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Journal of Bio-molecule Research And Engineering
Published by Universitas Airlangga
ISSN : -     EISSN : 2962343X     DOI : https://doi.org/10.20473/jbiome.v1i2.45225
Core Subject : Science,
Biochemistry, Genetics & Molecular Biology Chemistry Immunology & microbiology
Journal of Bio-Molecule Research and Engineering [JBIOME] is a peer-reviewed, open-access journal that publishes original research articles, review articles, as well as short communication in the following areas: Biochemistry, Biotechnology, Bioengineering, Microbiology, Molecular Biology, Synthetic Biology, Natural Product Exploration and Extraction, Organic synthesis, Drug discovery, Bioinformatics, Interdisciplinary approaches to Biomolecule Engineering.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 19 Documents
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Isolation and Enzymatic Degradation of Hemicellulose from Corncobs Waste Fithri, Lailatul; Damayanti, Mamik; Ayu, Anna Kartika
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35855

Abstract

Corncobs are rich in hemicellulose, which has very important applications in the food industry and biofuels. Hemicellulose is a heteropolysacharide which contains hexosan such as glucan, mannan, galactan and pentosan such as xylan and arabinan. The aims of this research are determining the optimum condition of hemicellulose isolation and identifying enzymatic degradation products of hemicellulose. Hemicellulose is extracted from corn cobs using various NaOH concentrations and extraction times. Acetic acid was added to the mixture after hemicellulose A reflux process, whereas hemicellulose B was precipitated with ethanol 96%. Enzymatic hydrolysis is carried out using xylanolytic enzyme from a recombinant of E. coli DH5α. The yield of hemicellulose is nearly 64.74% (w/w) using NaOH 4 M for 2 h of extraction time. Based on High Performance Liquid Chromatography data indicating that the enzymatic hydrolysis products of hemicellulose A are xylose and arabinose. While xylose, arabinose, and xylooligosaccharide are hemicellulose B and unextracted hemicellulose hydrolysis products.
In Silico Design Gene Encoding CYP71AV1 for Expression in Escherichia coli Ulfa, Evi Umayah
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35856

Abstract

Cytochrome P450 monooxygenase (CYP71AV1) is a crucial enzyme in the artemisinin biosynthesis pathway. This enzyme oxidized Amorpha 4,11 diene to produce artemisinic acid. This study aimed to in silico design high-level expression of CYP71AV1 in the E.coli system. In silico techniques are highly suitable for designing protein recombinant production before entering the laboratory. The amino acid sequence of CYP71AV1 was back-translated to the DNA sequence and adapt to E.coli codon usage by using Gene Designer. The DNA sequence of optimized CYP71AV1 was analyzed using Rare Codon Analysis to assess the expression efficiency in E.coli. The protein solubility prediction was determined using the SoDoPe tool. The optimized CYP71AV1 was determined to have a CAI 0.81, a GC content of 53.08 %, CFD with low frequency, and no negative cis or repeat elements. The result of the probability of solubility of CYP71AV1 was 0.6207 when expressed in E.coli. The MBP fusion partner can be used to increase the solubility of CYP71AV1. The in silico results showed the possibility of high-level protein expression of optimized CYP71AV1 in the E.coli system.
Isolation and Characterization of Uricase Produced from Chicken Liver Wuryanti Handayani; Nasrul Amaliyatun Naja; Muhamad Kiki Afindia Joenata; Ratnadewi, Anak Agung Istri
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35859

Abstract

Uricase is an enzyme that degrades uric acid into allantoin. One of the uricase sources is obtained from chicken species (Gallus gallus domesticus) liver which are broiler and native chicken. This study aims to determine the maximum uricase activity in broiler and native chicken liver. The uricase activity was obtained by measuring the uric acid concentration as uricase substrate using spectrophotometric method and wavelength at 291 nm. Uricase isolation was carried out into extraction process, ammonium sulfate fractionation (0-60% saturation of ammonium sulfate), and dialysis. During isolation process, centrifugation speed was also optimized to obtain the maximum uricase crude extract and uricase activity. The molecular weight of uricase was also determined by SDS PAGE. The result showed that the highest uricase activity remained using centrifugation speed of 15,000 rpm. The optimum uricase fraction for broiler chicken liver was obtained at 20-40% saturation of ammonium sulfate with uricase activity was 1.854 x 10-2 U/mg, and the uricase fraction for native chicken liver was obtained at 40-60% saturation of ammonium sulfate with uricase activity was 2.496 x 10-2 U/mg. The optimum fraction for uricase production and isolation is carried out to the dialysis process. The optimum uricase activity of broiler chicken liver crude extract was 4.921 x 10-4 U/mg, the uricase fraction was 3.989 x 10-3 U/mg, and the dialysate was 5.120 x 10-3 U/mg. While the native chicken liver crude extract was 2.980 x 10-4 U/mg, the uricase fraction was1.415 x 10-2 U/mg, and the dialysate was 1.753 x 10-2 U/mg. The molecular weight of the uricase was around 35 kDA according to the SDS PAGE result.
Isolation and Characterization of Thermophilic Bacillus subtilis subsp. inaquosorum CGR-1 from Cangar Hot Springs Geraldi, Almando; Aulia Azzahra; Dimas Aryq Ijlal Wafi; Febriani Sukma Maghfirotul Chasanah; Lillah Asritafriha; Rizki Amaliah Zain; Us Watun Nurul Khasanah
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35860

