Biotechnology Commons^™

Functional Analysis Of Ligand Binding Domain 2 Of Outer Surface Protein C Of Borreliella Burgdorferi, Gavin Z. Chambers

Theses and Dissertations

Lyme disease, caused by the spirochete Borreliella burgdorferi, is the most common vector-borne infection in North America. A critical determinant of early mammalian infection is outer surface protein C (OspC), a highly variable lipoprotein that is indispensable for spirochete survival but whose precise function remains unresolved. OspC has been proposed to mediate diverse roles, including complement evasion, adhesion, tissue dissemination, and antiphagocytic activity, supporting the view that it is a multifunctional virulence factor. Structural studies have identified two putative ligand-binding domains (LBD1 and LBD2), with LBD2 forming a solvent-exposed crown at the membrane-distal end of the OspC dimer.

To …

Development Of Dna Nanoswitches With Aptamer Based Detection For Thrombin, Camryn A. Beckles

Electronic Theses & Dissertations (2024 - present)

Bio-transducers are devices capable of converting the binding signals from molecular recognition events into readable signals for analytical detection. There is a need for modular bio-transducers that can specifically detect a wide range of analytes using a unified readout technique, as this approach could dramatically reduce costs of healthcare diagnostics and environmental monitoring.

To create such a modular transducer, the molecular recognition properties of aptamers will be used and integrated with the already established biosensing capabilities of DNA nanoswitches that reconfigure their shape in the presence of their target molecule. In this design, the detector strands of the nanoswitch will …

A Novel Silver-Ruthenium-Based Antimicrobial Kills Gram-Negative Bacteria Through Oxidative Stress-Induced Macromolecular Damage, Patrick O. Tawiah

Theses and Dissertations

The rise in drug-resistant bacteria, together with the decline in antibiotic development, requires new strategies for infectious disease control. Gram-negative pathogens are particularly challenging to combat due to their outer membrane. This study highlights the effectiveness of the silver-containing antimicrobial AGXX® against the Gram-negative bacterium Escherichia coli. AGXX® is a promising silver coating that presumably kills bacteria through the generation of reactive oxygen species (ROS). However, neither AGXX®’s mode of action is fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms towards AGXX® been studied in detail. Here, I report that the bactericidal …

Minimizing Cpu Utilization For Job Scheduling Problems By The Advanced Round Robin Method: A Pragmatic Perspective, Haribhau R Bhapkar, Pankaj R Chandre, Parikshit Mahalle

ASEAN Journal on Science and Technology for Development

CPU scheduling issues include minimizing waiting time for processes, ensuring fairness in resource allocation, and optimizing throughput. Balancing these objectives can be challenging, as improving one aspect may negatively impact another, making it essential to design efficient scheduling algorithms. This work presents an innovative approach to enhance CPU utilization through the development of a Result-Based Round Robin Scheduling Algorithm. Traditional Round Robin Scheduling methods often face challenges in efficiently allocating CPU time, leading to suboptimal system performance. In response to these limitations, the proposed method introduces a result-oriented strategy that dynamically adjusts time quantum allocations based on the execution progress …

Distance Metric Learning Techniques For The Performance Improvement Of Ml-Knn And Ranking-Svm-Based Multi-Label Pattern Classification, Shajee Mohan B. S., Sneha S Mohan

ASEAN Journal on Science and Technology for Development

A multi-label pattern classification system tries to predict the set of class labels of a test example by learning from the training examples with the relevant label sets. Classification that involve datasets having multiple labels found immense of applications in pattern analysis tasks involving image, music and video. A test sample can be labeled to indicate different objects, people, music categories or concepts. Classification problems involving data having multiple labels, have to consider training dataset associated with variety of labels. Multi-label extensions of popular algorithms, kNN and Support Vector Machine (SVM) called Multi-label kNN (ML-kNN) and Ranking-SVM are commonly used …

Solid Waste Management Strategies In Coastal Areas Affected By Seawater Flood Disaster, Adib Khoirul Anas, Maryono Maryono, Hartuti Purnaweni

