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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 189 Documents
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Medium Chain and Long Chain Alkanes Hydroxylase Producing Whole Cell Biocatalyst From Marine Bacteria Thontowi, Ahmad; Yetti, Elvi; Yopi, Yopi
Annales Bogorienses Vol. 22 No. 1 (2018): Annales Bogorienses
Publisher : BRIN

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Abstract

Alkanes are major component of crude oil that could be hydrolyzed by the enzyme of alkane hydroxylase. The are three types of alkane hydroxylase based on the chain length of alkane such as short-chain length/SCL (C2-C4), medium-chain length/MCL (C5-C17), and long-chain length/LCL (C>18). The aims of this study were to characterize and identify alkanes-degrading bacteria from these bacteria. The 30 strains from marine were grown on MCL (Pentane-C5H12, Decane-C10H22, and Pentadecane-C15H32) and LCL (n-Paraffin-C12H19C17 and branch of Pristane-C19H40). The study showed twenty-nine isolates have the ability to degrade alkanes compounds, whereas 14 isolates have grown ability on MCL and LCL medium, 11 isolates have the ability to grow on MCL and n-LCL, 3 isolates have the ability only to grow on MCL medium and 1 isolate has the ability only grow on n-LCL medium. The growth test result indicated that 29 isolates have medium-chain alkane monooxygenase and long-chain alkane hydroxylase. Based on 16S rDNA gene analysis, we obtained twenty nine of oil- degrading bacteria, namely a-proteobacteria (57 %), g-proteobacteria (30 %), Flavobacteria (7 %), Bacilli (3%) and Propionibacteriales (3 %). g-Proteobacteria and a-proteobacteria which seems to play an important role in the alkane biodegradation.
Biological Analysis of Leydig Cells-Conditioned Medium to Support Rat Bone Marrow Mesenchymal Stem Cells Differentiation Kaiin, Ekayanti Mulyawati; Prasetyaningtyas, Wahono Esthi; Mohamad, Kusdiantoro; Djuwita, Ita; Yusuf, Tuty Laswardi; Setiadi, Mohamad Agus
Annales Bogorienses Vol. 22 No. 1 (2018): Annales Bogorienses
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Abstract

The developed Leydig cells-conditioned medium (LCM) contains bioactive materials secreted by Leydig cells in vitro. LCM was used to evaluate the ability of bone marrow mesenchymal stem cells differentiation. Bone marrow mesenchymal stem cells (1x 106 cell/ml) were cultured in : 1) DMEM supplemented with 10% NBCS as a control (M), 2) M supplemented with 10 ng/ml testosterone; 3) M supplemented with 50% LCM ; 4) M supplemented with 50% LCM and 2.5 IU/ml hCG. Bone marrow mesenchymal stem cells that were cultured with LCM has a positive reaction (57.4%) to histochemistry staining 3β-HSD and produced 1.87 ng/ml testosterone. Supplementation of hCG to LCM increased the positive number of Leydig cells and testosterone production by 74.6% and 12.33 ng/ml (P<0.05). It can be concluded that Leydig cells-conditioned medium can support differentiation of bone marrow mesenchymal stem cells into Leydig cells.
Molecular Detection of Resistance To Bacterial Leaf Blight on Conde Indonesian Rice Variety Fatimah, Fatimah; Prasetiyono, Joko; Polosoro, Aqwin; Baroya, Mushlihatun
Annales Bogorienses Vol. 22 No. 1 (2018): Annales Bogorienses
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Abstract

Rice bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) affected grain yield and decreasing rice production in rice growing countries. Conde, Indonesian rice variety, exhibits high resistance to most of the Indonesian races of (BLB) and has been used in Indonesia for cultivated rice. This study was aimed to conduct the molecular detection between proximal markers in chromosome 6 and relative expression of Conde rice variety compare to IRBB7 in Xa7 region. The population screening, BLB evaluation and molecular detection around the Xa7 region were conducted. The results showed from the collection of individual recombinants between resistant and susceptible parents narrow the region containing the BTBPOZ domain. The sequence alignment of Xa7LD37 in two resistant and three susceptible cultivars demonstrated a perfect association. The sequence alignment in exon region of Loc_Os06g46240 in Nipponbare, IRBB7, and IR64 identified indel/SNPs in this region leading to nucleotide substitution and frameshift resulting in amino acid change between resistant and susceptible cultivars. It was predicted that Conde revealed the similar gene action with Xa7 gene for BLB that encodes a BTB POZ domain.
Growth and Proline Content of Irradiated in Vitro Shoots of Ubi Kuning Cassava Genotype Cultured at Different Temperatures Supatmi, Supatmi; Rahman, Nurhamidar; Hartati, N. Sri
Annales Bogorienses Vol. 22 No. 1 (2018): Annales Bogorienses
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Abstract

