Life Sciences Commons^™

The Deep Darkness Microbiome: Functional And Taxonomic Diversity In An Oligotrophic Temperate Cave, Philips O. Akinwole, Nina G. Shaffer '25, Emma E.C. Jacobs '25, Zoe Green '27, Thi Doan '27, Crimson Hickman '28, Kaija M. Carr '25, Kenneth L. Brown

Biology Faculty publications

Many subterranean ecosystems are chronically energy limited, yet the mechanisms governing microbial community assembly and metabolic function under extreme carbon scarcity remain poorly resolved. We combined 16S rRNA gene sequencing with community-level physiological profiling (CLPP) to examine how physicochemical gradients regulate microbial diversity and carbon-use strategies across a surface-subsurface transition into the Deep Darkness zone of Indiana Caverns. Progressive isolation from surface inputs resulted in sharp declines in microbial biomass, total organic carbon, and nitrogen, accompanied by increased water content and C:N ratios, indicating strong attenuation of allochthonous organic matter and intensified resource filtering. Microbial communities spanned 42 bacterial phyla, …

The Development Of An In Silico Vaccine Design-Based E-Module To Improve Students' Biological Literacy, Qairinasherin Qwine Ferendi, Rusdi Rusdi, Hanum Isfaeni

Jurnal Pendidikan Sains

Low levels of biological literacy among students, particularly in biotechnology, highlight the need for innovative digital learning media that facilitate meaningful and contextual learning experiences. This study aimed to develop and evaluate an interactive biotechnology e-module based on in silico vaccine design to improve students’ biological literacy. The study employed Educational Design Research (EDR) using the Hannafin and Peck model, which consists of three phases: needs assessment, development, and implementation. The participants included 73 tenth-grade science students and one biology teacher from SMAN 68 Jakarta, Indonesia. The e-module was developed using Canva and Heyzine to create an interactive flipbook integrating …

Principal Leadership As A Predictor Of Teacher Performance: Evidence From An Indonesian Elementary School, Irminapinem Pinem, Antonius Remigius Abi, Hamela Sari Sitompul

Jurnal Pendidikan Sains

Teacher performance is a critical determinant of educational quality and student achievement, making the identification of factors that influence teacher effectiveness an important area of educational research. Among these factors, principal leadership has been recognized as a key organizational variable that shapes teachers’ professional practices and instructional performance. This study aimed to examine the relationship between principal leadership and teacher performance at State Elementary School Raya Kahean, Simalungun Regency, Indonesia. The study employed a quantitative correlational research design involving 52 teachers selected through total sampling. Data were collected using two structured questionnaires measuring principal leadership and teacher performance. The principal …

Lesson-1 On Mni Wiconi (Water Is Life): Understanding The Problem Of Water Contamination, Reycel Jugo, Madhav P. Nepal

iLEARN Teaching Resources

Students investigate a scenario of water contamination in a fictional community. They define the engineering problem of dirty water and explore the cultural and ecological significance of water through the lens of indigenous principles. This lesson introduces students to the concept of water contamination and the need for purification, grounding the learning in a real-world problem and connecting to Indigenous knowledge about the land and water.

Problem-Based Learning (PBL) Scenario: Students receive a letter from a fictional community whose water source has become cloudy and is making people sick. They are tasked with becoming “Water Engineers” to investigate the …

Lesson-2 On Mni Wiconi (Water Is Life): Designing And Testing Solutions (Water Filtration), Reycel Jugo, Madhav P. Nepal

iLEARN Teaching Resources

Students apply the engineering design process to build, test, and refine a simple water filter prototype. This hands-on experiential learning activity focuses on the properties of filtering materials and iterative problem-solving.  In this lesson, students will apply the engineering design process to build and test their own simple water filters. They will use their newfound knowledge to begin developing a practical solution to the problem presented in Lesson 1 - Mni Wiconi: A Water Engineering Challenge for 4th Graders.

Problem-Based Learning (PBL) Scenario: Having identified the problem, students are now tasked with designing and building a prototype water filter …

Developing Biodegradable Packaging Films And Beads From Agricultural Residues, Sandeep Paudel, Santosh Rijal, Srinivas Janaswamy, Madhav P. Nepal

iLEARN Teaching Resources

Agricultural waste is produced in large amounts worldwide. These are often discarded despite being valuable sources of cellulose and renewable, biodegradable products. At the same time, rising environmental concerns about petroleum-based plastic packaging have created demand for sustainable alternatives. Introducing K-12 students to biodegradable packaging materials developed from agricultural waste can enhance understanding of sustainability, basic materials science, and circular bioeconomy concepts while encouraging interest in STEM fields. Another concern is the presence of microplastics and nanoplastics in drinking water, which can pose serious risks to human health. Traditional coagulation agents, such as ferric and aluminum salts, are less effective …

