Digital Commons Network^™

Comparative Methylation Analyses Across Juglans Species To Investigate Epigenetic Contributions To Fungal Resistance, Keertana Chagari

Honors Scholar Theses

Juglans cinerea (butternut) is a critically threatened North American tree species experiencing severe declines due to the fungal pathogen Ophiognomonia clavigignentijuglandacearum. In contrast, its Asian relative, Juglans ailantifolia (Japanese walnut), shows natural resistance. To investigate the genomic and epigenetic factors underlying this difference, we constructed and analyzed high-quality, chromosome-level genome assemblies for both species from long-read sequencing data (J. ailantifolia: 527Mb; J. cinerea: 586Mb), focusing on transposable element (TE) content, DNA methylation patterns, and regulation of pathogen resistance genes (PRGs).

Repeat analysis revealed that J. cinerea has a slightly higher overall transposable element (TE) content, with …

Effectiveness Of A Contextualized Interactive Multimedia For Grade 8 Science Students, Richard G. Cadizal, Ma. Cristina Bandarlipe

Annual Research Congress for High School and Elementary Teachers, Researchers, and Scholars (ARCHERS)

The Computer-Assisted Instruction is undertaken widely to catch interest and to improve student’s performance. This Descriptive and Quasi- Experimental research was anchored in determining the effects of the developed and validated Contextualized Interactive Multimedia (CIMM) to the non-equivalent groups of grade 8 students of Tanglag National High School in their Science subject. To determine the level of interest of the population toward Science subject, the researcher utilized a 10-item survey-questionnaire called Test of Related Science Attitude (TORSA). Additionally, a researcher-made pretest and posttest questionnaires were administered to determine the academic performance of the respondents. Findings showed that there is an …

Antibiotic Resistance And Molecular Characteristics Of Upcoming Pathogenic Kocuria Spp. Isolated From Iraq And Egypt, Maisam B. Al-Khamesi, Mohamed Khaled Ibrahim, Einas Hamed El-Shatoury, Iman Mohamed Amin El Kholy, Eslam Es Mikawye, Sahar T. M. Tolba

Baghdad Science Journal

Kocuria spp. isolates were collected from different clinical samples from Medical City Educational Laboratories/ Baghdad and Ain Shams Specialized Hospital, Cairo. Identification was carried out by VITEK2 automated compact system. Antibiotic susceptibility, biofilm formation, and detection of macrolides resistance genes ermA, ermB, ermC, msrA & mef, integron intI1 and intI2 were also investigated. Results indicated that 60 isolates were collected from the two countries, 42 isolates from Iraq, and 18 isolates from Egypt. The bacterial isolates were identified by their morphological and biochemical characteristics. They were susceptible to pipracillin/Tazobactam and vancomycin, resistant to …

Antimicrobial And Antibiofilm Activity Of Local Wheat Bran Extract And Bacteriocin Combination Against Gastrointestinal Pathogens, Omer Natheer Abbas, Majid Rasheed Majeed

Baghdad Science Journal

Gastrointestinal microbial infections have increased especially between children and represent a community burden. The present experiment was designed to examine the combined impact of local wheat bran bioactive compounds and Bacteriocin over locally isolated pathogens including S. aureus, E. coli and C. albicans and evaluate their antimicrobial and antibiofilm eligibility. Local wheat Ibaa99 bran extract consists of phenolic compounds, phytic acid and inulin, Bacteriocin was purified from Lacticaseibacillus paracasei that was identified as a new strain (namely MOIQ35) by the 16S rRNA gene using the PCR technique and after its registration with The National Center for Biotechnology Information (NCBI). The …

Amplification Of D18s51, D8s1179, And Fes Loci Of Dna Samples Isolated From Guitar String Stored At Room Temperature, Abdul Hadi Furqoni, Anindita Riesti Retno Arimurti, Meri Meri, Ni Luh Ayu Megasari, Indah Nuraini Masjkur, Qurrota A’Yunil Huda, Intan Sari Nuraini, Luluk Hermawati