Abstract

Bioindustries often involve biochemical processes that occur at higher temperatures. However, most proteins, including enzymes, lose their structural integrity and functionality at higher temperatures. Thus, thermostable enzymes from thermophilic microorganisms are best suited candidates for successful bioprocessing under such conditions. Indonesia is one of the best study sites for performing bioprospecting of thermostable enzyme-producing thermophilic microorganisms due to the numerous hot springs. To explore the biodiversity of thermophilic microorganisms with potential industrial applications, we isolated and characterized thermophilic bacteria from the Cangar hot spring, Batu, East Java, Indonesia. One isolate (CGR-1) showed growth at 60°C and was identified as Bacillus subtilis subsp. inaquosorum based on 16s rRNA gene sequencing followed by bioinformatic analysis. This is the first report on the isolation of Bacillus subtilis subsp. inaquosorum CGR-1 from Indonesia, especially from a hot spring environment. This isolate showed cellulolytic and amylolytic activity at 50°C, which would encourage further exploration on the industrial and environmental applications.
Partial Purification of Thermophilic Pectinase from Local Isolate Anoxybacillus flavithermus TP-01 Putri, Kartika Dwi Asni; Galih Ayhusta Laras; Ismi Aulia Syafira; Afaf Baktir
Journal of Bio-Molecule Research and Engineering Vol 1 No 1 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i1.35861

Abstract

Pectinase is an enzyme that can hydrolyze substances of pectin. It has several applications in daily life, for example in juice factories, wine factories, pulp and paper factories, coffee and tea factories that use fermentation. Pectinase consists of pectate lyase, pectin lyase, and polygalacturonase. The aim of this research is to partially purify pectinase protein by ammonium sulfate precipitation and dialysis. A preliminary test of pectinase activity used halo zone analysis. The partial purification was needed to optimize ammonium sulfate and get the optimal condition in 40–90% of the ammonium sulfate composition. Pectinase activity was measured using DNS method, and the concentration of protein was measured using Bradford method. The result of this partial purification of Anoxybacillus flavithermus TP-01 was 70%. Decreasing od pectinase activity was resulted in this research due to the loss of cofactor. Based on the result, it can be concluded that the pectinase from Anoxybacillus flavithermus TP-01 was polygalacturonase.
Phylogenetic analysis of DENV-1 isolated in Surabaya, Indonesia Rahmafitria, Fistara Lesti; Mahfudhah, Dzikra Nasyaya; Sucipto, Teguh Hari; Herdyastuti, Nuniek; Anggarani, Mirwa Adiprahara; Fauziyah, Shifa; Damayanti, Mamik
Journal of Bio-Molecule Research and Engineering Vol 1 No 2 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i2.41463

Abstract

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.
Functional group identification of Mimosa Pudica by UV-Visible and FT-IR spectroscopy Gurushankar, K.; K. Viswanathan; Karthik Kannan; S. Christopher Jeyaseelan
Journal of Bio-Molecule Research and Engineering Vol 1 No 2 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i2.41643

Abstract

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 Abdjan, Muhammad Ikhlas; Aminah, Nanik Siti; Kristanti, Alfinda Novi; Takaya, Yoshiaki; Siswanto, Imam
Journal of Bio-Molecule Research and Engineering Vol 1 No 2 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i2.43982

Abstract

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 ≤ 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 (∆Gbind) of each complex using the MM/GBSA approach. The results show ∆Gbind (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.
Screening and Identification of Nitrogen-Fixing Bacteria from Rhizosphere of Mangrove Jenu Tuban Salsabila, Syarifah; Rahmawati, Hanif Nur; Fatimah, Fatimah
Journal of Bio-Molecule Research and Engineering Vol 1 No 2 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i2.45225

Abstract

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.
Elimination of Dengue Virus with Antiviral Compound and Appropriate Technology Farihah, Neni Isna; Wijayanti, Alvia Rachma; Sucipto, Teguh Hari; Putri, Deva Permata; Ihsan, Anaqi Syaddad; Fauziyah, Shifa; Saputri, Ratih Dewi; Damayanti, Mamik
Journal of Bio-Molecule Research and Engineering Vol 2 No 1 (2023)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v2i1.44803

Abstract

Infection with the dengue virus by the Aedes aegypti mosquito vector is in the form of dengue hemorrhagic fever (DHF), which can cause a decrease in platelets and even death. The parasitic drug niclosamide, which is effective against dengue virus serotype 2 (DENV-2) is used to prevent further dengue virus infection. Many tests were carried out using inhibitors such as doxorubicin (SA-17), glycoside inhibitors in the form of deocynojirimycin (DNJ) and castanospermine (CSP), carbohydrate-binding agents (CBA), and the use of heparan sulfate aimed at inhibition of the adsorption process and replication process, as well as improper protein folding to prevent the conformation of virus merger. The elimination process can also be carried out using antiviral compounds found in the leaves of Psidium guajava and Carica papaya, which have inhibitory activities of 92.6% and 89.5%, respectively; propyl gallate, with a percent inhibition of dengue virus envelope protein serotype 2 of 53-9.85%; isobutyl gallate, with CC50 values of 167.19 g/mL and an inhibitory value (IC50) of 4.45; Cissampelos Pariera Linn methanol extract, with progressive inhibition as the Cipa extract concentration increased with an IC50 value of 6.1μg/ml Preventive methods are also carried out in several ways, namely by utilizing hydrophobic liquid in the form of silicone oil (low-viscosity polydimethylsiloxane, or L-PDMS), the use of eave tubes in home tubes inserted with insecticides, and utilizing ultrasound with a frequency of 100 kHz and 90 dB to repel mosquitoes carrying dengue virus vectors.

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