Association Of Household Economic Status And Birth Order With Stunting Among Children Aged 24-35 Months: Malawi Mics 2019–20, Sibongire B. Ngoma, Asri C. Adisasmita, Renti Mahkota, Septyana Choirunisa, Melisa Nyamukondiwa

Jurnal Epidemiologi Kesehatan Indonesia

Stunting remains a major public health concern in Malawi, with a national prevalence of 35.5% among children under five. However, evidence on the independent and combined effects of household economic status and birth order on stunting among Malawian children aged 24-35 months remains limited. This study aimed to examine the independent and combined association of household economic status and birth order with stunting among children aged 24-35 months in Malawi. A secondary data analysis of a cross-sectional 2019-20 Malawi Multiple Indicator Cluster Survey (MICS) was conducted, and the final sample comprised 2,764 children aged 24-35 months with complete data. Stunting …

Comparing The Effects Of Project-Based Learning, Inquiry Learning, And Conventional Instruction On Students' Learning Motivation In Biology, Yeyen Angraini, Irwandi Irwandi, Jayanti Syahfitri

Jurnal Pendidikan Sains

Learning motivation is an important factor influencing students’ engagement, persistence, and success in Biology learning. However, classroom instruction at the senior high school level is often dominated by teacher-centered approaches, which may limit students’ active participation and motivational development. This study aimed to compare students’ learning motivation across Project-Based Learning (PjBL), Inquiry Learning, and conventional instructional approaches in Biology learning. The study employed a quantitative quasi-experimental design with a pretest–posttest approach involving three groups. Participants consisted of 85 Grade XI students from SMA Negeri 1 Talang Padang, South Sumatra, distributed across three classes: PjBL (n = 28), Inquiry (n = …

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 …

Economic Performance And Technical Efficiency Of “Small-Scale” Vegetable Production In Ido Local Government Area Of Oyo State, Nigeria, Taiye Oluwasola Babatunde, Oluyemisi Omowunmi Babatunde

Journal of Bioresource Management

A study was carried out to examine the economic performance of small-scale vegetable farmers and how effectively they are using their resources in Ido Local Government Area of Oyo State. The study involved eighty vegetable farmers who were chosen randomly, and information was gathered from them using structured questionnaires. Different tools such as budget analysis, linear regression, frequency distribution, percentages, and the stochastic frontier production function were used to examine the data that was collected. The results indicated that about 41.3 % of the farmers were between the ages of 41 and 50. Most of the people who answered were …

Crispr/Cas9-Based Genome Editing: Understanding Differences In Dna Repair Pathways, Profiles, And Outcomes, Samuel Effah, Shirley Barrera, Nahia Urturi Ortiz, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the …

Antimicrobial Resistance Profiles And Clinical Dynamics Of Listeriosis In Small Ruminants: A One Health Review, Muhammad Aqeel, Pervez Ahmed Khoso, Amjad Hussain Mirani, Dildar Hussain Kalhoro, Abdul Ahad Soomro

Journal of Bioresource Management

Although the incidence of listeriosis is much lower in small ruminants, it has implications for food safety, herd health and appropriate antibiotic usage as well as zoonotic potential. Both have been reported to be robust pathogens and Listeria monocytogenes is generally recognized as the most common etiologic agent, but in ovine or caprine abortion it should be included as a significant differential diagnosis. This is a narrative one health review that summarizes status of the information published to date on the epidemiology and clinical signs of infection, resistance patterns found and diagnosis and prevention methods employed in small ruminant populations. …

Essential And Non-Essential Amino Acid Composition Of Hilsa (Tenualosa Ilisha) Fish In Different Fishing Regions Of Bangladesh, Mohajira Begum, Md. Moshfekus Saleh-E-In, Md. Zia Uddin Al Mamun, Umma Fatema Shahjadee, Farha Matin Juliana, Md. Sabir Hossain

Journal of King Abdulaziz University: Marine Science

Hilsa, Tenualosa ilisha (Hamilton, 1822), is one of the favourite and popular tropical fish in the people of South-East Asia due to its delicious taste and flavour. This study investigates the comprehensive amino acid profiles of various fishing locations of Bangladesh to assess the protein quality and nutritional values. Fourteen free amino acids were identified from the six riverine locations of Bangladesh. The total free amino acid (TAA) contents were ranged from 11.60 g/100 g in Cox's Bazar to 13,40 g/100 g in Kirtonkhola for raw fish. In the case of smoked treated, the TAA ranged from 14.01 g/100 g …