Baghdad Science Journal

The act of criminality is an unlawful behavior that constitutes a criminal offense. Criminals use various ways to hide evidence at the crime scene. Forensic experts often find DNA on items found at the crime scene, one of the types of evidence is a guitar. Guitar is one of the musical instruments often played by humans that can be used as a comparison. Methods: This study used 18 guitar string samples that had been used for five minutes and incubated at room temperature. The 18 samples were then divided into three groups, in which each group consisted of six samples …

Downregulation Of Biofilm Formation Genes In Some Pathogenic Bacteria By Extracts From Two Algal Genera, Nishtiman S Hasan, Janan J Toma, Abdulilah S Ismaeil, Suzan A Shareef, Muhsin J Abdulwahid

Baghdad Science Journal

Most infectious diseases are primarily caused by the growth of microorganisms called biofilms. The formation of bacterial biofilms enables microorganisms to inhabit biotic and abiotic surfaces which increases their resistance to antimicrobials. To control this issue, there is a critical need for novel approaches and compounds can suppress the expression or regulation of virulence genes. A potential method for disarming rather than eliminating bacterial pathogens is antivirulence therapy based on the blockage of biofilm pathways. In current study, the action of water, diethyl ether and acetone extraction on two types of algae namely Scenedesmus quadricauda and Chlorosarcinopsis eremi in their …

The Effect Of Bio And Nano Fertilizer On Growth And Yield Of Basil Plant And Its Content Of Active Ingredients, Radhiyah Ali Hasan Ahmad, Hayder Abdulmunem A. Turk, Suha Dhia Abid Ali Twaij

Baghdad Science Journal

A factorial experiment was conducted at the College of Education for Pure Sciences Ibn al-Haitham/University of Baghdad for the 2023 growing season to study the effect of the biofertilizer represented by the mycorrhizae vaccine and the NPK Nano fertilizer on some indicators of vegetative and root growth, yield, and volatile oil production of the basil plant, Ocimum basilicum L., the experiment included two factors. The first factor was mycorrhizae inoculum at 2 levels: 0 (no addition) and an addition of 25 g plant^–1, as the seeds were inoculated upon planting. The second factor was spraying the plant’s shoots …

From The Sea To The Classroom: Harmful Algal Blooms, Northern Sea Otters, And Engaging Curriculum, Emily Mailman

Biological Sciences

Harmful Algal Blooms (HAB) consist of a myriad of phytoplankton that can produce multiple potentially lethal biotoxins, which are ingested by shellfish as they consume algae in their diet. HAB events can occur when sunlight, nutrients, temperature, and turbidity conditions combine optimally. These bloom events are expected to increase as ocean temperatures continue to rise. The present study takes a multifaceted approach to evaluate the concentrations of paralytic shellfish toxins (PST), in northern sea otters (Enhydra lutris kenyoni), and provides a curriculum for students in grades 9-12 to support student’s conceptualization of microscopic phytoplankton and their roles in coastal ecosystems. …

Performative Biomechanics : Evolving Buildings Into Inhabitable Organisms, Josh Lopez

Bachelor of Architecture Theses - 5th Year

There has always been a connection between biology and architecture. Michael Pawlyn, in Biomimicry in Architecture, coined “biomechanical designs” to describe structural techniques derived from creatures. This study investigates chitin-based creatures. Crustaceans, insects, and microscopic organisms all have exoskeletons in nature. With a focus on crabs, other crustaceans and bugs, this study examines and evaluates the formal characteristics of chitin-based organisms. The architectural creations of OXMAN, NOX, which was founded by Lars Spuybroek; and Lebbeus Woods are among those that are analyzed and studied due to their inspiration from living things. They follow functional effectiveness in nature, which is why …

Advancing Mitochondrial Dna Visualization And Dynamics In Plants: Application Of The Mt-Hi-Ness Fluorescent Marker, Madeleine H. Faber

Honors Program: Senior Projects (Public)

