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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 523 Documents

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Decolorization and detoxification of batik dye effluent containing Indigosol Blue-04B using fungi isolated from contaminated dye effluent Ratna Stia Dewi; Rina Sri Kasiamdari; Erni Martani; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.32332

Fungi are capable of treating various synthetic dye effluents. Previously, we isolated seven strains of fungi from contaminated batik dye effluent at Banyumas, Central Java. The aims of this study were to screen the ability of these fungi to decolorize batik dye effluents containing Indigosol Blue-04B and to investigate the phytotoxicity effects of biodegraded effluent on the germination of corn seeds Zea mays L. and green bean seeds Vigna radiata (L.) Wilczek. In addition, the decolorized effluents were tested for toxic effect on the agriculturally important gram-positive and gram-negative soil bacteria Bacillus cereus and Azotobacter sp., Staphylococcus aureus and Escherichia coli, respectively. Study of decolorization showed that fungi were able to decolorize Indigosol Blue-04B batik dye effluents by 21.04% to 99.89% at room temperature after three days of incubation. The assay of phytotoxicity showed that both plumule and radicle length of Z. mays and V. radiata grown on the decolorized effluent was longer than on untreated effluent. The percentage of Z. mays and V. radiata seed germination in decolorized effluent was higher than in untreated effluent. There was no inhibition zone found around the decolorized effluent samples after incubating the bacteria for 48 hours. Aspergillus sp. 3 was the most effective for degradation and could be used for batik effluent mycoremediation processes.

In vitro anticancer activity of N-benzyl 1,10-phenanthroline derivatives on human cancer cell lines and their selectivity Eti Nurwening Sholikhah; Jumina Jumina; Sitarina Widyarini; Ruslin Hadanu; Mustofa Mustofa
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.33997

This research was conducted to evaluate the anticancer activity of new compounds of benzyl-1,10- phenanthroline derivatives and their selectivity. In vitro anticancer activity of 11 benzyl-1,10-phenanthroline derivatives were conducted on three human cancer cell lines, cervical cancer (HeLa), myeloma (NS-1), and breast cancer (MCF-7) using MTT-based cytotoxicity assay. The cytotoxicity of each compound was assessed to normal Vero cell line by the same method. The in vitro anticancer activity and cytotoxicity was expressed by the concentration inhibiting 50% of the cell growth (IC50), and the selectivity index (SI) was determined by calculating ratio of the IC50 on Vero cell line and the human cancer cell lines. The results showed that among the 11 compounds tested, the (1)-N-(4-butoxybenzyl)-1,10-phenanthrolinium bromide exhibited the best in vitro anticancer activity with an IC50 27.60 ± 2.76 µM on HeLa, 6.42 ± 5.53 µM on NS-1 and 9.44 ± 2.17 µM on MCF-7 cell lines. Its SI were 377.65 ± 39.97 on HeLa, 6158.72 ± 5306.34 on NS-1 and 1140.11 ± 261.85 on MCF-7 cell lines. This study demonstrated that (1)-N-(4-butoxybenzyl)-1,10-phenanthrolinium bromide possessed a potential in vitro anticancer activity on cancer cell lines with high selectivity

Anti-metastatic effect of curcumin analog pentagamaboronon-0-fructose (PGB-0-F) against 4T1 breast cancer cells Yogi Ertanto; Rohmad Yudi Utomo; Riris Istighfari Jenie; Ratna Asmah Susidarti; Edy Meiyanto
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Development of a chemotherapeutic agent and boron carrying pharmaceutical based on triple-negative breast cancer is important due to its metastatic progression. Metastases are often more dangerous than the primary tumor and they are responsible for 90% of all cancer deaths. The purpose of this study was to explore the anti-metastatic activities of the PGB-0 complex with fructose (PGB-0-F) against 4T1 breast cancer cells. A scratch wound healing assay was carried out to determine the migration inhibition ability of PGB-0-F, while MMP-9 expression was analysed using gelatin zymography. The testing of anti-migration activity showed that PGB-0-F inhibited in 4T1 cells, whereas the gelatin zymography assay revealed a suppression of MMP-9 expression. PGB-0-F inhibited closure on 4T1 metastatic breast cancer cells line compared with the control. PGB-0-F decreased the MMP-9 expression level compared with the control. Based on these results, PGB-0-F has the potential to be developed as a chemotherapeutic agent, and especially as an anti-metastatic agent.