Cassava (Manihot esculenta) is an important crop to food security under climate change due to its various tolerance mechanism under stress conditions. However, the sustainable growth of cassava in the field depends on many factors especially temperature. The objective of the research was to investigate the growth performances and proline contents of irradiated Ubi Kuning at dosage of 10 Gy, cultured in Murashige Skoog (MS) hormone-free solid medium for 4 weeks at three different temperature treatments i.e 25oC, 28oC and 30oC. Each treatment consisted of 3 clone explants with 5 replicates. Results show that growth performances of irradiated plantlets were better compared to that of non-irradiated plantlets in terms of plant height and number of leaves at all temperature tested. The best growth performances were obtained from irradiated plantlets grown under 30oC. The proline content of irradiated Ubi Kuning was high when they were grown under 25 oC and 30oC, implying that these plantlets had the possibility to tolerant to lower and higher-temperature condition. This study is initially useful to find out the growth ability of irradiated Ubi Kuning in response to lower and higher temperature.
Optimization of Substrate and Starter Cell Concentrations for Dibenzothiopene Biodegradation by Indigeneous Marine Bacteria Mauricauda olearia LBF-1-0009, Alcanivorax xenomutants LBF-1-0018, and Stakelama pacifica LBF-1-0031 Yetti, Elvi; Thontowi, Ahmad; Yopi, Yopi
Annales Bogorienses Vol. 21 No. 2 (2017): Annales Bogorienses
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Dibenzothiophene (DBT) and its derivatives have been widely used as model organic sulfur compounds in petroleum, included their biodegradation process. The abilities of microorganisms to degrade pollutants are significantly influenced by various factors such as microbial species, nutrients and environmental parameters. In this research, we carried out further study to determine optimal condition for DBT biodegradation regarding with substrate and strains cell concentration by several indigenous marine bacteria from Indonesia. These three isolates were belong to Mauricauda olearia, Alcanivorax xenomutants, and Stakelama pacifica, with homology result 99% each. Optimal dibenzothiophene as substrate reached by all isolates is 100 ppm, while cell concentration or microbial numbers that gave highest growth for all isolates is 20 based on conversion of OD600 nm measurement.
Optimization of Somatic Embryogenesis Induction of Cassava (Manihot esculenta Crantz) Susanti, Idha; Suharsono, Suharsono; Widyastuti, Utut; Siregar, Ulfah Juniarti; Tjahjoleksono, Aris
Annales Bogorienses Vol. 21 No. 2 (2017): Annales Bogorienses
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The embryogenesis (SE) has important role for genetic engineering of cassava (Manihot esculenta Crantz). However, the success of SE induction depend on plant growth regulator s (PGR)s and treatment enriched in induction media. This experiment tried to induce callus formation of cassava from several in vitro explants: immature leaf, apical bud, and internode; and to develop somatic embryogenesis of cassava in several media enriched with tyrosine and copper sulphate (CuSO4) added into media enrich with picloram as treatment. Different response of explants source to callus induction treatment from those three varieties in callus induction as well as friable callus formation were found in this experiment. The best medium to induce varied with variety; MS media supplemented 12 mg/L picloram + 0.5 mg/L CuSO4 was the best for “Adira 4” and half MS and half GD media supplemented 12 mg/L picloram + 100 mg/L tyrosine for “Malang 6”. All treatments resulted somatic embryo which developed indirectly and in morphologically normal somatic embryos
Improvement of HER2I655V TARMS-PCR Performance by DNA Quality Analysis Budiarto, Bugi Ratno; Azamris, Azamris; Desriani, Desriani
Annales Bogorienses Vol. 21 No. 2 (2017): Annales Bogorienses
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Reliable TARMS-PCR is a prerequisite in constructing a solid conclusion in genetic diagnostics. The validity of data generated by this molecular technique is hampered by a false positive result. In attempt to develop a TARMS-PCR for HER2I655V genotyping with no interfering of bias we used DNase I to eliminate DNA contaminant resided in PCR reagent. TARMS-PCR without enzyme treatment using recombinant plasmids that contained HER2I655V gene with represented its alleles was used to evaluate the presence of false positive result while DNase I treated-PCR reagent was used in TARMS-PCR to evaluate the effective dose of the enzyme and further to adjust the TARMS-PCR conditions. PCR master mix kit used in this study produced a false positive result on HER2I655V TARMS-PCR as proven by the presence of multiple PCR products in Non-Template Control (NTC) and 0.1 U of the enzyme could eliminate this DNA contaminant effectively, although this pretreatment altered the specificity of HER2I655V TARMS-PCR genotyping on certain genotype. Combination of touchdown TARMS-PCR with another allele-specific primer recovered specificity of detection on this model system. Interestingly, this optimized HER2I655V TARMS-PCR can only be used for genotyping the clinical samples if only further optimization was done using genomic DNA as template