Operational Risk Assessment Of Ship To Shore Petroleum Transfer Using Fuzzy Rule-Based Bayesian Networks, Ayman F. Alghanmi

Journal of King Abdulaziz University: Marine Science

Petroleum ports represent critical infrastructure in global energy supply chains, where operational risks during ship-to-shore transfer operations can lead to catastrophic consequences including environmental damage and human casualties. Despite rigorous safety protocols, these facilities remain vulnerable to operational hazards in dynamic maritime environments. This research aimed to develop and apply a hybrid Fuzzy Rule-Based Bayesian Reasoning (FRBBR) model to identify, evaluate, and prioritize operational hazards during crude oil transfer operations at petroleum port berths, with a case study conducted in Saudi Arabia, addressing the challenge of risk assessment where historical data is limited.
The research employed a mixed-methods approach combining …

Revolutionizing Coral Research: The Power Of Holo-Omics, Mohammad M. Binsarhan

Journal of King Abdulaziz University: Marine Science

This mini-review highlights the emerging field of holo-omics and its application in unraveling the complex dynamics of the coral holobiont. Corals exist as meta-organisms, closely interacting with a diverse microbiota including bacteria, archaea, microeukaryotes, viruses, and algal symbionts. Understanding these intricate relationships is critical for assessing coral health, stress responses, and resilience to environmental change. We explore the application of meta-omics approaches such as metabarcoding, metagenomics, meta-transcriptomics, metabolomics, and proteomics in profiling coral-associated microbial communities and their functions. The review sheds light on the methodological advantages and limitations of each approach, as well as some of the technical challenges involved …

Microalgae As Sustainable Biofactories For Bioplastic Production: Challenges And Future Perspectives: A Review, Zahraa Hussein Obaid, Noor S. Naji, Jasim M. Salman, Layla Mustafa A.A. Alkatrani

Journal of King Abdulaziz University: Marine Science

The widespread use of traditional plastics, combined with their slow breakdown, has exacerbated environmental and health problems. Therefore, it has become imperative to find alternatives. Due to their simplicity of cultivation, quick growth, tolerance to challenging growing conditions, and low cost, microalgae are being used more frequently as a bio-source for bioplastics lately. Additionally, a variety of biopolymers, including polyhydroxybutyrate, polylactic acid (PLA), starch, polyhydroxyalkanoates (PHA), protein, and cellulose, could be produced by microalgae. These polymers show promising qualities including biodegradability, biocompatibility, and non-toxicity under various cultivation conditions. The purpose of this study is to demonstrate the potential of microalgae …

Magnetically Treated Water: Enhancing Stocking Density, Water Quality, And Growth In Nile Tilapia (Oreochromis Niloticus), Mortada M. A. Hussein, Ayatollah A. H. Abd-El Said, Asmaa N. Mohammed, Fatma M. M. Korni

Journal of King Abdulaziz University: Marine Science

This study aimed to explore the potential of using magnetic treated water (MTW) to increase stocking densities of growing Nile tilapia, Oreochromis niloticus, in storage, productive, and/or rearing holding facilities with limited mortality and water loss. The experimental period was 12 weeks, with 1500 O. niloticus fingerlings acclimated with maintained water parameters. After acclimation, 1350 were randomly selected and used for experiment setting up, including its triplicates. For each replicate, 225 fingerlings were distributed in three experimental tanks of MTW units as group set A, B and C, each received 50, 75, and 100 fingerlings, respectively. Besides, 225 fingerlings …

Environmental Assessment Of The Shatt Al-Basra Canal: Petroleum Hydrocarbons, Heavy Metals And Water Quality, Mohammed A. Jasim Aldoghachi, Bassam A. B. Alabdul Aziz, Shurooq Al-Mosawi

Journal of King Abdulaziz University: Marine Science

The environmental assessment of the Shatt al-Basra Canal in the area of the regulatory was studied. Petroleum hydrocarbons and heavy elements (cobalt (Co), zinc (Zn), lead (Pb), cadmium (Cd), and chromium (Cr)) in the waters of this area were analyzed. In addition, some water quality characteristics were evaluated (salinity, total dissolved solids (TDS), pH, oxygen, biological oxygen demand (BOD₅), chemical oxygen demand (COD), nitrate (NO_3^-), nitrite (NO_2^-), phosphate (PO₄ ^-3), and ammonia (NH₃). Petroleum hydrocarbons had been recorded in studied area and dominated with medium-chain alkanes, namely decane …

Impacts Of Coastal Development And Tourism On Fisheries And Aquatic Biodiversity Of The Red Sea: A Review, Lafi S. Al Solami

