented in wild boar (Sus scrofa) populations. Leucism, characterized by partial loss of melanin while retaining normal eye pigmentation, represents one of the least frequently reported coloration anomalies in the species. During a camera-trap survey in Bamo Mountain, Zagros Mountains of Iraqi Kurdistan, an unusually pale-colored wild boar consistent with leucism was recorded. The individual exhibited cream to light-blond pelage with retained darker pigmentation on the snout and distal limbs, while the eyes remained normally pigmented. Its morphology and behavior were otherwise consistent with those of a typical wild …

Uti, Delirium, And Dementia: A Conceptual Bioinformatics Framework For Clinical Attribution, Rob E. Carpenter, Andrew Krouse

Human Resource Development Faculty Publications and Presentations

Urinary tract infection (UTI) is frequently invoked to explain delirium, confusion, and functional decline in persons with dementia. Yet urine positivity in this population often reflects asymptomatic bacteriuria, colonization, chronic pyuria, contamination, or sampling noise rather than clinically attributable infection. For biomedical informatics and computational diagnostics readers, this narrative review contributes an integrative conceptual bioinformatics framework for probabilistic clinical attribution of suspected UTI in dementia under uncertainty. We formalizes the attribution problem by distinguishing organism detection from a clinically plausible infection-related contribution to neurocognitive decline. The framework integrates clinical, laboratory, biological, and longitudinal data to clarify whether urinary findings are …

Endophytic Actinobacteria: Deciphering Therapeutic And Industrial Potential, And Prospects Of Genome Mining In Novel Products Discovery, Yusra Waheed, Rabia Shahdin, Imran Sajid

Journal of Bioresource Management

Endophytic actinobacteria are a diverse group of Gram-positive bacteria with high G+C content, which inhabit plants’ internal tissues, and represent a significant yet underexplored reservoir of bioactive secondary metabolites. In host plants, a remarkable repertoire of metabolites, including broad-spectrum antibiotics, anticancer, antiviral, antifungal, antioxidant, and immunomodulatory compounds, is synthesized by these microbial allies, carrying significant medicinal and agricultural potential. These endophytes, in contrast to their soil relatives, have developed unique biosynthetic gene clusters (BGCs) strongly influenced by plant-associated factors, leading to the production of structurally novel metabolites. In recent years, the advances in genome mining, metagenomics, and metabolomics have accelerated …

In Vitro Anticancer Evaluation Of Tamoxifen And Paclitaxel-Loaded Chitosan Nanoparticles Against Breast And Lung Cancer With In Silico Docking, Arshia Amaan, Farah Mehak, Amer Jamil, Fatma Hussain

Journal of Bioresource Management

Breast and lung cancer are the primary cause of death worldwide, underlining the need for an improved therapeutic strategy. In the current study, tamoxifen (TAM) and paclitaxel (PTX) loaded chitosan nanoparticles (NPs) were produced for the evaluation of sustained drug delivery and enhanced anticancer potential of nanocarriers over conventional chemotherapy against breast and lung cancers, respectively. Nanoparticles were produced by the ionic gelation method and characterized by UV-visible spectroscopy, Dynamic Light Scattering and Fourier Transform Infrared Microscopy (FTIR), verifying the nanoscale morphology, stability and successful encapsulation. A drug release profile study (in vitro) (78 %, 60-75 %) and …

A Review On Nanoparticles: Classification And Roles In Plant Systems, Muhammad Junaid Zafar, Muhammad Shafiq, Muhammad Azeem Rana

Journal of Bioresource Management

Nanotechnology has been a new paradigm of the twenty-first century with several good breakthroughs. These tiny particles, known for their outstanding qualities, are enjoying an increasing influence in many research fields concerning foodstuff, cosmetics, electronics, and pharmacology. Synthesis of nanoparticles includes utilizing chemical processes with reducing agents, alongside employing physical techniques such as top-down and bottom-up approaches for NP formation. The biological approach, known as green synthesis, utilizes plant extracts to ensure increased safety. Biological methods also involve bacteria and fungi, known as the major sources of nanoparticles. It is acknowledged as the most effective and environmentally conscious approach, attributed …