Mitochondrial DNA (mtDNA) plays a crucial role in cellular energy production and inheritance, yet its dynamics and exchange remain poorly understood in plant systems due to limitations in visualization techniques. Traditional visualization methods such as exogenous DNA stains and fluorescent protein markers present challenges in specificity and live-cell imaging. To address this challenge, we adapted the MT-HI-NESS fluorescent marker, originally developed for mammalian cells, for use in plant mitochondrial studies. Using Arabidopsis thaliana as a model system, we employed mitochondrial targeting sequences (IVD and AOX) to ensure accurate localization and to confirm mtDNA binding specificity. The validation process included fluorescence-based …

A Cross-Taxa Comparison Of Avian Telomere Dynamics, Age, And Lifespan, Benjamin Konigsberg

Honors Theses

When eukaryotes replicate cells throughout their life, the end regions of chromosomes naturally degrade as a result of the 5' to 3' directionality of DNA polymerase. There is a point when the chromosome is too damaged to provide normal cellular functions, so the cell will die. Telomeres act as a buffer by providing repetitive sequences of non-coding nucleotides. While telomeres do shorten during replication events, the enzyme telomerase can extend telomeres to prevent senescence. Telomere lengths vary between individuals based on different stressor and stress mitigation. Telomeric rate of change is a metric that can capture telomerase activity by measuring …

Population Dynamics, Life History Characteristics, And Environmental Drivers Of Neomysis Americana In The Damariscotta River Estuary, Allison Fogg Ms '25

All Student Scholarship

Mysid shrimp (Neomysis americana) play a pivotal role in estuarine food webs by linking primary producers to higher trophic levels and serving as an important food source for commercially valuable fish. Despite their ecological significance, mysids are often under sampled, leading to gaps in our understanding of their population dynamics and life history traits. My study investigated N. americana over a full year (June 2023 to May 2024) in the temperate Damariscotta River Estuary in Maine. My research focused on how environmental factors such as temperature, turbidity, salinity, chlorophyll-a, and zooplankton biomass affect mysid density and reproduction. Temperature emerged as …

Mesenchymal Stem Cell Secretome For Ischemic Stroke: Cd31 And Vegf Expression, Sisca Silvana, Iskandar Japardi, Muhammad Rusda, Rini Savitri Daulay, Agung Putra, Irawan Mangunatmadja, Dewi Masyithah Darlan, Sri Sofyani, Yana Andreas

Baghdad Science Journal

Standard treatments for ischemic stroke are intravenous thrombolysis and endovascular recanalization. In the acute phase (

Detection Of Mthfr C677t Genotyping For Spina Bifida Defects Using Arms-Pcr Technique, Halah Kamal Al-Qazzaz, Zahraa F. Al-Khero, Hameed Husham Hameed

Baghdad Science Journal

Neural tube defects (NTDs) are complex structural deformities in newborn infants. These defects are caused by a blend of genetic and environmental factors in the abnormal phenotype. The current study aims to determine the genetic variation polymorphism for methylenetetrahydrofolate reductase (MTHFR) C677T rs180133 genotyping and to detect single nucleotide polymorphisms (SNPs) in a DNA sample of Spinal Bifida (SB) and compare it with control newborn children. Blood samples were collected from newborns (50 children under one year old) (25 cases of spinal bifida (SB) and 25 controls). The DNA was extracted and amplified by the tetra ARMS-PCR technique (Amplification Refractory …

Quantifying The Relationship Between Biomass And Edna​, Andrew K. Hogan

Biology Student Scholarship

Andrew K. Hogan ’27, Environmental Biology and English Literature major

Faculty mentor: Dr. Jeffrey Markert, Biology

In this project, we compared eDNA concentration in water to the biomass of present creatures and the time the eDNA in each sample took to decay. With this data, standard curves for both variables can be created and can be used for future experiments and field research. This data will give researchers a greater level of understanding about what animal populations might look like based on the eDNA obtained.

