Journal of Bio-molecule Research And Engineering

Phylogenetic analysis of DENV-1 isolated in Surabaya, Indonesia

2022-12-13T09:54:48+07:00

Dengue virus (DENV1-4) belongs to the Flaviviridae family, which is transmitted by the Aedes mosquito vector and is the main cause of dengue fever and dengue hemorrhagic fever. Since one of the DENV serotypes, DENV1, has become an endemic known to be circulating worldwide, including in Indonesia, it becomes necessary to carry out molecular epidemiological research using phylogenetic analysis with two methods, neighbor-joining (NJ) and UPGMA. This study aims to analyze the DENV-1 relationship and obtain information regarding the differences between those methods, including the level of accuracy. This study used one DENV-1 sequence isolated in Surabaya, aligned with similar sequences on the GenBank. The results showed two comparisons. First, in the NJ method, the DENV-1 sequence samples in Surabaya with branch length 0,000 were similar to the DENV-1 in Malaysia, and Singapore, with branch lengths 0,000; 0,002;. which belong to Genotype 1. The UPGMA method resulted in the DENV-1 sequence in Surabaya with branch length 0,000 were similar to the DENV-1 in Malaysia with with branch length 0,000, which belong to Genotype 1. Second, their level of accuracy, which is in the NJ method, the construction of phylogenetic trees is based on periodic evolutionary times. In contrast, UPGMA assumes that each sequence is found at the same evolutionary time, which makes this method less accurate than the NJ method. We can conclude that the construction and analysis of the phylogenetic tree of the DENV1 sequence isolated in Surabaya have higher similarity and accuracy using the NJ method.

Screening and Identification of Nitrogen-Fixing Bacteria from Rhizosphere of Mangrove Jenu Tuban

2023-07-31T09:04:06+07:00

this study aims to determine nitrogen-fixing bacteria isolates from Jenu mangrove soil, their macroscopic and microscopic characteristics, and species based on the 16S rRNA gene. nitrogen-fixing bacteria were filtered qualitatively using a selective nitrogen-free bromothymol (NFB) medium. screening results showed that six bacterial isolates from Jenu Tuban mangrove soil had potential as nitrogen -fixing bacteria, namely 1,8,10,15, and 16. the six nitrogen-fixing bacteria had varied microscopic characteristics and were gram-positive. based on the identification of the 16S rRNA, it was found that the six isolates were detected as a Bacillus cereus group with 99% query cover and 99.58% identitiy; Bacillus toyonensis with 99% query cover and 99.79% identity; Bacillus altitudinis with 99% query cover and 99.72% identity; Bacillus megaterium with 99% query cover and 99.79% identity; and Bacillus aerius with 98% query cover and 99.86% identitiy.

Functional group identification of Mimosa Pudica by UV-Visible and FT-IR spectroscopy

2022-12-19T11:32:55+07:00

Medicinal plant research involves much more than drug discovery. This area has been expanded to include various topics, such as power negotiations based on medicinal plant lore. A wide range of modern medicines is derived directly or indirectly from plants. Some of these drugs are no longer synthesized in significant quantities by competitors because they have been toxic to humans and other animals. Therefore, this study focuses on scientific research to confirm the knowledge of the phytocompounds of Mimosa pudica by UV-Visible and FT-IR spectroscopy. It also provides clues for evaluating its performance in various fields.

The comparative of free energy binding between Pyrimethamine-pDHFR double mutant and Pyrimethamine-pDHFR quadruple mutant: Structure-based approach

2023-08-15T18:33:59+07:00

Structure-based was performed to understand the mechanism inhibition of pyrimethamine (CP6) against Plasmodium Falciparum mutants at the molecular level. A molecular docking process was carried out to obtain the initial conformation of each system. The data showed in the form of RMSD values, hydrogen bonds, and grid scores. The results show that the RMSD value in the redocking process meets the criteria of the CP6-1J3J and WRA-1J3K complexes with a value of â‰¤ 2 í…. Several hydrogen bonds bind to receptor-active sites, including Ile14, Asp50, Ile164, and Asn108. Additionally, the grid score (kcal/mol) binds well on the active site: CP6-1J3J (-46.86), WRA-1J3K (-65.40), and CP6-1J3k (-44.71). Furthermore, molecular dynamics simulation was carried out to determine the free energy (âˆ†G_bind) of each complex using the MM/GBSA approach. The results show âˆ†G_bind (kcal/mol) in each complex, namely CP6-1J3J (-28.24), WRA-1J3K (-36.62), and CP6-1J3k (-24.23). Information on this research was expected to provide molecular insight into pyrimethamine as an antimalaria inhibitor.