Biotechnology Commons^™

Identification Of Conserved Eukaryotic Gene Products In Novel Mycobacteriophage, Brandon Mar, Jade Coxon, Lily Esterline, Sydney Clifford, Gabriella Burke, Mallory Motz, Alaina Gartner, Kioni Bush, James Lin, Lizzie Adams, Sophia Palant

The Journal of Purdue Undergraduate Research

Bacteriophage, a type of virus that infects bacteria, was discovered 100 years ago, initially isolated with a plaque assay in the 1940s. A mycobacteriophage is a subtype of bacteriophage that specifically infects mycobacteria. Since the introduction of DNA technologies and efforts to identify a plethora of bacteriophages, over 10,000 bacteriophages have been identified with 1,500 sequenced. Bacteriophage discovery has aided in genetic editing techniques, the development of synthetic biology tools, and disease treatment. However, to be able to expand on these capabilities, there is a need to identify more bacteriophages and sequence the genomes of these viruses, as they outnumber …

A Mini Review Of Plant Tissue Culture: The Role Of Media Optimization, Growth Regulators In Modern Agriculture, Callus Induction And The Applications, Norrizah Jafaar Sidik, Hasan M. Agha, Abdulmutalib Alabeed Alkamil, Muneer Mohammed Saleh Alsayadi, Amjad Abdulhadi Mohammed

AUIQ Complementary Biological System

Plant tissue culture is an innovative biotechnological approach developed to meet the escalating global demand for agricultural production with enhanced nutritional value. This aseptic, in vitro technique allows for the cultivation of plant cells, tissues, or entire plants under controlled environmental and nutritional conditions, facilitating the generation of genetically identical clones. The method is indispensable in preserving endangered plant species, boosting crop yield and quality, and enabling year-round production of disease-free plants. Central to plant tissue culture is the composition of the growth medium, which must include a precise balance of macronutrients, micronutrients, amino acids, vitamins, and plant growth regulators …

Analysis Of Natural Structures And Chemical Mapping Data Reveals Local Stability Compensation In Rna, Robert L. Cornwell-Arquitt, Riley Nigh, Michael T. Hathaway, Joseph D. Yesselman, David A. Hendrix

Department of Biochemistry: Faculty Publications

RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for therapeutic applications. However, our ability to design new RNA structures remains limited by an incomplete understanding of their folding principles. While global metrics such as the minimum free energy are widely used, they are at odds with naturally occurring structures and incompatible with established design rules. Here, we introduce local stability compensation (LSC), a principle that RNA folding is governed by the local balance between destabilizing loops and their stabilizing adjacent stems, challenging the focus on global energetic optimization. Analysis …

Clinical Utility Of Opencap Motion Analysis In Lower Limb Prosthesis Users, Sarahi Fernandez Leon

Honors Program Theses and Research Projects

The use of prosthetics has gradually increased due to various diseases, and it is estimated that 35-40 million people are prosthetic/orthotic users, with the number estimated to increase to two billion by 2050. Mobility has been determined to be a strong predictor of quality of life. There are various ways to measure mobility and predict outcomes in lower-limb amputees (LLA), such as self-report and performance-based measures. However, these come with many limitations, showcasing the need for quantitative measures of gait parameters to allow for better development of prosthetic components. Motion analysis tools are expensive and time consuming, but an inexpensive, …

Trend And Awareness Of E-Cigarettes Among Students In A Private College In Sabah Malaysia, Vitalis Ronald Eden, Hazrina Hamid, Sreemoy Das, Regidor Iii Dioso

AUIQ Complementary Biological System

Objective: This study aims to investigate the trend and awareness of e-cigarette use among students in a private college located in Sabah, Malaysia. Research Methods: The cross-sectional study was conducted in a private college in Sabah. A self-administered questionnaire was adapted and distributed to 300 randomly selected students regardless of their e-cigarettes vaping status. IBM SPSS Statistic 27 was utilized to analysed accumulated data. Results: A-245 students participated in the study with a response rate of 81.6%. Majority of the respondent were female (69.8%), Bumiputera Sabah (72.2%), Diploma students (90%) aged 22-25 years’ old. The study revealed that almost all …

Investigate The Possibility Of Producing Healthier, Safer Peanuts Through Molecular Breeding And Novel Fungal Pathogen Management Strategies, Tariq Alam