Assessing The Efficacy Of Soil Amendments On Water Use Efficiency And Wheat Productivity For Different Soil Textures, Saadi Sattar Shahadha, Ammar Al-Zubade, Mahmood Raam Sh., Mohamed Ahmed Youssef

Baghdad Science Journal

Irrigation practices on agricultural fields use more water than any other human activity. As a result, the sustainability of water use and food output is intimately tied to how fields are managed. This research was conducted to enhance the long-term viability of water and agricultural production. Soil amendments of compost and perlite were applied in an experiment to investigate the possibility of enhancing soil textures (sandy clay and silty clay) and, consequently, improving the production of crops and water sustainably. The Root Zone Water Quality Model (RZWQM2) was utilized to simulate the water dynamics and water requirement for wheat production …

Jadriyah And Umm Al-Khanazeer Island Sites, Baghdad, Iraq: Status And Eligibility As An Important Bird Area, Aya Yaqoob Jasim, Nadheer Abod Fazaa

Baghdad Science Journal

In Baghdad, the site of Jadriyah and Umm Al-Khanazeer Island (JUKI) was the only IBA nominated by the Birdlife International in 1994 (based on data from 1984). Unfortunately, the JUKI site was deleted from the IBA list in 2017 without proper investigation. We compared our 2022 data with two previous surveys and successfully calculated the trend of the site for the first time. JUKI, as compared to 1984 as baseline data, has currently a medium level of threats (land use change and climate change). Status assessment shows that the site in 2022 has 58.9 % of its 1984 potential habitat …

Serological Detection Of Toxoplasma Gondii In Local Duck Birds, And Gallus Gallus In Basrah Province, Iraq, Ameer Ibrahim Abdulzahra, Alaa Ismail Saood, Afaq Talib Farhood

Baghdad Science Journal

Toxoplasma gondii was widely spread in humans and other animals, including domestic poultry, worldwide and depends on a unique collection of secretory and cytoskeletal organelles for host cell invasion. The meat of T. gondii infected poultry which includes chickens and ducks was widely consumed in most countries and was known as a primary source of human infection. In Iraq generally and in Basrah province especially, the prevalence of T. gondii in local ducks (Anas platyrhynchos domesticus) and domestic chicken (Gallus gallus) was scarcely known. In the current study, the Latex Agglutination Test (LAT) and (TOX) Toxoplasma IgM/IgG Antibody Rapid Test …

Interference With Quorum Sensing Of Klebsiella Pneumoniae By Some Plant Extracts Can Affect The Biofilm Formation And Antibiotic Resistance, Zahraa Eisaa Sadeq, Inam Jasim Lafta, Samah Ali Lamburne

Baghdad Science Journal

Quorum sensing (QS) is a perfectly orchestrated molecular communication system. It is a boon for Klebsiella pneumoniae, and bane for the host. This system is believed to make K. pneumoniae a leading cause of multidrug-resistant (MDR) nosocomial infections. This study aimed to investigate the antibacterial and anti-biofilm potential of medicinal plant extracts through interfering with QS of K. pneumoniae. The effect of different concentrations of ethanolic extracts of cinnamon and clove on K. pneumoniae was determined by analyzing the growth curve, survival assay (MTT), Qualitative and quantitative biofilm formation, antibiotic resistance, along with studying gene expression of the …

The Isolation And Characterization Of Acidovorax And Brevundimonas Bacteriophages With Preliminary Biocontrol Study On Arabidopsis Thaliana, Minh Quynh N. Vu

Senior Theses

As antibiotic-resistance becomes an increasing global concern, researchers are looking for alternatives to combat phytopathogenic rhizobacteria – one of which is through the application of phage biocontrol. To elucidate the complex tripartite relationships between phage, bacteria and plant interactions, nine novel phages were isolated from potential phytopathogenic strains of Acidovorax (RBW13) and Brevundimonas (RBW18). These phages were isolated from root samples obtained from the Rocky Branch Creek and the Broad River located in Columbia, SC. Using Pulsed-Field Gel Electrophoresis (PFGE), we identified seven “medium sized” phages (~40 kbp), one “large-sized” phage (~200 kbp), and one “small-sized” phage ( < 25 kbp). Three phages were determined to be lambda-like due to their “ladder-building” patterns on PFGE. Although spot-tests revealed that all phages seemed to have broad host ranges that spanned over multiple genera, plaque-formations must be observed in future experiments to determine if these phages can infect their hosts productively. Preliminary in planta experiments were performed on Arabidopsis thaliana …