http://http://repository.i3l.ac.id:80/handle/123456789/84 Final Paper of Biomedicine Student 2026-04-21T16:59:28Z http://http://repository.i3l.ac.id:80/handle/123456789/1413 Title: Prediction of T-Cell and B-Cell Epitopes from Protein Allergen Tropomyosin That Are Presented by Major Hla Alleles in The Indonesian Population Authors: Lee, Virginia Gladys Abstract: Shellfish allergy is one of the highest prevalence allergies in the world, accounting for 7.7% of the population including Indonesia. Thus, the development of T cell epitope and B cell epitope based vaccines play an important role in future prospects for alternative treatment for allergy. The vaccine aims to induce the immune system so it will not react towards the allergen though the body already went through sensitization. In this experiment, immunoinformatics methods were used to predict the T cell and B cell epitopes from Pen a 1 allergen, tropomyosin from Penaeus aztecus. T cell epitopes were obtained from NetCTLpan for HLA Class I binding peptide and NetMHCIIpan for HLA Class II binding peptide. As for B cell epitopes, three different servers that are complementary to each other were used; BepiPred 2.0, IEDB B Cell Epitope Prediction Tool, and ABCpred. T cell epitopes were analyzed further for their immunogenicity, IFN-gamma-inducing ability, cross-reactivity against human peptides, and conservancy in other tropomyosin sequences. The vaccine was then constructed using promiscuous T cell and B cell epitopes using beta-defensin as adjuvant and appropriate linkers. The vaccine construct has good population coverage and therefore potential to be developed as an allergen immunotherapy for the Indonesian population. 2023-08-31T00:00:00Z http://http://repository.i3l.ac.id:80/handle/123456789/1312 Title: Optimization of Isothermal Amplification Methods for Identifying Drug-resistant Strains of Plasmodium Falciparum Authors: Deandre Abstract: Plasmodium falciparum, a type of single-celled parasite, is the main cause of malaria and remains a major problem for public health worldwide, especially in areas where healthcare is not easily accessible. A major obstacle in the effort to eradicate malaria is the rise and spread of drug-resistant forms of P. falciparum. These specific strains of malaria parasites have been discovered to reduce the effectiveness of antimalarial drugs. It is crucial to quickly and properly detect these strains of medicine resistance to customize treatment plans and apply effective containment measures. This study addresses the important problem of detecting drug-resistant strains of P. falciparum by providing innovative techniques of isothermal amplification that were specifically designed for this purpose. In this thesis, both the loop-mediated isothermal amplification (LAMP) assay and PCR are utilized as the primary methods for detecting target nucleic acids. Gel Electrophoresis is employed to visualize and compare the amplification results from each technique. By examining the band patterns on the gels, we can compare the results of LAMP to conventional PCR. The findings of this thesis revealed that the LAMP test is a feasible alternative to PCR for application in rural regions. The findings showed that LAMP generated results that were similar as those acquired using PCR. This makes LAMP an appealing choice owing to its simplicity and lack of specific equipment and technical skills. This study introduces an innovative and easily available approach that can aid in identifying and describing drug-resistant strains of Plasmodium falciparum, hence improving efforts to control malaria and optimizing patient results. 2025-08-31T00:00:00Z http://http://repository.i3l.ac.id:80/handle/123456789/1311 Title: Optimization of Isothermal Amplification Reactions for Detecting Drug-resistant Plasmodium falciparum Strains Authors: Valentine, Yeshaya Abstract: Malaria is primarily caused by Plasmodium falciparum, a single-celled parasite that poses a significant public health challenge, particularly in remote locations with little access to healthcare. The emergence of drug-resistant P. falciparum strains poses a significant challenge to malaria eradication efforts. Certain malaria parasite strains have been found to impair the efficiency of antimalarial medicines. Early detection of drug resistance strains is critical for tailoring treatment programs and implementing successful containment strategies. This study introduces novel isothermal amplification techniques to detect drug-resistant strains of P. falciparum. This thesis uses both the LAMP test and PCR to detect target nucleic acids. Gel electrophoresis is used to visualize and compare amplification results from different techniques. Using gel band patterns, we may compare the sensitivity and specificity of LAMP to traditional PCR. The results obtained suggest that the LAMP test condition has been successfully optimized and that it can be further integrated into downstream detection methods or used as it is. The study found that LAMP produced comparable and reliable results to PCR. LAMP is an enticing alternative because of its simplicity and lack of required equipment and technical abilities. This study provides proof of initial development of a novel approach for detecting and defining drug resistant strains of Plasmodium falciparum, leading to improved malaria control and better patient outcomes. 2025-08-31T00:00:00Z http://http://repository.i3l.ac.id:80/handle/123456789/1310 Title: Development of an Isothermal Amplification Reaction Based on LAMP for The Identification of High-Risk HPV Serotypes Authors: Aurelia, Angel Abstract: Human Papillomavirus (HPV) infects mucous membranes and skin, with two main types: low-risk, causing warts, and high-risk, linked to cervical cancer. Accurate identification of HPV serotypes is crucial for developing effective treatment strategies. However, current methods lack precision in distinguishing HPV types. This study aims to develop an accurate detection method for high-risk HPV using newly designed Loop-mediated Isothermal Amplification (LAMP) primers. In this thesis, PCR, LAMP, and colorimetric LAMP were employed to identify target regions of HPV. Gel electrophoresis was used to visualize and compare amplification results. Findings revealed that LAMP and colorimetric LAMP serve as effective alternatives to PCR for HPV detection. Primers targeting HPV18 E7 and L1 genes, and HPV16 E6 gene were designed and tested on HeLa cells. The LAMP results closely matched those of PCR, with optimal primer temperatures between 60–65°C. Primer sensitivity was highest at 50–100 ng/μl DNA concentrations. However, the primer for HPV16 E6 showed non-specific amplification. The colorimetric LAMP assay demonstrated greater accuracy compared to PCR and conventional LAMP, making it a promising tool for HPV detection, especially in rural areas lacking advanced laboratory equipment. This simpler, rapid approach can improve HPV diagnostics, specifically for high-risk types, supporting better treatment strategies and infection control. Overall, this thesis contributes to enhancing HPV detection methods, aiding efforts to manage and reduce HPV-related diseases. 2025-08-31T00:00:00Z