ASEAN Journal on Science and Technology for Development

Solid waste in areas affected by seawater floods must be handled specifically because people often dispose of solid waste on flooded land. This research aims to identify the performance of the community to manage solid waste and solid waste management strategy, solid waste measurement using SNI method 19-3964-1994. Analysis of land affected by seawater floods shows that 12 villages are flooded. Communities in coastal areas are not optimal in managing solid waste because the government has never given directions to manage solid waste in a good way, the facilities and marketing are inadequate so that solid waste is often not …

Potential Of Green Synthesis Of Silver And Gold Nanoparticles For The Management Of Metabolic Associated Steatotic Liver Disease: A Mini Review, Atiqah Suhaili, Ya Chee Lim, Mei Ann Lim, Lee Hoon Lim, Mohammad Mansoob Khan, Monowarul Mobin Siddique

ASEAN Journal on Science and Technology for Development

Metabolic-associated steatotic liver disease is a metabolic disorder with limited pharmacological treatment options and only one approved medication to date. MASLD can be asymptomatic in its earlier stage and hence, prevention of this disease progression is the most effective approach. Recently, green-synthesized nanoparticles, particularly silver (AgNPs) and gold nanoparticles (AuNPs), have gained interest due to their eco-friendly production, biocompatibility, and bioactive properties. This review highlights the biosynthesis of AgNPs and AuNPs using medicinal plant extracts and their reported biological effects relevant to MASLD management including anti-hyperlipidemic, anti-diabetic, antioxidant and anti-inflammatory activities. While findings are promising, further mechanistic studies and preclinical …

Unwritten Rules And Oral Transmission In Architectural Proportion Systems: Case Study Of Bubungan Tinggi House, Huzairin. Muhammad Deddy, Dila Nadya Andini, Rudi Hartono, Anna Oktaviana, Dahliani Dahliani

ASEAN Journal on Science and Technology for Development

The proportional systems in vernacular architecture often exist without formal written codification, raising questions about their transmission across generations. Bubungan Tinggi House which is a replica of the Banjar Kingdom palace was built by Banjarese merchants and aristocrats from the 16th to the 19th centuries, showing a uniform aesthetic quality, which indicates a regularity in the proportions of its form. However, no historical written manuals detailing these proportions are known to exist. To prove the existence of regularity in the Bubungan Tinggi House proportion system, research was conducted by taking 7 Bubungan Tinggi House samples spread across South Kalimantan province, …

Numerical Modeling Of Performance And Phenomena In A Single Proton Exchange Membrane Fuel Cell, Doan Nguyen Cong, Hiep Nguyen Ha

ASEAN Journal on Science and Technology for Development

One of the methods to protect our environment is to convert the fuel's chemical energy directly into electricity, bypassing the fuel's combustion process. This method is implemented in devices called fuel cells. Among them, the proton exchange membrane fuel cell (PEMFC) is widely used in practice because it has outstanding advantages such as high power density and efficiency, low operating temperature and noise, compactness, fast start-up, and, most importantly, only releases water, entirely safe for the environment. The paper presents a method for selecting materials for manufacturing PEMFC components, making a single PEMFC model based on the materials chosen, then …

Ribomoe: An Application Of Mixture Of Experts On Artificial Riboswitch Classification, Hainian Audrey Long

Master's Projects

Urban water sewage is a potential health concern due to its possibility to spread contagious RNA viruses such as Coxsackievirus B3. However, detection of viral particles remains challenging because of low viral concentrations in wastewater and high mutation rates of the RNA virus. To address this, this study proposes a novel viral detection method using synthetic riboswitches that bind to the target virus and trigger a reporter gene, amplifying the detection signals. To support the design of effective riboswitches, we present a machine learning model for classifying riboswitch performance, integrating RNA sequence data with secondary structural features. This model used …

Study Of The Incorporation Of Date Stone Powder On Technological And Rheological Characteristics Of Common Wheat Flour, Djilali Bouhadi, Hamza Belkhodja, Zouaoui Benattouche, Abderrahmane Remil, Ahmed Hariri

Journal of Bioresource Management

The fortification of bakery products with bioactive and functional substances is the main focus of food sciences. These nutrients include date fruits (Phoenix dactylifera L.) and their byproducts. This work aims to illustrate the effects of using date components in bakery products and to determine how these effects affect the products' technological, rheological, and sensory qualities. To achieve this purpose, date powder was introduced in bread making procedure with different rates (1, 3, 5, 7 and 9 %). Then, the physicochemical, sensorial and rheological characteristics was determined. In terms of bread qualities, date powder improved the volume and form …

