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Annales Bogorienses
Published by Badan Riset dan Inovasi Nasional
ISSN : 05178452     EISSN : 24077518     DOI : https://doi.org/10.55981/ann.bogor
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Annales Bogorienses aims to disseminate high-quality scientific research in the field of life sciences, with a strong emphasis on advancing knowledge and applications in biotechnology, molecular biology, biochemistry, bioinformatics, and bioengineering. The journal serves as a platform for researchers, academicians, and practitioners to share original findings, innovative methodologies, and critical reviews that contribute to scientific progress and sustainable development. The journal covers research in biotechnology, molecular biology, biochemistry, bioinformatics, and bioengineering. It publishes original research articles, reviews, and short communications, and is committed to rigorous peer review and open access for the widest possible dissemination of scientific knowledge.
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Articles 203 Documents
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EDITOR'S PREFACE Puspita Lisdiyanti
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

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Abstract

Optimization of Culture Conditions for Production of β-Mannanase by Strain Nonomuraea sp. ID06-379 using Submerged Substrate Fermentation Shanti Ratnakomala; Yopi Yopi; Maggy Thenawidjaja Suhartono; Anja Meryandini; Bambang Prasetya
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2014.v18.n2.1-11

Abstract

The objective of this study was to investigate the effect of media compositions on the production of β-mannanase by Nonomuraea sp. ID06-379. The study was focused on the influence of carbon, nitrogen, phosphorus and detergents on β-mannanase synthesis through manipulating media compositions on production medium. The results indicated that for carbon sources, locus bean gum (0.745 ± 0.036 U/ml) showed maximum mannanase activity. Malt extract was the best nitrogen source for producing β-mannanase (1.075 ± 0.006 U/ml), (NH4)2HPO4 as phosphate source (1.733 ± 0.026 U/ml) and Tween 80 (1.145 ± 0.003 U/ml) as surfactants effect on increasing permeability of bacterial cell membrane, enhancing membrane transport and excretion of extracellular enzymes into the production media. The results showed that 1% malt extract, 0.5% locus bean gum and 0.05% (NH4)2HPO4 were good substances for nitrogen source, carbon source and phosphate respectively. The highest production of β-mannanase by Nonomuraea sp. ID06-379 (5.33 U/mg) was reached in the medium optimization (Vogel’s minimal medium) contained the following ingredients: 0.5% locus bean gum, 1% malt extract and 0.05% (NH4)2HPO4, under submerged fermentation with shaking at 120 rpm and 28C for 2 days incubation.
Identification of nifD and nifH Genes of Methanotrophic Bacteria from Rice Field Ari Fina Bintarti; Iman Rusmana; Aris Tri Wahyudi
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2014.v18.n2.13-25

Abstract

Metanotrophic bacteria have ability to oxidize methane and fix atmospheric nitrogen, hence the bacteria has an important role as a nitrogen source provider on wetland area like rice fields. Nitrogen fixation process is catalyzed by the nitrogenase enzyme complex, encoded by nifD and nifH genes. However, characteristic of these genes from indigenous-methanotrophic bacteria still poorly understood. Hence, nifD and nifH genes of methanotrophic bacteria isolated from rice fields in Indonesia (BGM3, BGM9, SS1, SS3, SS10, ST18, SP3, and INP4) were identified and characterized. Detection of nifH and nifD genes was conducted by polymerase chain reaction (PCR) amplification. nifH and nifD gene sequences were analyzed using BLAST-X and phylogenetic trees were constructed using Neighbour Joining method. Based on nifH sequences analysis, SS1 closely related to Beijerinckia mobilis and SS3, SS10, ST 18 closely related to Beijerinckia indica subsp. indica ATCC 9039, while, BGM3, INP4, and BGM9 related to nifH of uncultured nitrogen-fixing bacterium. In other hand, sequence analysis of nifD gene showed that SS1, SS3, SS10, ST 18 closely related to B. indica subsp. indicaATCC 9039 and BGM3, BGM9, INP4 closely related to Xanthobacter autotrophicus Py2. Identification by 16S rRNA gene indicated that SS1, SS3, SS10, and ST18 had closeness to Beijerinckia sp. P310-1, while INP4 closely related to Xanthobacter sp. M5C24.
Enhancement of β-Glucosidase Activity in Penicillium sp. by Random Mutation with Ultraviolet and Ethyl Methyl Sulfonate Vilya Syafriana; Sukma Nuswantara; Wibowo Mangunwardoyo; Puspita Lisdiyanti
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2014.v18.n2.27-33