All Dissertations

Peanut allergy, a critical health concern with high morbidity and mortality rates, is a leading cause of fatal anaphylactic reactions in the United States. Managing peanut allergy is challenging due to the prevalence of peanuts in processed foods and the risk of contamination. This dissertation evaluates the U.S. peanut mini-core collection for four major immunogenic proteins, Ara h1, Ara h2, Ara h3, and Ara h6, using gel electrophoresis, enzyme-linked immunosorbent assay, liquid chromatography, and mass spectrometry. The study identified 26 genotypes with reduced concentrations of allergenic proteins. Genome-wide association studies (GWAS) of protein traits revealed 10 significant SNPs and identified …

Assessment Of Drought Tolerance In Mung Bean [Vigna Radiata (L.) Wilczek] Through Phenology, Growth, Protein Yield, And Cluster Heatmap Analysis, Rafiqul Islam, Jamil Hossain, Shamsul Huda, Mohammad Golam Azam, Faruk Hossain, Aktar Uz Zaman, Safiqul Moula, Nasir Uddin Ahmed, Jamal Hossain, Ayman El Sabagh, Mohammad Sohidul Islum

The Philippine Agricultural Scientist

Mung bean [Vigna radiata (L.) Wilczek] cultivation is challenging under the changing climate as less precipitation during the summer season, which is becoming increasingly common, results in soil moisture deficiency and affects production especially at the early growth stages. Hence, this study was conducted to assess the phenology, growth, and protein yield traits of mung bean related to drought tolerance. Eight mung bean genotypes were grown in pots inside a rain-out shelter under well-watered (WW) and water-deficit (WD) conditions. These genotypes included four water stress-tolerant genotypes: G-1 (BARI Mung-8), G-2 (BMX-010015), G-3 (BMX-08010-2), and G-4 (BMX-08009-7), as well as four …

Polymeric Sumo-2/3 Chain Signals Are Antagonistically Regulated By The Sumo-Targeted Ubiquitin E3 Ligase Rnf4 And The Sumo-Specific Isopeptidase Senp6, Shaniah A. Irving M.A., Xiang-Dong Zhang Ph.D.

Biology Theses

Polymeric SUMO-2/3 chain modification is critical for chromosome segregation, DNA damage repair, genome stability, stress responses, and protein degradation. However, how these signals are regulated remains poorly understood. Both the SUMO-targeted ubiquitin E3 ligase (STUbL) RNF4 and the SUMO-specific isopeptidase SENP6 recognize poly-SUMO-2/3 chains through multiple SUMO-interacting motifs (SIMs). RNF4 contains four tandem SIMs within a short (~80 amino acids) region, whereas SENP6 possesses eight SIMs spanning a much larger (~500 amino acids) domain.

Our preliminary results show that overexpressing an RNF4 N-terminal fragment containing four tandem SIMs (wild type, WT), but not an inactive SIMs mutant (Mut), increases levels …

Timigp: A Computational Framework To Determine The Tumor Immune Microenvironment Associated With Prognosis And Immunotherapy Response, Chenyang Li

Dissertations and Theses (Open Access)

Accumulating evidence has suggested that the tumor immune microenvironment (TIME) drastically impacts cancer patients’ clinical outcomes, including prognosis and immunotherapy response. However, understanding TIME remains challenging due to its complexity and heterogeneity. In this dissertation, we introduce TimiGP (Tumor Immune Microenvironment Illustration based on Gene Pairs), a computational framework designed to address this challenge. Leveraging single-cell RNA-seq (scRNA-seq) and bulk gene expression data alongside clinical information, TimiGP constructs a cell-cell interaction network that elucidates the relationship between immune cell function and relevant clinical outcomes, such as prognosis and treatment response. With immunological insights, these cell-cell interactions also facilitate the development …

A Pan-Cancer Single-Cell Analysis Of Intratumoral Copy Number Diversity And Evolution, Hanghui Ye

Dissertations and Theses (Open Access)

Aneuploidy is a hallmark of human cancers, with many copy number aberrations (CNAs) being associated with disease progression. Previous studies have revealed extensive inter-patient heterogeneity (IPH) in copy number profiles. However, the extent of intratumoral heterogeneity (ITH) and its evolutionary dynamics remain poorly understood.