Biotechnological Applications Of Microalgae: Advances, Potential And Future Challenges: A Review, Samiha M. Gharib, Mohamed Z. Nassar

Blue Economy

This review highlights the diverse biotechnological applications of microalgae, emphasizing their significance in human health, nutrition, and sustainable development. Microalgae are among the most widespread photosynthetic microorganisms in aquatic environments, characterized by remarkable metabolic diversity and the ability to produce a wide range of valuable bioactive compounds. These compounds include proteins, lipids, essential fatty acids, pigments, vitamins, and antioxidants, which support their applications in food, feed, pharmaceuticals, and cosmetic industries. In addition to their nutritional and therapeutic potential, microalgae play a crucial role in environmental management through carbon dioxide sequestration, wastewater treatment, and bioremediation processes. Their capacity to convert solar …

Screening For The Suitable Signal Peptide For Secreted Nattokinase Expression In E. Coli Using An In Silico Approach: Precursor Vs. Mature Forms, Dewi Purwani Caya Ningsih, Kartika Sari Dewi, I Wayan Martadi Santika, Ade Andriani, Joko Pebrianto Trinugroho, Muhammad Yusuf

Makara Journal of Science

Nattokinase (NK), an enzyme with thrombolytic activity, has been widely used in treating cardiovascular disease. The expression of NK in the E. coli cell host is favored due to its several benefits, though it often results in inclusion bodies. Appropriate signal peptides can be attached to the N-terminus of a protein to initiate a secretory expression system, thus preventing the nascent protein from aggregating in the cytoplasm. This study aimed to identify suitable signal peptides for the secretory expression of active NK in E. coli and to investigate the impact of pre-protein in NK secretion using an in silico approach. …

Contribution Of Animals To Biomedical Advancements In The Current Era: A Narrative Review, Leena Rajathy Port Louis, Mani Rajarathinam, Prithiviraj Nagarajan, Divya Sekar, Nisha Perumal

The Thai Journal of Pharmaceutical Sciences

Animal research has played a major role in the development of vaccinations and therapies for illnesses such as tetanus, polio, meningitis, hepatitis, and Severe Acute Respiratory Syndrome Coronavirus 2. For every prescription drug available today, animal testing and research have contributed immensely. This narrative review aims to explore the contribution of animals to biomedical advancements in the current era, which involved a search of peer-reviewed literature using electronic databases such as Scopus, Web of Science, and PubMed. In current biomedical research, animals help develop new treatments for long-term illnesses such as cancer, HIV, and Alzheimer’s. Animals also aid in 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 …

Metal Oxide Nanoparticle‑Integrated Phema Hydrogels: Morphology, Chemical Properties, And Biological Interaction, Venkateswar Rao, Collin Cox, Brandon Clark, Arushi Rai, Erick S. Vasquez-Guardado, Madhuri Kango-Singh, Soubantika Palchoudhury

Chemical and Materials Engineering Faculty Publications

Hydrogels offer attractive matrices for incorporating inorganic metal oxide nanoparticles (NPs) to generate multifunctional hybrid materials, but challenges remain in scalable synthesis and correlating their properties to bio-interaction. Therefore, we report the synthesis and characterization of poly(2-hydroxyethyl methacrylate) (pHEMA) hydrogels, and pHEMA hydrogels encapsulating iron oxide or zinc oxide NPs, using a modified free-radical polymerization. Dose-dependent survivorship studies on Drosophila melanogaster revealed that both NP-embedded hydrogels are tolerated over a wide dose range (e.g., 50–200 mg), although ZnO NP-gels exhibit lower survivorship at some concentrations due to their inherent composition and a wider size distribution of iron oxide NPs.