Black Soldier Fly Larvae (Bsfl) Bioconversion For Circular Economy: A Study In Polaman Village, Siswo Sumardiono, Rizka Amalia, Syaikha Butsaina Dhiya’Ulhaq, Nurika Nazilatul Ilmi, Hermawan Dwi Ariyanto

ASEAN Journal of Community Engagement

Conventional organic waste management methods often lead to environmental degradation and underutilization of valuable resources. In rural areas, such as Polaman Village, limited awareness and inefficient disposal systems exacerbate these issues, thus necessitating innovative and sustainable solutions. This study explores black soldier fly larvae (BSFL) bioconversion as a community-based solution for organic waste management, addresses environmental challenges, and promotes economic empowerment by converting waste into valuable by-products. The study employed a mixed-methods approach, beginning with baseline assessments of waste generation and existing management practices to identify community needs. Educational workshops and hands-on training sessions introduced BSFL bioconversion techniques to local …

Green Synthesis Of Titanium Oxide Nanoparticles From Leaves Extract Of Cassia Fistula And Evaluation Of Their Antimicrobial Activities, Anum Sadiq, Muhammad Shahbaz, Ayesha Shahbaz, Badra Younis, Shmsa Manzoor, Syeda Sabahat Fiaz

Journal of Bioresource Management

The fields of biotechnology, pharmacy, agriculture, and health could all benefit greatly from advances in Nano science and nanotechnology. The synthesis, characterizations, and antibacterial qualities of titanium dioxide (TiO2) nanoparticles made using Cassia fistula leaves in a green synthesis procedure are the main objectives of this work which was carried out between September 2021 and June 2022. Four methods were used to analyse the structure of titanium dioxide nanoparticles: FTIR, XRD, and SEM. According to FTIR research, TiO2 exhibited stretching vibrations at 1500–1600 cm-1 and a UV absorption peak between 250 and 400 nm. Nanoparticle diameters ranged from 145.6 to …

Determination Of The Kinetic Parameters Of Cholesterol Oxidation Using Cholesterol Oxidase From Streptomyces Sp., Meka Saima Perdani, Heri Hermansyah, Muhamad Sahlan, Dwini Normayulisa Putri, Teguh Pambudi, Anggi Khairina Hanum Hasibuan

Makara Journal of Technology

Cholesterol oxidase (CO) was successfully produced from Streptomyces sp. via the submerged fermentation method, and 69 U/mL enzyme activity was obtained. This study aimed to determine cholesterol oxidation kinetics and the production of CO as a catalyst. The enzyme was diluted to 0.15, 0.075, and 0.00375 U/mL for the oxidation reaction. The substrate was also prepared in three concentrations: 3.23, 6.46, and 12.93 mM. The optimization of conditions for enzymatic cholesterol oxidation was investigated through measurement of the effect of initial cholesterol and enzyme concentrations. Cholesterol concentration was rapidly measured via high-performance liquid chromatography (HPLC). The kinetics of CO were …

Assembly Of Ppsu-Oligomers, Mariam Nesterov

Student Theses and Dissertations

The development of nanostructures for delivering multiple proteins to targeted antibodies has become a promising avenue in biotechnology, driven by advancements in synthetic polymers like poly(propylene sulfone), PPSU. However, the PPSU polymer faces a major limitation - its high insolubility. To address this challenge, this study investigates whether PPSU oligomers can enhance both the solubility and stability of lysozyme, a model protein that is cost-effective and widely accessible. Using dimer, trimer, tetramer, and hexamer configurations, we analyzed the interactions between PPSU oligomer and lysozyme under varying conditions. Our results show that the dimer and trimer are water soluble (no aggregate …

Chilling- And Dark-Regulated Photoprotection In Miscanthus, An Economically Important C4 Grass, Jared Haupt, Katarzyna Glowacka