Journal of King Abdulaziz University: Marine Science

The Red Sea boasts a diverse coastal environment, unique coral reef biodiversity, and fisheries that support rapidly growing marine tourism. Its excellent tourism facilities make it a popular destination. However, intensive tourist activities such as swimming, boating, diving, and fishing have a negative impact on the coastal and marine ecosystem. Additionally, in line with Vision 2030, Saudi Arabia has launched mega projects along the Red Sea coast, increasing tourist activity and leading to human intrusion into critical yet vulnerable marine ecosystems like coral reefs, fish, sea grass beds, and mangrove stands. With the rise in tourism activities and disruptions to …

Coastal Landforms Analysis Of Al-Kharrar Lagoon And Rabigh Coast Using Aster (Ast_L1t) Imagery, Western Saudi Arabia, Omar A. Alharbi

Journal of King Abdulaziz University: Marine Science

The current study sought to examine the coastal geomorphology throughout the entire length of the Al-Kharrar Lagoon, in addition to the coastal region of Rabigh City, situated on the western coast of Saudi Arabia. The mechanisms underlying the formation of the wide variety of natural land features were also studied. These include sandy, pebble and rocky beaches and sand dunes; intertidal areas; salt flats (sabkhas) and marshes; elevated, terraced or fringing coral reefs; water inlets; and the deposition of terrigenous or alluvial materials, all reflecting the swift transformation that has impacted the region. Evaluation of the ASTER (AST_L1T) data enabled …

The Influence Of Reef Shape On The Fish Community Structure Around Coral Reefs Off Jeddah Coast, Red Sea, Kingdom Of Saudi Arabia, Safaa Alowaidi, Lara Aljarafi, Lina Aloufi, Zekra Albeishi, Fay Al-Salem, Lama Alnebehi, Mohamed Abu El-Regal

Journal of King Abdulaziz University: Marine Science

The purpose of this study is to investigate the effect of the reef profile on the associated fish community. Two stations with different reef shape and depth, Bayada and Abotair islands located off Jeddah coast on the Saudi Arabian Red Sea were studied. The reef check was used to determine the proportion of hard coral, soft coral, algae, and other benthic components. A 20 m long by 5 m belt was used to determine the number and colonies and genera of hard and soft corals. Fish were counted using the underwater visual census (UVC) technique along a transect that is …

Microplastics Contamination In Marine Environment: Sources And Management Strategies, Aishah Hamdi, Mohammad Oves, Naser Alkenani, Majed Alshaeri

Journal of King Abdulaziz University: Marine Science

Microplastics (MPs) have been identified as emerging global pollutants because of their persistence, mobility, and significant ecological impacts. These particles, which result from the degradation of plastic waste and from various industrial and consumer activities, are now widespread in marine environments. The capacity of MPs to adsorb contaminants and bioaccumulate within food webs increases their ecological and health risks, prompting substantial concern regarding their long-term consequences for marine ecosystems and human health. This review synthesizes current knowledge regarding the composition, sources, transport, mechanisms, and environmental behavior of microplastics (MPs), with particular emphasis on marine systems. In these environments, the persistence …

Multi-Label Seabed Image Classification: A Comparative Study Of Deep Learning And Machine Learning Models, Anis Bel Hadj Hassin, Elyes Omri

Journal of King Abdulaziz University: Marine Science

This study evaluates the effectiveness of deep learning and machine learning models for classifying seabed images into three ecologically significant categories: algae, rocks, and sand. We investigated five models: ResNet50, VGG16, a custom-designed convolutional neural network (CNN), support vector machines (SVM), and random forests (RF). Deep learning models were fine-tuned on 1259 seabed images, with the custom CNN architecture optimized using depthwise separable convolutions and global average pooling. For SVM and RF, features were extracted using a pre-trained VGG16 network. Class weighting was applied to address potential imbalances in the dataset. The custom CNN achieved the highest validation accuracy (82.01%), …

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 …

The Multifaceted Medicinal Properties Of Momordica Charantia: Insights Into Phytochemistry And Therapeutic Applications, Maham Ashfaq, Haroon Ur Rashid, Javaria Ashfaq, Shazia Ramzan, Fatma Hussain

Journal of Bioresource Management

Momordica charantia (bitter melon) is a significant medicinal plant, having been long used in traditional medicine in Asian, African and South American systems. M. charantia is more than a traditional medicine; by consolidating existing evidence, it is a promising source of drug discovery and can serve as a complementary in contemporary therapeutics. Over the last several decades, it has become the subject of contemporary biomedical studies due to its abundance of phytochemicals, such as saponins, flavonoids, alkaloids, and polypeptides. These bioactive compounds present a wide range of pharmacological processes that M. charantia can be a natural solution to some of …