Evaluation of potential gene expression as early markers of insulin resistance and non-alcoholic fatty liver disease in the Indonesian population Eunice Limantara; Felicia Kartawidjajaputra; Antonius Suwanto
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Early detection of insulin resistance (IR) or non-alcoholic fatty liver disease (NAFLD) is crucial to preventing future risks of developing chronic diseases. The Homeostatic Model Assessment of Insulin Resistance (HOMA-IR), Liver Fat Score (LFS), and Fatty Liver Index (FLI) are generally employed to measure severity stages of IR and NAFLD. The study of gene expressions could explain the molecular mechanisms that occur early on in IR and NAFLD; thus providing potential early markers for both diseases. This study was conducted to evaluate the gene expressions that could potentially be early markers of IR and NAFLD. All participants (n = 21) had normal blood glucose and were categorized as without hepatosteatosis (n = 10), at higher risk of hepatosteatosis (n = 6), and hepatosteatosis (n = 5). Gene expression analysis was performed using the 2-∆∆CT relative quantification method. There were significant differences in galnt2 (p < 0.002) and sirt1 (p < 0.010) expression between the first and the third tertiles of HOMA-IR; and in ptpn1 (p < 0.012) expression between the first and the second tertiles of LFS. In conclusion, the expressions of galnt2 and sirt1 could be used as early markers of IR, while the expression of ptpn1 could be employed as an early marker of NAFLD.

NMR metabolomics revealed metabolites and bioactivity variation in Torbangun leaves Plectranthus amboinicus L. with different origins Nancy Dewi Yuliana; Muhammad Anwari Sugiharto; Hanifah Nuryani Lioe; Masao Goto; Yuko Takano Ishikawa
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Plectranthus amboinicus has been reported to have antidiabetic and antioxidant activities. Environmental factors might influence the plant’s secondary metabolite profile and its beneficial properties. NMR-based metabolomics was used to show phytochemical variations between specimens of P. amboinicus grown in Japan and Indonesia. The results showed that flavonoids and triterpenes were among the discriminating factors of the variation between the two groups. Targeted comparative analysis of the concentration of the specific flavonoids of the plants using a validated HPLC-MWD method showed that the Japanese samples contained a higher concentration of total flavonoids compared with the Indonesian samples. The Japanese and Indonesian samples contained 1100.6 ± 5.1 and 532.4 ± 1.8 µg/g luteolin, and 584.5 ± 7.4 and 571.7 ± 11.6 µg/g apigenin, respectively. Eriodyctiol was detected only in the Indonesian samples. Contrarily, more intensive DPPH reduction and α-glucosidase inhibition activities were found in the Indonesian samples (IC50 14.4 ± 1.2 and 24.0 ± 0.3 µg/mL for the DPPH assay, 1181.9 ± 113.5 and 4451.4 ± 290.0 µg/mL for α-glucosidase inhibition, respectively). Thus, flavonoids might not be the only group of compounds related to the aforementioned bioactivities. This should be confirmed by further research targeting other groups of compounds, such as triterpenes.

Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing Benediktus Yohan; Rama Dhenni; Rahma F Hayati; Frilasita Aisyah Yudhaputri; Dionisius Denis; Yanuarni WB Pamai; Anna Matiana Afida; Ingrid A Hutagalung; Sotianingsih Haryanto; Hidayat Trimarsanto; Khin Saw Aye Myint; R. Tedjo Sasmono
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.38788

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies.

Secretory expression of human insulin precursor in Pichia pastoris employing truncated α-factor leader sequence and a short C-peptide Dini Nurdiani; Hariyatun Hariyatun; Wien Kusharyoto
Indonesian Journal of Biotechnology Vol 23, No 2 (2018)
Publisher : Universitas Gadjah Mada

In the past ten years, diabetes prevalence has increased rapidly in low- and middle-income countries due to lifestyle changes. This increased number of diabetic patients leads to the escalation of recombinant insulin demand, which is creating a large global insulin market. Pichia pastoris has appeared as an alternative host to produce recombinant proteins. It has excellent qualifications as an expression host for large-scale production of recombinant proteins for therapeutic use. In this study, we attempted to express the insulin precursor (IP) in P. pastoris. We used a synthetic IP-encoding gene constructed in frame with the truncated α-factor secretory signal and a short C-peptide (DGK) linked A- and B-chain of human insulin in a pD902 expression vector. Several zeocin resistant clones were successfully obtained and verified with PCR using AOX1 specific primers for the integration of the expression cassette into the P. pastoris genome and for the identification of Mut phenotypes. The secretion of IP by the Pichia pastoris clone in the culture supernatant was confirmed using SDS-PAGE, where a single band of the secreted IP with a molecular mass above 6.5 kDa was found.

