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Indonesian Journal of Biotechnology

ijbiotech
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Published by Universitas Gadjah Mada

ISSN : 08538654 EISSN : 20892241 DOI : -

Core Subject : Science,

Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology

The Indonesian Journal of Biotechnology (IJBiotech) is an open access, peer-reviewed, multidisciplinary journal dedicated to the publication of novel research in all aspects of biotechnology, with particular attention paid to the exploration and development of natural products derived from tropical—and especially Indonesian—biodiversity. IJBiotech is published biannually and accepts original research articles featuring well-designed studies with clearly analyzed and logically interpreted results. A strong preference is given to research that has the potential to make significant contributions to both the field of biotechnology and society in general.

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Articles 8 Documents

Search results for , issue "Vol 23, No 1 (2018)" : 8 Documents clear

MicroRNA-21 as a biomarker for ovarian cancer detection Aprilia Indra Kartika; Siti Nur Chasanah; Akbar Satria Fitriawan; Dewi Sahfitri Tanjung; Addin Trirahmanto; Heru Pradjatmo; Teguh Aryandono; Sofia Mubarika Haryana
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Ovarian cancer is a lethal disease. One of the problems faced by patients with ovarian cancer is the lack of symptoms in its early stages, which results in it only being detected when it is at an advanced stage. Therefore, there is an urgent need for biomarkers that can predict ovarian cancer precisely. The purpose of this study was to determine the expression of microRNA-21 as a predictive biomarker candidate in both early- and advanced-stage ovarian cancer. This was a cross-sectional study using the blood plasma of 21 healthy control subjects and 37 blood plasma samples from patients with ovarian cancer. Blood plasmas were collected, from which the RNA was isolated. Based on the RNA, the cDNA was synthesized and run through qPCR, the results of which were analyzed using the Livak method. The results showed an upregulation of microRNA-21 in the advanced stage by 2.14 fold compared with the early stage, and 6.13 fold compared with the healthy controls (p < 0.05). The upregulation of microRNA-21 in early-stage ovarian cancer was 2.86 fold compared with the healthy control subjects (p < 0.05). In addition, there was an increase in the expression of microRNA-21 in ovarian cancer by 4.14 fold compared with the healthy controls (p < 0.05). Based on these results, it can be concluded that the expression of microRNA 21 upregulated with the severity of the disease.

Isolation of actinomycetes from maize rhizosphere from Kupang, East Nusa Tenggara Province, and evaluation of their antibacterial, antifungal, and extracellular enzyme activity Umi Fatmawati; Yulin Lestari; Anja Meryandini; Abdjad Asih Nawangsih; Aris Tri Wahyudi
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Actinomycetes are the one of the components of the rhizospheric microbial population and useful for producing secondary metabolites such as lytic enzymes, antibiotics, and antifungal. The aim of the study was to isolate the actinomycetes from maize rhizosphere collected from Kupang, East Nusa Tenggara. The screening was focused on the actinomycetes that showed the ability to produce antibacterial, antifungal, and extracellular enzymes such as amylase, cellulase, and protease. The actinomycetes were isolated using Humic-Acid Vitamin B (HV) agar media. The antagonistic assay was tested against Escherichia coli, Staphylococcus aureus, Sclerotium rolfsii and Fusarium oxysporum. Isolate JKP-8 was an isolate that showed the highest activity in inhibiting the growth of E. coli and S. aureus bacteria. Isolate JKP-5 showed the highest activity in inhibiting the growth of F.oxysporum. There were no actinomycetes isolates that showed an ability to inhibit the growth of S. rolfsii fungus based on dual culture assay. JKP-3 and JKP-4 isolates exhibited the highest ability to hydrolyze amylum, while JKP-5 and JKP-8 isolates exhibited the highest ability to hydrolyze CMC. The results of the amplification of 16S rRNA gene in selected potential isolates JKP 5 and JKP 8 indicated that both isolates belong to the genus Streptomyces.