Metabolic Markers And Gut Microbiota In Big Cats: A Relationship Between Diet, Health And Environment, Javeria Saman, Saima Sharif, Bushra Nisar, Shagufta Naz

Journal of Bioresource Management

The wild animals that occupy large territories were found to adapt less easily to captive environments compared to those with small home ranges. Among big cats, captivity posed a range of challenges, with stress emerging as central factor influencing overall welfare. Transition into captive environment was shown to alter both behavior and physiological processes, largely due to changes in their natural habitat, environmental complexity and diet. Several health issues reported in big cats including alopecia, gastrointestinal issues, neuromuscular disorders such as hindquarter paralysis were associated with underlying metabolic dysregulation. Metabolic health was recognized as critical component of overall well-being, closely …

Modeling Framework To Demonstrate Elimination Of A Vector Population: Tsetse Elimination In Chad, John Hargrove, Mahamat Hissene Mahamat, Moukhtar Aldjibert, Wilfrid Yoni, Djoukzoumka Signaboubo, Justin Darnas, Ernest Salou, Inaki Tirados, Albert Mugenyi, Priscille Barreaux, Philippe Solano, Antoine Marc Gaby Barreaux

All Peer-Reviewed Publications

Every year, over 700,000 people, particularly children under five, die from vector-borne diseases worldwide. Effectively controlling endemics and preventing new outbreaks requires an integrated approach that can lead to the elimination of both vectors and diseases. In the last two decades, integrating medical interventions and vector control has significantly reduced the incidence of Gambian Human African Trypanosomiasis (g-HAT), with the World Health Organization validating eight countries as having eliminated the disease as a public health problem. However, elimination of the tsetse vector has not been confirmed, leaving the possibility of re-emergence. We developed a six-step modeling framework to assess vector …

Haematological Responses Of Nile Tilapia (Oreochromis Niloticus) To Diets Supplemented With Varying Levels Of Plant Leaf Meals, Isaack V. Makombe, Harishchandra Pratap, Felister Urasa, Blandina R Lugendo

Tanzania Journal of Science

Plant leaf meals have the potential to replace fishmeal in fish feed formulation, hence reducing its cost and increasing fish production. This study evaluated the effects of plant leaf meals (PLMs) on haematological parameters in Nile tilapia (Oreochromis niloticus). The PLMs of cassava, sweet potatoes, cowpeas and common beans were substituted at the rate of 100% (mixed leaves of all four species, Diet 5), followed by each separate leaf meal at 100% (Diet 4), 75% (Diet 3), 50% (Diet 2) and 0% (control diet containing fish meal, Diet 1). Fish collected from Mbegani Fisheries Institute were kept in five, 80 …

Dynamical Behavior, Extinction And Persistence In A Stochastic Delayed Two-Strain Epidemic Model With A Generalized Crowley-Martin Incidence Rate, Amina Allali, Dounia Bentaleb, Saida Amine

Mathematical Modelling and Numerical Simulation with Applications

This paper develops and analyzes a novel delayed stochastic SIR epidemic model with two interacting strains and general incidence functions. By establishing the existence and uniqueness of a positive global solution, the well-posedness of the model under stochastic perturbations is ensured. Extinction occurs when the stochastic reproduction number falls below unity, as demonstrated through Itô calculus and martingale convergence theorems, while persistence is guaranteed under the Crowley–Martin incidence when it exceeds one. Numerical experiments based on the Positive Preserving Truncated Euler–Maruyama (PPTEM) scheme confirm the analytical predictions and highlight the influence of time delay and noise intensity on the long-term …

Urban-Rural Differences In The Association Between Physical Activity And Overweight/Obesity Among Indonesian Adolescents: A Cross-Sectional Study, Wahyu Wulandari, Mufti As Siddiq M. Irzal, Lady Farah Fatmawati

Jurnal Epidemiologi Kesehatan Indonesia

Adolescent overweight/obesity is an increasing public health concern and contributes to the risk of non-communicable diseases later in life. Physical activity plays an important role in weight regulation. However, its association with overweight/obesity may vary according to residential setting. This study aimed to examine the association between physical activity and overweight/obesity among adolescents living in rural and urban areas of Indonesia. A cross-sectional study was conducted using data from the 2023 Indonesian Health Survey. The study included 115,372 adolescents aged 10–18 years. Physical activity was classified based on total Metabolic Equivalent of Task (MET)-minutes per week (≥600 MET-minutes/week), while nutritional …