cover
Article Per Year (5 Year)
All
Home Page
OAI Link
Editorial Team
Contact
Reviewer
Google Scholar
Contact Name
-
Contact Email
-
Phone
-
Journal Mail Official
-
Editorial Address
-
Location
Kab. sleman,
Daerah istimewa yogyakarta
INDONESIA
Indonesian Journal of Biotechnology
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.
Arjuna Subject : -
Articles 523 Documents
 40   41   42   43   44 
Analysis using top‐k skyline query of protein‐protein interaction reveals alpha‐synuclein as the most important protein in Parkinson’s disease Mohammad Romano Diansyah; Annisa Annisa; Wisnu Ananta Kusuma
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63023

Abstract

Parkinson’s disease is the second‐most‐common neurodegenerative disorder and can reduce patients’ quality of life. The disease is caused by abnormalities in dopaminergic neurons, such as reactive oxygen species (ROS) imbalance leading to programmed cell death, protein misfolding, and vesicle trafficking. Protein‐protein interaction (PPI) analysis has been demonstrated to understand better candidate proteins that might contribute to multifactorial neurodegenerative diseases, particularly in Parkinson’s disease. PPI analysis can be obtained from experiments and computational predictions. However, experiment data is often limited in interactome coverage. Therefore, additional computational prediction methods are required to provide more comprehensive PPI information. PPI can be represented as protein‐protein networks and analyzed based on centrality measures. The previous study has shown that top‐k skyline query, a method using dominance rule‐based centrality measures, reveals important protein candidates in Parkinson’s diseases. This study applied the top‐k skyline query to PPIs containing experiment and prediction data to find important proteins in Parkinson’s disease. The result shows that alpha‐synuclein (SNCA) is the most important protein and is expected to be a potential biomarker candidate for Parkinson’s disease.
Isolation and identification of protease‐producing bacteria from sludge and sediment soil around Adama, Ethiopia Yeshaneh Adimasu Lemenh; Teshome Geremew Biru; Adinew Zewdu Chernet; Feleke Belachew Lema
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63987

Abstract

Proteases are enzymes used in industries such the production and processing of detergents, food, leather, and silk. The aim of this study was to isolate and identify protease‐producing bacteria from a sludge disposal site and from sediments. Soil samples were collected separately from the selected area. Samples weighing 1 g were serially diluted and spread onto skim milk agar. A total of 16 bacteria species were isolated from the study samples. Four bacterial isolates showed high proteolytic activity and were selected for enzymatic study based on their zone of proteolysis. The isolates were identified based on biochemical tests. The results indicated that the isolated bacteria were E. coli (99.69%), Pseudomonas putrefaciens (Shewanella putrefaciens) (91.61%), Bacillus carboniphilus (92.78%), and Lysinibacillus sphaericus (98.4%). The crude protease enzymes produced by these bacterial isolates showed promising results for application in dehairing and destaining as detergent additives. Bacillus carboniphilus showed the best level of activity and was selected as the most potent protease‐producing bacteria for both dehairing and destaining ability. Soils from sludge disposal sites and sediments from around tannery wastes could be good sources from which to isolate alkaline protease‐producing bacteria.
Performance of CO1 and ITS2 nested PCR in molecular identification of ordinary scabies (Sarcoptes scabiei var. hominis) Gita Dwi Prasasty; Miftahurrizqiyah Miftahurrizqiyah; Chairil Anwar; Dwi Handayani; Dalilah Dalilah; Ahmad Ghiffari; Inda Astri Aryani; Nunuk Dyah Retno Lastuti; Afiat Berbudi
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64472