Department of Biochemistry: Faculty Publications

Tolerance of chilling dictates the geographical distribution, establishment, and productivity of C4 crops. Chilling reduces enzyme rate, limiting the sink for the absorbed light energy leading to the need for quick energy dissipation via non-photochemical quenching (NPQ). Here, we characterize NPQ upon chilling in three Miscanthus accessions representing diverse chilling tolerance in C4 grasses. High chilling tolerant accessions accumulate substantial amounts of zeaxanthin during chilling nights in both field and growth chamber settings. Chilling-induced zeaxanthin accumulation in the dark enhances rate of NPQ induction by 66% in the following morning. Based on our data, the emerging ways for the unique …

Distinct Effects Of Extra- And Intracellular Trehalose Supplementation In Freezing Medium On The Post-Thaw Developmental Capacity Of Feline Oocytes, Saengtawan Arayatham, Wirakan Kallayanathum, Panuwat Padungros, Theerawat Tharasanit

The Thai Journal of Veterinary Medicine

Oocyte cryopreservation is a crucial technique for preserving the genetic material of female cats, yet maintaining post-thaw oocyte developmental competence remains a significant challenge. This study investigated the impact of intra- and extracellular trehalose on the developmental competence of feline oocytes following cryopreservation. In Experiment 1, immature feline oocytes were matured in vitro (IVM) with varying concentrations (0, 1.5, and 3 mM) of intracellular trehalose hexaacetate (Tre-(OAc)6). The matured oocytes were then cryopreserved and thawed prior to in vitro fertilization and embryo culture. Experiment 2 examined the effects of extracellular trehalose supplementation at concentrations of 0, 0.125, 0.25, and 0.5 …

Activities Of Cellulolytic, Amylolytic, And Secondary Metabolites From Thermophilic Actinomycetes Collected From The Heated Soil Around Cisolok Geyser, Dhian Chitra Ayu Fitria Sari, Fitria Ningsih, Mazytha Kinanti Rachmania, Akira Yokota, Wellyzar Sjamsuridzal

Makara Journal of Science

This study investigated the antimicrobial activity, cellulolytic, and amylolytic abilities of eight thermophilic Actinomy-cetes isolated from the heated soil around the Cisolok geyser, West Java, Indonesia. Cellulolytic and amylolytic abili-ties were screened for on media by adding 1% (w/v) soluble starch and carboxymethylcellulose (CMC), respectively. Antimicrobial activity was screened for using the agar-plug diffusion method by cultivating strains on various growth media. Growth at various temperatures showed that six strains could grow up to 50 °C. Seven out of eight strains showed amylolytic ability at 40 °C and 45 °C, and only four strains did so at 50 °C. Screening …

Observations On The Biodegration By Solid State Fermentation Of The Giant Swamp Taro (Cyrtosperma Merkusii) Biomass By Two Endolichenic Fungi Isolates, Maria Helena, Helen Joan Lawalata, Dino Rahardiyan, Livana Dethris Rawung, Emma Mauren Moko

Makara Journal of Science

Giant swamp taro (GST/Cyrtosperma merkusii), a local North Sulawesi coastal plant, is underutilized but has high po-tential for cultivation as a paludiculture plant on rewetted peatland restorations. GST has high starch content and is currently being explored for potential use. This study explored the potential of using the biomass pulp yielded as resi-dues of the starch extraction process. Endolichenic fungi (Trichoderma reesei and Aspergillus aculeatus) isolated from local lichens, were inoculated on the GST biomass in a solid state fermentation (SSF). Findings of this study indicate that both isolates were effective in degrading the lignocellulosic biomass of GST over an …

Total Organic Carbon Analysis Of Residual Contaminants In Bioreactor Equipment: A Cleaning Verification Study Using Surface Swabbing, Ciara E. Fitzpatrick, James J. Roche

SURE Journal: Science Undergraduate Research Experience Journal

Contamination is a major issue in the biopharmaceutical industry. Bioreactors must be meticulously cleaned to remove residual impurities and avoid cross-contamination. Cleaning validation is necessary to ensure residual contaminants are reduced to the lowest acceptable limits. Bacterial cells represent the paramount challenge in manufacturing equipment cleaning because they are composed of insoluble organic contaminants. Total organic carbon (TOC) analysis is a fast, highly sensitive, and inexpensive analytical technique commonly used to evaluate the approximate level of organic contamination.

A study was conducted to assess the effectiveness of cleaning procedures in the removal of contaminants from bioreactor equipment by measuring the …