To address these gaps, we developed Acoustic Cell Tagmentation (ACT), an advanced single-cell single-molecule DNA sequencing (scDNA-seq) technology, to resolve the copy number substructure of human tumors and investigate the evolution of aneuploidy. Applying ACT to eight triple-negative breast cancer (TNBC) patients to profile 9,765 aneuploid tumor cells, we discovered that following initial punctuated copy number …

Derivation Of A Novel Antimicrobial Peptide From The Red Sea Brine Pools Modified To Enhance Its Anticancer Activity Against U2os Cells, Mona Elradi, Ahmed I. Ahmed, Ahmed M. Saleh, Khaled M.A. Abdel-Raouf, Lina Berika, Yara Daoud, Asma Amleh

Faculty Journal Articles

Cancer associated drug resistance is a major cause for cancer aggravation, particularly as conventional therapies have presented limited efficiency, low specificity, resulting in long term deleterious side effects. Peptide based drugs have emerged as potential alternative cancer treatment tools due to their selectivity, ease of design and synthesis, safety profile, and low cost of manufacturing. In this study, we utilized the Red Sea metagenomics database, generated during AUC/KAUST Red Sea microbiome project, to derive a viable anticancer peptide (ACP). We generated a set of peptide hits from our library that shared similar composition to ACPs. A peptide with a homeodomain …

Effects Of Culture Media And Duration On In Vitro Maturation And Production Of Cỏ Goat Embryos, Van Khanh Nguyen, Huong Thi Thu Vu, Au Thi Hoang, Yen Thi Kim Pham, Dat Van Le, Lan Anh Thi Nguyen, Huu Xuan Quan, Lan Doan Pham

The Philippine Agricultural Scientist

This study aimed to evaluate the effects of maturation media and duration on the in vitro maturation (IVM) of Cỏ goat oocytes for the in vitro production of Cỏ goat embryos. In Experiment 1, the highest percentage of matured oocytes and blastocyst rates were observed in the IVM medium consisting of tissue culture medium (TCM) 199 + 10% fetal calf serum (FCS) + 50 ng/mL follicle stimulating hormone (FSH) + 100 μM cysteamine + 10 ng/mL epidermal growth factor (EGF) + 100 units/mL penicillin G potassium + 0.1 mg/mL streptomycin sulphate (P < 0.05). In Experiment 2, Cỏ goat oocytes were cultured in the same IVM medium for 20, 22, and 24 h, respectively. The matured oocyte and blastocyst rates of the 20-h group were lower than those of the 22- and 24-h groups (61.56% vs. 76.81% and 73.48%; 13.76% vs. 24.75% and 24.72% respectively; P < 0.05), while there was no difference between the 22- and 24-h groups (P > 0.05). In conclusion, the TCM 199 medium supplemented …

Student Comprehension Of Biochemistry In A Flipped Classroom Format, Ed Harris, Evan A. Schroder, Teryn J. Berks

Department of Biochemistry: Faculty Publications

Concept-heavy courses such as Biochemistry in life and physical science curricula are challenging for many college-aged students. It is easy for students to disengage in a lecture and not learn the subject matter while in class. To improve student learning and participation, we employed a flipped format for the first half of the course and compared learning outcomes and attitudes with the traditional lecture in the second half of the course. The experimental course was an upper-level biochemistry course taken primarily by juniors (49%), seniors (40%), and some graduate students (10%) at the college level. Our results indicate that lower-performing …

Isolation And Characterization Of Lignin From Oil Palm Shells Using A Precipitation Method With Sulfuric Acid And Polyaluminum Chloride As Coagulant, Eny Kusrini, Ria Yolanda Arundina, Anwar Usman, Resti Marlina, Bambang Subiyanto, Volkan Degirmenci, Nofrijon Sofyan, Yudan Whulanza

AUIQ Complementary Biological System

Lignin has useful and significant properties such as stiffness, resistance to UV radiation, antioxidant, antimicrobial, high thermal stability, and high carbon content. Due to these properties, lignin can be used for several applications including wood adhesive, carbon-based material, and can be developed as a functional material composite. Isolation and utilization of lignin from lignocellulosic biomass offers significant opportunities in various now and future industrial applications mainly for development advanced materials. In this study, isolation and characterization of lignin from oil palm shells (OPS) was conducted. Lignin was isolated from OPS using the precipitation method with sulfuric acid and coagulation using …

Analysing Sound Characteristics Of Cello And Violin Using Fast Fourier Transform, Sinin Hamdan, Khairul Anwar Mohamad Said, Ahmad Faudzi Musib, Marini Sawawi, Aaliyawani Ezzerin Sinin

ASEAN Journal on Science and Technology for Development

The unique sound characteristics of music are based on multiple harmonic frequencies that exist within the sound waves. Through Fast Fourier Transform (FFT) software, the wave can be broken down into frequency and amplitude components. Spectrum analysis can be used quantitatively to describe these sound characteristics. In this paper, the frequency range present in the spectrum and the average intensity of the first 10 high notes in the sound are used to classify the sound characteristics of the cello and violin. This is done by generating a frequency (x-axis) and amplitude (y-axis) graph for the sounds of the cello and …