Abstract

The genus Penicillium has a potential ability to produce β-glucosidase. The aim of the study was to improve the β-glucosidase activity of Penicillium sp. ID10-T065 with physical (Ultraviolet = UV), chemical (Ethyl Methyl Sulfonate = EMS), and combined mutation (UV-EMS). The spores of Penicillium sp. ID10-T065 were exposed into UV irradiation for 3 minutes with dose of 0.1 J/cm2 and 13 cm of distances. Chemical mutation was done by treated spores into 3% of EMS solution for an hour. Combined mutation of UV and EMS were also performed by UV for 3 minutes (0.1 J/cm2, 15 cm) and continued with soaking into 2-3% of EMS solution. The developed mutants were screened, selected and assayed. Comparison of enzyme activities with the wild- type (1.78 U/ml), mutant UV13 (5.53 U/ml) showed a 3.1 fold increase; mutant EM31 (4.26 U/ml) showed a 2.4 fold increase. Meanwhile, mutant UM23 obtained from the multiple exposures showed a decreased activity (1.75 U/ml). Mutant UV13 showed the best enzyme activity to be considered as a potential strain for β-glucosidase producer. This result needs to be further elaborated especially on its genetic stability studies in order for the ascertained as a stable mutant.
Preparation of An scFv-Based Immunoliposome Specific towards Transferrin Receptor Wien Kusharyoto; Ira Handayani; Martha Sari; Asrul Muhamad Fuad
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2014.v18.n2.35-44

Abstract

An ideal therapeutic for cancer would be one that selectively targets to tumor cells, is nontoxic to normal cells, and that could be systemically delivered, thereby reaching metastases as well as primary tumor. Immunoliposomes directed by monoclonal antibody or its fragments are promising vehicles for tumor targeted drug delivery. Transferrin receptors (TfR) levels are elevated in various types of cancer cells and considered to correlate with the aggressive or proliferative ability of tumor cells. Therefore, TfR levels can be elaborated as a prognostic tumor marker, and TfR is a potential target for drug delivery in the therapy of malignant cells. Here, we report the preparation of an anti-TfR single-chain antibody variable (scFv) immunoliposome for tumor targeted delivery vehicle. The cDNA encoding the variable heavy and light chain domains of the anti-TfRscFv antibody fragment was derived from the murine monoclonal antibody Clone E6, which is specific towards transferrin receptor. The gene encoding the anti-TfR scFv fragment was codon optimized for expression in Escherichia coli, subsequently synthesized, and cloned into the expression vector pJexpress404. The His6-tagged anti-TfR scFv fragment was expressed in E. coli and purified by means of immobilized metal-ion affinity chromatography on TALON™ matrix. SDS-PAGE revealed that the scFv fragment had the size of approximately 27 kDa, which corresponded with the predicted size of the protein based on its amino acid sequence. Liposome containing 5% MPB-DOPE were prepared by ethanol injection method. Afterwards, the anti-TfR scFv fragments were covalently conjugated to the liposome to produce the anti-TfR scFv immunoliposome with the size of around 200 to 300 nm.
Isolation and Characterization of OsNAC6 cDNA from Rice (Oryza sativa L.) cv. Nipponbare, Batutegi, and Rojolele Agus Rachmat; Satya Nugroho; Dini Nurdiani; Maria Swastika; Dewi Sukma; Hajrial Aswidinnoor; Sudarsono Sudarsono
Annales Bogorienses Vol. 18 No. 2 (2014): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2014.v18.n2.45-55

Abstract

Transcription factors have an important function in regulating gene expression and plant responses to stresses. The ERF, bZIP, WRKY, MYB, and NAC are stress inducible transcription factors. The OsNAC6 is a member of the NAC transcription factor family in rice and its expression is induced by abiotic stresses, wounding and blast disease. Characterization of OsNAC6 gene sequences would give a better understanding on how OsNAC gene functions biologically. The objectives of this research are to isolate the OsNAC6 cDNA from Nipponbare, Batutegi, and Rojolele cultivars, to characterize their DNA sequences, and to compare their sequences to other NAC genes from other plants available in GenBank DNA databases. Isolated cDNA and sequencing of the fragments resulted in a 912 bp DNA sequences. Translation of the sequences yielded a protein consisted of 303 amino acid residue. Blast analysis of amino acid sequences indicated identity of isolated cDNA from three Indonesian rice cultivars are the OsNAC6 gene. Deduced amino acid residues from amplified cDNAs of Nipponbare, Batutegi, and Rojolele cultivars shared 100% sequence identities to rice OsNAC6 (Acc. # BAA89800), 71-100% sequence identity to a number of OsNAC protein from Oryza sativa and 63-83% sequence identity to NAC protein from other plants.
EDITOR'S PREFACE Puspita Lisdiyanti
Annales Bogorienses Vol. 19 No. 1 (2015): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