Abstract

Scabies is a global disease with a high prevalence, causing morbidity and even mortality, especially in poor and developing countries. However, it is often misdiagnosed due to varied and unspecified lesions. The gold standard technique for diagnosis is a microscopic examination, which requires experienced experts in finding mites, mainly in ordinary scabies. CO1 and ITS2 genes have been widely used in molecular identification to detect Sarcoptes scabiei and its variants. This study aimed to determine and compare the sensitivity and specificity of CO1 and ITS2 S. scabiei genes to the microscopic examination of scabies skin scrapings. The skin scrapings of 52 subjects with scabies diagnosed by anamnesis, physical examination, and dermoscopic examination were examined under a microscope and analyzed by nested PCR. The diagnostic test result showed that the sensitivity of nested PCR of both CO1 and ITS2 genes to micro‐ scope examination was 100%. However, the specificity of both CO1 and ITS2 nested PCR was poor (24% and 0%). Hence, CO1 and ITS2 nested PCR could be more suitable for screening ordinary scabies in humans than the microscopic examination.
Plant growth‐promoting activity of endophytic bacteria from sweet sorghum (Sorghum bicolor (L.) Moench) Charlie Ester de Fretes; Donny Widianto; Yekti Asih Purwestri; Tri Rini Nuringtyas
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64893

Abstract

Application of high levels of chemical fertilizers for optimal growth of sweet sorghum causes environmental degradation. Plant growth‐promoting bacteria have biotechnological importance because they can improve the growth and health of important agronomic plants. This study aimed to isolate, characterize, and identify endophytic bacteria associated with sweet sorghum (cv. KCS105), and also to study the inoculation effects of selected isolates on sorghum growth. In this study, 35 isolates were evaluated for their ability to support plant growth. The results showed that seven isolates were diazotrophic, six were capable of dissolving phosphate, six produced IAA and could detect ACC‐deaminase activity, and three inhibited the growth of pathogenic fungi. Nine isolates exhibiting mechanisms for promoting plant growth from the Alphaproteobacteria (Devosia), Firmicutes (Bacillus, Paenibacillus, Staphylococcus), and Actinobacteria (Microbacterium, Brachybacterium) phyla were identified. In addition, the Paenibacillus sp. BB7, Bacillus sp. PIB1B, and Bacillus sp. PLB1B isolates showed increasing effects on plant growth in greenhouse tests. Endophytic bacterial isolates which display plant growth‐promoting features can potentially be employed as biofertilizer agents. They may also address environmental damage problems resulting from the use of chemical fertilizers and pesticides.
In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B Erdianty Setiabudi; Karlia Meitha; Fenny Martha Dwivany
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.65142

Abstract

Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.
Identification of mercury‐resistant Streptomyces isolated from Cyperus rotundus L. rhizosphere and molecular cloning of mercury (II) reductase gene Wahyu Aristyaning Putri; Hanum Mukti Rahayu; Anis Uswatun Khasanah; Langkah Sembiring; Masashi Kawaichi; Yekti Asih Purwestri
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.65989

Abstract

Streptomyces is one of mercury‐resistant bacteria which can convert Hg2+ into nontoxic Hg0 . This study aimed to identify mercury‐resistant Streptomyces present in the Cyperus rotundus rhizosphere from artisanal small‐scale gold mining (ASGM) area and clone merA gene to the cloning and expression vectors. Molecular identification was conducted using 16s rRNA gene with the maximum likelihood algorithms. Results revealed that the AS1 and AS2 strains were a group of Streptomyces ardesiacus and the BR28 strain was closed to Brevibacillus agri. The AS2 merA gene was cloned to pMD20 cloning vectors, pGEX‐5x‐1 and pET‐28c expression vectors. The transformation was successfully performed in BL21 and DH5α competent cells. The full length of the merA gene was confirmed to be 1,425 bp. This study is the first research on identifying mercury‐resistant Streptomyces and cloning the full‐length merA gene in Indonesia.
Increased serial levels of platelet‐derived growth factor using hypoxic mesenchymal stem cell‐conditioned medium to promote closure acceler‐ ation in a full‐thickness wound Pangesti Drawina; Agung Putra; Taufiqurrachman Nasihun; Yan Wisnu Prajoko; Bayu Tirta Dirja; Nur Dina Amalina
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64021