Pectinase Production and Clarification Treatments of Apple (Malus Domestica) Juice Berutu, Cocok Ana Maryani; Fahrurrozi, Fahrurrozi; Meryandini, Anja
Annales Bogorienses Vol. 21 No. 2 (2017): Annales Bogorienses
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Pectinases are a group of an enzyme that break down pectin, a polysaccharide that is found in plant cell walls. Today, the application of pectinolytic enzymes plays an important role in food technology for the maceration of fruits and vegetables, including for the extraction and clarification of juice. This research aimed to produce pectinase enzyme for clarifying of apple juice. A microbial culture was selected from cocoa bean fermentation samples and identified as Bacillus sp.. The highest enzyme activity was investigated after 48 hours of incubation. Citrus pectin as the carbon source and peptone as the nitrogen source was found as the best component for pectinase production. The optimum condition of pectinase activity was observed at pH 5, temperature 40 °C and the crude enzyme had the higher activity at one hour storage. Apple juice was treated with the enzyme at different concentrations (0%, 0.5%, 1%, 2%, 4%). Apple juice clarification was evaluated for its percent clarity and viscosity. The result showed that enzyme treatment at 4% in apple juice promoted juice clarification and decreased pH and viscosity. In conclusion, the quality of apple juice can be improved by enzymatic treatment using pectinase.
ILE655VAL Genotyping Study of HER2 - Positive Breast Cancer of Patients from Padang - Indonesia With High Resolution Melting Technique Wulandari, Dwi; Azamris, Azamris; Nurhayati, Isna; Warisman, M. Ali; Budiarto, Bugi Ratno; Desriani, Desriani
Annales Bogorienses Vol. 21 No. 2 (2017): Annales Bogorienses
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Transtuzumab has proven to be a great improvement in the treatment of HER2 + of breast cancer patients, but it is associated with relevant adverse cardiac events and with significantly elevated cost of treatment. One of the risk factors for cardiotoxicity due to transtuzumab is the I655V HER2 polymorphism (GTC> ATC mutation) in which the allele mutant (Ile val or val / val) has a higher risk than the wild type (Ile/Ile). The detection of specific alleles is very important for therapeutic decision-making. In this study, our group have developed a HRM with EvaGreen dye method to discriminate specific allele of I655V HER2 (wild type, heterozygote mutant or homozygote mutant) in 66 frozen section samples of HER2+ of breast cancer patients. Our group reported the wild type is the most prevalent allele (77,27%), whereas heterozygous mutation is significantly present in this research (21,21%) and only 1,52% of sample detected as minor allele. It showed that only one sample detected as a minor allele (val/val) and may have relatively low abundance in the population. This method has been compared with sanger sequencing and giving 100% of validity.
The Emergence of Biosimilars in Indonesia: Guidelines, Challenges, and Prospects Wardiana, Andri; Ningrum, Ratih Asmana
Annales Bogorienses Vol. 20 No. 2 (2016): Annales Bogorienses
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According to the Food and Drug Administration (FDA), biosimilar is defined as a product which is highly similar to the reference product without clinically meaningful differences in safety, purity and potency. Indonesia is a developing country which has more than 250 million people. In 2008, the world market of biosimilar was USD 100 billions with 10-20% of domestic need from total market. Even though the need is very high, Indonesia still has not been able to produce Biosimilar independently. To stimulate the domestic production on biosimilar, National Agency for Drug and Food Control (NADFC) Republic of Indonesia has assigned Regulation of Biosimilar as Peraturan Kepala Badan Pengawas Obat Dan Makanan Republik Indonesia Nomor 17 Tahun 2015 Tentang Pedoman Penilaian Produk Biosimilar. The guidance covers the quality requirement and evaluation of Biosimilar products. Indonesian Ministry of Health has a strategic plan in biopharmaceutical covering biosimilar, which is going to be developed from 2015 to 2025. The strategy is expected to initiate biosimilar production in Indonesia. This review focuses on the guidelines of biosimilars in Indonesia compared to other international regulatory bodies, as well as the challenges and prospects of biosimilars development. 

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