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Abstract

Optimization Expression and Stability Test of Recombinant Human Interferon Alfa 2a Fusion Protein in Escherichia coli BL21 (DE3) Adi Santoso; Arizah Kusumawati
Annales Bogorienses Vol. 19 No. 1 (2015): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2015.v19.n1.1-8

Abstract

The rhIFN α2a is expressed as a fusion protein containing thioredoxine and polyhistidine sites at its N terminal. Our previous research has obtained recombinant human IFN α2a (rhIFN α2a) protein that expressed predominantly as a soluble form in E. coli BL21 (DE3). Through systematic approach of various culture conditions, the aim of current this research is to acquire the best condition and its stability of recombinant rhIFN α2a fusion protein in a culture under study. Expression optimization performed by using three parameters, i.e.: temperature, induction time and inducer concentration. Various IPTG concentrations are 0.25, 0.5, 0.75, and 1.0 mM. The incubation time of bacterial cell culture carried out in 3, 4, and 5 hours at temperature 28, 30, and 37°C. The best condition was used to analyze the stability of rhIFN α2a protein expression up to ten generation. The expressed protein was analyzed using SDS PAGE and CBB staining. The optimal culture condition was found to be 37 °C temperature with 4 hours time of induction and 1 mM IPTG concentration. Stability analysis revealed that the rhFN α2a protein expression remained stable until the tenth generation with molecular weight, approximately, 36 kDa. 
Optimizaton of Cationic Lipid Mediated Transfection of pEGFP-c1 and pJ-EPO Plasmids in Chinese Hamster Ovary (CHO) Cells Attached Culture for Transient and Stable Recombinant Human Erythropoietin (rhEPO) Expression Endah Puji Septisetyani; Arizah Kusumawati; Adi Santoso
Annales Bogorienses Vol. 19 No. 1 (2015): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2015.v19.n1.9-16

Abstract

Cationic lipid is one of transfection agents which show high efficiency and low cytotoxicity. The transfection efficiencies can be varied depending upon the type or amount of cationic lipids, the cell line or DNA plasmid being used for transfection. The purpose of this study was to find optimal condition for transfection of CHO-K1 and CHO-S cells with pJ-EPO plasmid (containing human erythropoietin/ hEPO gene) compared with pEGFP-c1 plasmid (containing green fluorescence protein/gfp gene) by cationic lipid Lipofectamin 2000TM (lipofectamin) to generate stable transfectant expressing recombinant human erythropoietin (rhEPO). Optimization was carried out regarding the amount of lipofectamin, DNA concentration, and concentration of antibiotic Geneticin (G418) for selection of stable transfectants. By using standard amount of lipofectamin (10 μl/well) in 6-well plate, highest expression level of green fluorescent protein (GFP) was shown after transfection of CHO-K1 cells with 3 μg/well pEGFP-c1 while highest expression level of rhEPO was observed after transfection of CHO-K1 cells with 6, 8, or 10 μg/well pJ-EPO plasmid. The data also indicated that optimal transfection conditions of CHOK1 and CHO-S cells with pJ-EPO were shown with the use of 4 μg/well DNA in combination with 15 μl lipofectamin. Concentration of G418 used during cells selection also affected the expression where strongest rhEPO expression was shown at 750 ng/μl G418 concentration. Similar to GFP expression profile, rhEPO signal was detected very low during selection process sbased on Western blot data at day 9. Stronger rhEPO signal was observed after day 20 when the stable transfectants have been obtained.
In-Silico Cloning and Analysis of Divalent Subunit OMP31-SODc Proteins As A Prophylaxis Vaccine Against Brucella melitensis Infection Sri Kartika Wijaya; Arizah Kusumawati; Andri Wardiana; Yana Rubiyana; Ulfatul Husnaa; Adi Santoso
Annales Bogorienses Vol. 19 No. 1 (2015): Annales Bogorienses
Publisher : National Research and Innovation Agency (BRIN)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2015.v19.n1.17-28

Abstract

The urgency to develop a new protein subunit based vaccine candidate against Brucella was provoked by its frequent infection to human and livestock. Since Brucella melitensis is found as the most frequently isolated Brucella species from human, thus the outer membrane of B. melitensis becomes a prominent subcellular localization to search for promising antigen to be developed as vaccine candidate due to its interaction with host cell. Among outer membrane proteins suggested by Vaxign program, OMP31 was found as the most promising candidate. Moreover, analysis on other subcellular localization led our interest to SODc protein, which was expected to support OMP31 in triggering immune response. The OMP31-SODc divalent vaccine candidate was analysed in silico to predict its stable three-dimensional structure, cloning process and expectation on the ease during expression, purification and vaccine delivery to elicit the expected immune response.

Page 15 of 21 | Total Record : 203

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