Low cost and comprehensive pork detection in processed food products with a different food matrix Fenny Aulia Sugiana; Henni Widyowati; Muhammad Ali Warisman; Suryani Suryani; Desriani Desriani
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

The adulteration of processed beef-based meat products with pork is a sensitive issue in Indonesia. In this study, we developed a detection method for the low cost identification of pork in processed meat products. We used the cost-efficient Taq DNA polymerase, DreamTaq Green PCR master mix (2x), and duplex PCR method to recognize pork simultaneously with 18S rRNA detection. A positive control containing a pork gene inserted into pGEM®-T easy was prepared, along with a negative control. The results of the duplex PCR were used to assess its specificity, detection limit, and its ability to recognize pork in processed meat products with a different food matrix. 18S rRNA detection was for confirming DNA integrity of DNA extracted from the processed food, while the positive control confirmed that the reagents were working well and the negative control confirmed a non-contamination problem. Following this, the duplex PCR was optimized and the optimum concentration primer for duplex PCR detection was found to be 3 µm for pork and 0.2 µm for 18S rRNA. As little as 3.125 ng of the DNA template could be used to detect whether a sample contained pork. Duplex PCR is a simple, fast, sensitive, specific, and low cost method of detecting pork in processed meat products.

Determination of secondary and tertiary structures of cervical cancer lncRNA diagnostic and siRNA therapeutic biomarkers Arli Aditya Parikesit; Didik Huswo Utomo; Nihayatul Karimah
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Cervical cancer is one of the primary causes of mortality in women due to human papilloma virus (HPV) infection. The fingerprint of an HPV infection could be detected using a long non-coding RNA (lncRNA) biomarker, enabling it to be utilized in molecular diagnostics. The primary structure or sequences of RNA should be annotated within conventional bioinformatics tools. Therefore, this study aimed to determine the fine-grained 2D and 3D structures of lncRNA PVT1 and its respective siRNA inhibitors. lncRNA PVT1 sequences from Homo sapiens, Mus musculus, and Rattus norvegicus were retrieved from Genbank (NCBI). Prediction of the 2D structure and analysis of the interactions of the lncRNA and siRNA were performed using the Vienna RNA package. The 3D structure of the RNA was computed using the SimRNA and ModeRNA software programs. The results showed that lncRNA PVT1 from H. sapiens and M. musculus had a conserved region. However, the lncRNA from both H. sapiens and M. musculus showed a low conserved region, and the 2D structure could not be determined; thus, the annotation and 2D model focused only on H. sapiens. Both of their lncRNA PVT1 also had a short half-life in the cell. Based on the 3D modeling pipeline, the 3D model of lncRNA PVT1 showed the stability and possible function as molecules, while the PVT1 siRNA-lncRNA interaction analysis revealed that the molecules could bind well. Based on these findings, the structures of both lncRNA PVT1 and its siRNA have the potential to be utilized as biomarkers.

Amylolytic ability of bacteria isolated from termite (Coptotermes sp.) gut Putri Dwi Mulyani; Radhiyah Mardhiyah Hamid; Rifqi Zahroh Janatunaim; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

BSR 2, BSR 3, BSR 8, and BSR 9, different bacteria isolated from the termite gut, have been shown to possess cellulolytic activities, but their amylolytic ability has heretofore been unknown. This study attempted to fill in this knowledge gap. The formation of a clear zone using the iodine test showed that the bacteria were able to produce and secrete amylase. Based on the results, the best cultivation times for strains BSR 2, BSR 3, BSR 8, and BSR 9 were 6, 3, 2, and 2 d, respectively, yielding amylase activities of 2.59 ± 0.13 U/mg, 2.00 ± 0.08 U/mg, 1.67 ± 0.10 U/mg, and 1.55 ± 0.12 U/mg, respectively. BSR 2 had the highest amylase activity compared with the other bacterial isolates. The optimum ph for bacterial amylase activity of BSR 2 was 7.0, and the optimum temperature was 40°C. The molecular characterization of isolates BSR 2, BSR 3, BSR 8, and BSR 9 was based on 16S rRNA gene sequences. Isolates BSR 8 and BSR 9 were thus identified as Brevibacillus parabrevis and Brevibacillus sp. With similarities amounting to 92.48% and 95.91%, while the BSR 3 isolate was identified as Pseudomonas alcaligenes with a similarity of 94.29%, and the BSR 2 isolate could not be identified yet.