Exploring Pcat3 Expression In Arthritis: Proinflammatory Marker Patterns And P53 Involvement, Aida H. Alobaidi, Entkhab M. A. Alanisi, Khalid A. Alyodawi

AUIQ Complementary Biological System

This study investigated the role of long non-coding RNA (lncRNA) PCAT3 in arthritis, focusing on its impact on proinflammatory markers. Researchers analyzed both mRNA and protein levels of various proinflammatory markers (TNF-α, IL-1β, IL-4, IL-6, IL-8, IL-10, and IL-13) in arthritis patients and compared them to healthy controls. Additionally, PCAT3 expression was assessed in both patient groups and further investigated using siRNA knockdown in the human synovial cell line SW982. Results revealed distinct expression patterns of proinflammatory markers in arthritis patients, with TNF-α and IL-6 showing the highest levels. PCAT3 expression was significantly elevated in arthritis patients compared to controls. …

Clinical Outcomes Of Isoniazid Preventive Therapy Amongst Persons Living With Hiv Attending A Referral Hospital: A Cross-Sectional Study, Mwaka Dick Odong, Wafula Bossa, Muhwezi Loyce, Nangobi Christine Faith, Mbusa Chrispus, Bontu Aschale Abebe, Daniel Chans Mwandah, Silas Ojuka, Tadele Mekuriya Yadesa

AUIQ Complementary Biological System

Tuberculosis (TB) is the most common opportunistic infection amongst persons living with HIV (Human Immunodeficiency Virus) (PLWHIV). World Health Organisation recommends tuberculosis preventive therapy (TPT) to avert the effects of TB/HIV co-infection. This study aimed at determining the incidence of active tuberculosis infection, assessing the burden of adverse drug events (ADEs) and identifying the associated factors. In this study, records of 379 patients who started isoniazid preventive therapy at Mbarara Regional Referral Hospital (MRRH) between 1^st July, 2017 and 30^th June, 2022 were retrospectively reviewed. Data was analyzed using a statistical software (SPSS version 20.0) and presented using …

Use Of Electrical Bone Growth Stimulators In High-Risk Patients Following Spinal Fusion, Soumya Malhotra, Khavir Sharieff

HCA-NSU MD Research Day

Title: Use of Electrical Bone Growth Stimulators in High-Risk Patients Following Spinal Fusion Authors: Soumya Malhotra, BA., MS1 & Khavir Sharieff, DO, MBA2 1Class of 2027, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Fort Lauderdale, FL 2Assistant Professor of Surgery, Nova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine, Tampa Bay, FLNova Southeastern University Dr. Kiran C. Patel College of Osteopathic Medicine Objective: This study aimed to elucidate the advantages of EBGSs following high-risk spinal fusions. Background: Pseudarthrosis is a condition where bones fail to fuse after an injury or surgery. It causes significant …

The Effects Of Wildfires On The Mental And Physical Health Of School-Age Children In North America: A Scoping Review, Sarah Oerther, Sarah Manspeaker, Alison Wix, Daniel Oerther, Carmen Marsit

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Background: Wildfires are occurring more often and with greater intensity, leading to longer and harsher fire seasons. As a result, children are more frequently exposed to wildfire smoke, which increases their risk of mental and physical health effects. Purpose: The purpose of our scoping review is to explore the current literature on what is known about the direct and indirect impacts of wildfires on the mental and physical health of school-age children in North America (5 to 18-year-olds). Methods: A health sciences librarian-assisted literature search, with input from the research team, was performed. Results: A total of 16 studies were …

Evaluating Uv-Protective Low-Emissivity Window Films: Implications For Thermal And Visual Comfort In Luminous Office Buildings, Lina M. Shaker

AUIQ Complementary Biological System

This review article explores the integration of thin window films and solar energy systems to enhance thermal comfort in luminous office buildings. Luminous office buildings, which prioritize natural lighting, often face challenges in maintaining thermal comfort for occupants. By integrating solar energy systems, such as photovoltaic (PV) and solar thermal systems, with thin window films, it is possible to optimize thermal comfort while harnessing sustainable energy sources. Thin window films act as a barrier against solar radiation, reducing heat gain while allowing therapeutic blue light (400-520nm) transmission. The advantages of thin window films include improved thermal insulation, glare reduction, and …