Abstract

The healing process of a full‐thickness wound involves a complex cascade of cellular responses to reverse skin integrity formation. These processes require growth factors, particularly platelet‐derived growth factor (PDGF). Conversely, hypoxic mesenchymal stem‐cell‐conditioned medium (HMSC‐CM)‐contained growth factors notably contribute to acceleration of wound healing. This study aims to investigate the role of HMSC‐CM in controlling the serial levels of PDGF associated with accelerated wound closure in full‐thickness wounds. Twenty male Wistar rats with full‐thickness wounds were developed as animal models. The animals were randomly assigned to four groups, comprising two treatment groups (treated using HMSC‐CM at a high dose as P1 and at a low dose as P2), a control group (administration of base gel), and sham group (healthy group). PDGF levels were examined using an enzyme‐linked immunosorbent assay. Using ImageJ software, wound closure percentages were determined photographically. The study showed that there was a significant increase in PDGF levels on days 3 and 6 after HMSC‐CM treatment, followed by a decrease in PDGF levels on day 9. In line with these findings, wound closure percentage also increased significantly on days 6 and 9. In the rat model, HMSC‐CM administration may promote acceleration of wound closure by increasing serial PDGF levels in the full‐thickness wound.
Tetra‐primer amplification refractory mutation system (ARMS) PCR used to detect 3’UTR rs1948 mutation in CHRNB4 Anggi Laksmita Dewi; Dewi Kartikawati Paramita; Jajah Fachiroh
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.64933

Abstract

Rs1948 A>G is a single nucleotide variation (SNV) in the 3’‐UTR of CHRNB4. Genotyping the synonymous CHRNB4 rs1948 may be useful in identifying a lung cancer susceptibility gene. The study aimed to develop a simple and easy tetra‐primer amplification refractory mutation system (ARMS PCR) for CHRNB4 rs1948. The following steps were taken to optimize tetra‐primer ARMS PCR: 1) determining the gene sequence and position of a single mutation; 2) developing outer and inner primers; 3) amplification of target gene fragments via PCR using an outer primer; 4) genotyping PCR product using Sanger sequencing; 5) determining the optimal annealing temperature and PCR cycle; 6) determining optimal outer and inner primer ratio; and 7) testing the reproducibility of the PCR program and final validation with Sanger sequencing. Genotype (PCR result) was visualized with 3% agarose gel electrophoresis. Optimum condition was determined as annealing temperature of 64.8 ºC and 35 cycles, outer and inner primer ratio of 1:6, and DNA volume of 3 µL. Sanger sequencing confirmed the results of the tetra‐primer ARMS PCR and it was shown that ARMS PCR was able to identify three different variants of CHRNB4 rs1948.
The relationship between morpho‐physiological changes and expression of transcription factors in NTT local rice cultivars as a response to drought stress Yustina Carolina Febrianti Salsinha; Alfino Sebastian; Ekris Sutiyanti; Yekti Asih Purwestri; Didik Indradewa; Diah Rachmawati
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.65728

Abstract

Response by plants to drought occurs through a series of mechanisms that involve transcription regulation. This research was conducted to study transcription factors (TF) and physiological changes in the drought response of local rice cultivars from East Nusa Tenggara (Nusa Tenggara Timur, NTT) during drought stress. Using three NTT local rice cultivars (Boawae Seratus Malam (BSM), Gogo Jak (GJ), and Kisol Manggarai (KM)) and the fraction of transpirable soil water (FTSW) method with two treatment levels, FTSW 1 (control) and FTSW 0.2 (severe stress), we analyzed the TF expression of OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6. Based on the result, the highest level of TF expression occurred in the BSM, followed by the GJ and KM cultivars. Analysis of physiological characteristics showed an association between TF expression levels and physiological response, with the BSM cultivar showing high pigment levels, high proline content, and lower H2O2 levels. A linkage was also found in relation to water conservation, as indicated by the higher relative water content and cell membrane stability index in the BSM cultivar in contrast to lower electronic leakage and malondialdehyde percentage when exposed to drought. Based on the results, it can be concluded that the BSM cultivar can be considered as a drought‐tolerant local cultivar according to morpho‐physiological analysis. In this study, all NTT local rice cultivars showed a subtle upregulation of stress‐responsive transcription factors OsDREB1A, OsDREB2A, OsWRKY45, and OsNAC6 as responses to drought stress.
The design of Indonesian SARS‐CoV‐2 primers based on phylogenomic analysis of the SARS‐CoV‐2 clades Tsania Taskia Nabila; Ata Rofita Wasiati; Afif Pranaya Jati; Annisa Khumaira
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.66854

