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All Journal JURNAL BIOLOGI INDONESIA Biosaintifika: Journal of Biology & Biology Education
Utomo, Didik Huswo
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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PROTEIN DOMAIN ANNOTATION OF PLASMODIUM SPP. CIRCUMSPOROZOITE PROTEIN (CSP) USING HIDDEN MARKOV MODEL-BASED TOOLS Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i2.3737

Abstract

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium  knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of  CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.  
Molecular Mechanisms of Increased Platelets: An In Silico of the Active Compounds in Psidium guajava Salwa, Khoerina; Susanti, R.; Utomo, Didik Huswo; Yuniastuti , Ari; WH, Nugrahaningsih
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 1 (2024): April 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v15i1.3519

Abstract

Dengue virus infection causes thrombocytopenia. Psidium guajava is widely used by people to increase platelet counts. This research aims to analyze in silico the molecular mechanisms of compounds in guava fruit in increasing platelets. The compounds in guava fruit were taken from Dr. Duke's Phytochemical and Ethnobotanical Databases, which include secondary metabolites such as flavonoids, terpenoids, tannins, alkaloids, and fatty acids. Target proteins were predicted using PharmMapper. Protein interaction networks were created using STRING, visualized, and analyzed using Cytoscape. Potential target proteins were identified by topology, modularity, functional, and KEGG pathway analysis. Degree and betweenness centrality are parameters in topological analysis and the cluster with the highest score is selected as the functional module. The results showed that MAPK1, MAPK14, and AKT1 are involved in many inflammatory pathways, and MMP9 is a target protein directly involved in increasing vascular permeability. The compounds arjunolic acid, farnesene, beta-carotene, and alpha-linolenic acid inhibit MAPK1, citral, ellagic acid, palmitic acid, and oleanolic acid inhibit MAPK14, guaijaverin, pantothenic acid, and citric acid inhibit AKT1, guaijaverin and pantothenic acid inhibit MMP9. It was concluded that the bioactive compounds in guava fruit play a role in increasing platelets by inhibiting the MAPK, PI3K-Akt pathways, and leukocyte trans-endothelial migration, thereby inhibiting or reducing the production and expression of inflammatory mediators and vascular permeability.
Anti-Inflammatory Effect of Phyllanthus niruri: A Meta-Analysis Susanti, R; Fitriya, Farikhatun Nur; Kristamtini, K; Utomo, Didik Huswo
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 2 (2024): August 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v16i2.10823

Abstract

Many studies report on the role of Phyllanthus niruri as an anti-inflammatory and there are variations in the results in every research, so a meta-analysis study is needed to obtain accurate results. This study aims to conduct a meta-analysis of the effect of Phyllanthus niruri as an anti-inflammatory. This study uses a meta-analysis research design with data collection from 12 databases. The screening process was carried out according to PRISMA, then analyzed using Comprehensive Meta-Analysis Version 3 (CMA3). Funnel plot and Egger’s test were used as methods to measure publication bias. The articles used were 438 articles from various research journals. After going through screening, as many as 5 articles were eligible to be incorporated in the meta-analysis. Data were analyzed using a random effect model to calculate standardized means difference (SMD). The cytokines analyzed were TNF-α and IL-6 because both were discussed in at least 3 studies. Phyllanthus niruri affected the reduction of inflammatory cytokines with an effect size of SMD on TNF-α is -17,611 (95% CI -29,347, -5,875; p=0.003) and IL-6 is -3,263 (95% CI -5,403, -1,222; p = 0.003). The results of this meta-analysis strengthen the concept/theory that Phyllanthus niruri has the potential as an anti-inflammatory by reducing the inflammatory cytokines TNF-α and IL-6. These results strengthen the scientific basis for the use of Phyllanthus niruri as a supplement for the community to prevent inflammation.
Co-Authors Arli Aditya Parikesit Fitriya, Farikhatun Nur Karimah, Nihayatul Kristamtini, K Martien Herna Susanti Nugrahaningsih WH, Nugrahaningsih Salwa, Khoerina Yuniastuti , Ari