Use of microsatellite markers to detect heterozygosity in an F2 generation of a black rice and white rice cross Kristamtini Kristamtini; Taryono Taryono; Panjisakti Basunanda; Rudi Hari Murti
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

The aim of this research was to know the heterozygosity of F2 generation from black rice and white rice crossing using microsatellite marker. The research material consisted of F2 Sx G plant population from black rice (S) and white rice Situbagendit (G) crosses, female parent of black rice (S), male parent of white rice (G), chemical and organic fertilizer, chemicals and tools for molecular activity and 3 microsatellite markers related to color properties (RM 220, RM 224 and RM 252). All of plant populations (generation F2, parent female, parent male) were planted in fields up to harvest. Young leaves (30 days after planting) all of plant populations were molecularly analyzed using 3 microsatellite markers (RM 220, RM 224 and RM 252). Stages of this activity include DNA isolation, PCR reaction, and visualization of PCR results using Metaphore Agarose Gel Electrophoresis. The results showed that the percentage of the number of individual plants showing heterozygous pattern in F2 S × G plant generation was 50% (RM 220); 40% (RM 224) and 60% (RM 252), so the RM 252 microsatellite marker was effectively used as a DNA-assisted selection tool on the crossbreed of black rice with white rice.

Bovine vitreous gel can reactivate replicative senescence of human dermal fibroblast Maria Vianny Sansan; Sunardi Radiono; Muhamad Eko Irawanto; Yohanes Widodo Wirohadidjojo
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

The most influential factor in the poor healing of chronic ulcers is replicative senescence of fibroblasts that are unresponsive to TGF-β1 stimulation. Cellular replicative senescence can be induced by cultivating normal human dermal fibroblasts (HDFs) in a serum-starved medium. In addition, increasing microenviroment mechanical forces by hyaluronic acid can ameliorate the TGF-β1 signaling of these senescent cells. One of natural resources of hyaluronic acid is bovine vitreous gel. In order to evaluate the effect of bovine-vitreous gel on replicative senescence of fibroblasts, we used various levels of bovine vitreous gel diluted in Dulbecco’s modified Eagle’s medium to stimulate cellular activities of serum-starved HDFs. Those cellular activities were compared to the control media, standardized hyaluronic acid, and to normal HDFs. Our results show that replicative senescence of HDFs treated with 50% bovine vitreous gel exhibited a significantly higher proliferation index, migration rate, and collagen deposition than those cultured in control media, and they displayed an equal level of cellular activity with the HDFs exposed only to standardized hyaluronic acid. We concluded that bovine vitreous gel can be used to stimulate replicative senescence of HDFs and therefore a potential candidate material to stimulate healing of chronic ulcers.

The aqueous extract of Gerrardanthus macrorhizus caudex enhanced doxorubicin activity in MCF-7 human breast cancer cells Sari Haryanti; Yuli Widiyastuti; Slamet Wahyono
Indonesian Journal of Biotechnology Vol 23, No 1 (2018)
Publisher : Universitas Gadjah Mada

Gerrardanthus macrorhizus (GM) caudex, is traditionally used in cancer therapy by the Tetun people in Belu District, East Nusa Tenggara Province, Indonesia, where it is known as “akar batu”. This study aimed to explore the cytotoxic effects of G. macrorhizus caudex aqueous extract, as well as its combination with doxorubicin, on MCF-7 cells. Also investigated were the possible mechanisms of interaction through cell cycle progression and apoptosis induction. Single treatments of 5–320 µg/mL of the extract showed morphological alterations in MCF-7 cells, but did not show any cytotoxic effect. Combining the extract with doxorubicin resulted in a synergistic cytotoxic effect. Doxorubicin concentrations equivalent to 1/12, 1/8, and 1/5 fold of the IC50 combined with 20 µg/mL decreased viability to 48%. We then explored the combination effect of doxorubicin 0.4 µM with GM 5 and 20 µg/mL using a flow cytometer. A low concentration of the extract (5 µg/mL) combined with 0.4 µM of doxorubicin resulted in slight cell cycle modulation by G1, G2M arrested and apoptosis induction. The combination of doxorubicin and a higher concentration of the extract (20 µg/mL) did not show cell cycle modulation, and led to necrosis. Therefore, G. macrorhizus caudex at low concentrations has the potential to be developed further as a co-chemotherapeutic agent.

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