Abstract

Molecular detection needs to be augmented for COVID‐19 detection in Indonesia using the PCR method with primer‐based gene analysis. This is necessary because the RNA of the SARS‐CoV‐2 virus, the causative infectious agent of the pandemic, has been mutated. Therefore, this study aimed to develop a primer design for determining SARS‐CoV‐2 clades in Indonesia using phylogenomic analysis. Data were obtained from 38 GISAID (Global Initiative on Sharing All Influenza Data) viruses and the relationships were analyzed using maximum likelihood (ML) phylogenomic analysis with a substitution model of generalized time‐reversible (GTR) to construct the tree topology. The results showed that the five types of SARS‐CoVs‐2 clades in Indonesia were L, G, GH, GR, and O. It also indicated that the GH region had the highest rate of clade at 50%, with the S clade affecting its formation. Furthermore, the genome sequences of the GH type used to design its primer were based on three genes, namely RdRp, S, and N. The RdRp and N genes were found to be conserved and hardy mutants, while the S gene occurred repeatedly. Several previous studies have stated that the designed primers produced missense mutations compared to another in silico. Therefore, three sets of primers were achieved from the GC contents and clamps, Tm range, and structural secondary indicator standards.

Page 42 of 53 | Total Record : 523

 40   41   42   43   44 

Filter by Year

2005 2025


Reset
Filter By Issues
All Issue Vol 30, No 4 (2025) Vol 30, No 3 (2025) Vol 30, No 2 (2025) Vol 30, No 1 (2025) Vol 29, No 4 (2024) Vol 29, No 3 (2024) Vol 29, No 2 (2024) Vol 29, No 1 (2024) Vol 28, No 4 (2023) Vol 28, No 3 (2023) Vol 28, No 2 (2023) Vol 28, No 1 (2023) Vol 27, No 4 (2022) Vol 27, No 3 (2022) Vol 27, No 2 (2022) Vol 27, No 1 (2022) Vol 26, No 4 (2021) Vol 26, No 3 (2021) Vol 26, No 2 (2021) Vol 26, No 1 (2021) Vol 25, No 2 (2020) Vol 25, No 1 (2020) Vol 24, No 2 (2019) Vol 24, No 1 (2019) Vol 23, No 2 (2018) Vol 23, No 1 (2018) Vol 22, No 2 (2017) Vol 22, No 1 (2017) Vol 21, No 2 (2016) Vol 21, No 1 (2016) Vol 20, No 2 (2015) Vol 20, No 1 (2015) Vol 19, No 2 (2014) Vol 19, No 1 (2014) Vol 19, No 1 (2014) Vol 18, No 2 (2013) Vol 18, No 2 (2013) Vol 18, No 1 (2013) Vol 18, No 1 (2013) Vol 17, No 2 (2012) Vol 17, No 2 (2012) Vol 17, No 1 (2012) Vol 17, No 1 (2012) Vol 16, No 2 (2011) Vol 16, No 2 (2011) Vol 16, No 1 (2011) Vol 16, No 1 (2011) Vol 15, No 2 (2010) Vol 15, No 2 (2010) Vol 15, No 1 (2010) Vol 15, No 1 (2010) Vol 14, No 2 (2009) Vol 14, No 2 (2009) Vol 14, No 1 (2009) Vol 14, No 1 (2009) Vol 13, No 2 (2008) Vol 13, No 2 (2008) Vol 13, No 1 (2008) Vol 13, No 1 (2008) Vol 12, No 2 (2007) Vol 12, No 2 (2007) Vol 12, No 1 (2007) Vol 12, No 1 (2007) Vol 11, No 2 (2006) Vol 11, No 2 (2006) Vol 11, No 1 (2006) Vol 11, No 1 (2006) Vol 10, No 2 (2005) Vol 10, No 2 (2005) Vol 10, No 1 (2005) Vol 10, No 1 (2005) More Issue