Isolation, identification, and detection of ACC deaminase gene-encoding rhizobacteria from rhizosphere of stressed pineapple Dori Kusuma Jaya; Giyanto Giyanto; Novik Nurhidayat; Sarjiya Antonius
Indonesian Journal of Biotechnology Vol 24, No 1 (2019)
Publisher : Universitas Gadjah Mada

ACC deaminase is a microbial cytoplasmic enzyme that cleaves ACC, a precursor of ethylene, in the stressed plant. The aims of this study were to isolate, identify, and detect the presence of ACC deaminase gene-encoding rhizobacteria from the rhizospheric soil of pineapple plants that have been exposed to abiotic and biotic stress, specifically herbicide, flooding, and Phytophthora spp. stress. A total of 49 rhizobacterial isolates were obtained, seven of which were observed for their growth on DF medium containing 3 mM L-1 ACC. The four best-growing isolates were selected for genomic DNA extraction. They were molecularly identified as Stenotrophomonas maltophilia (3), Burkholderia territorii (2A), Pseudomonas oryzihabitans (5B), and Bacillus tropicus (1E). A set of primers, 105F-acdS 5’-TGCCAAGCGTGAAGACTGC-3’ and 244R-acdS 5’-GGGTCTGGTTCGACTGGAT-3’, were constructed to amplify the ACC deaminase gene (acdS). Based on melt peak curve analysis, four products appeared to show a specific single peak at 86, 89, 87, and 89.5°C, indicating a single product was produced. In addition, a Blast search showed that these four products met the ACC deaminase feature and their acdS sequences were clustered into an ancestral group compared with the bacterial strains deposited in GenBank. These results suggest that ACC deaminase gene-encoding rhizobacteria from a pineapple plantation of tropical origin may affect the acdS sequences and may contribute to the host plant’s stress tolerance.

Modification of recombinant human epidermal growth factor (rh-EGF) expression vector by site-directed mutagenesis for therapeutic protein production Achmad Rodiansyah; Riyona Desvy Pratiwi; Sabighoh Zanjabila; Asrul Muhamad Fuad
Indonesian Journal of Biotechnology Vol 24, No 1 (2019)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.41859

Recombinant human epidermal growth factor (rh-EGF) has high value in therapies for h-EGF deficiency-related diseases. The expression of the h-EGF gene was designed by using the pET21b(+) vector and Escherichia coli BL21(DE3) as the expression host. In a previous study, the sequence of a 6xHis tag without any restriction sites was fused to the h-EGF gene, yet it was not possible to obtain a purified and single rh-EGF by this approach. In this study, we modified the rh-EGF expression vector using site-directed mutagenesis (SDM) to remove the sequence of the 6xHis tag. The vector modification was carried out by inserting a stop codon and the EcoRI restriction site, along with deleting the 6xHis tag sequence. The results of PCR showed non-specific bands, while 2-step cycles PCR produced one non-specific band, and 3-step cycles PCR produced two non-specific bands. After purification of the PCR products, the SDM-recombinant plasmids treated for template plasmid-free product were transformed into E. coli DH5a. Even though the transformation efficiency was low, the planned gene mutations including the deletion of the 6xHis tag and insertion of the stop codon and EcoRI restriction site in plasmid pET21b(+) were successfully carried out. When using this modified vector in expression studies, rh-EGF of a similar size to that of the rh-EGF standard and approximately 1 kDa smaller than the rh-EGF-6xHis of the previous study was obtained.

Identification of single nucleotide polymorphisms in GDF9 gene associated with litter size in Garut sheep Resti Yuliana Rahmawati; Sumadi Sumadi; Tety Hartatik
Indonesian Journal of Biotechnology Vol 24, No 1 (2019)
Publisher : Universitas Gadjah Mada

The growth differentiation factor 9 (GDF9) gene has been regarded as having major impacts on ovulation rate and litter size in sheep. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of the GDF9 gene and their association with litter size in Garut sheep. For this purpose, a total of 60 ewes of Garut sheep were included in this study. Based on the sheep GDF9 reference sequences (Genbank Acc. No. AF078545.2), one pair of primers (5’-CTGCTGTTTAACCTGGATCGTG-3 5’-GGAGAGCCATACCGATGTCC-3 as forward and reverse, respectively) was used for PCR amplification. The results revealed that four SNPs (g.54C>T, g.60G>A, g.304G>A, and g.333G>A) were found in Garut sheep by direct sequencing. For SNP g.54C>T, the sheep exhibited the highest frequency of allele C and genotype CC. On the other hand, SNPs g.60G>A, g.304G>A, and g.333G>A showed a higher frequency of allele G than allele A, and the GG genotype was predominant in the population. SNP g.333G>A had a significant effect on litter size (p < 0.05), and ewes with the GG genotype had a higher litter size than those with the GA genotype. Genotype distributions for all identified SNPs were in agreement with Hardy-Weinberg equilibrium. We highlight that SNP g.333G>A may be useful as a genetic marker for litter size in Garut sheep.

Page 36 of 53 | Total Record : 523

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