Indonesian Journal of Biotechnology
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In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B
No full textBanana 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
No full textStreptomyces 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
Obtaining of transgenic potato (Solanum tuberosum L.) cultivar IPB CP3 containing LYZ‐C gene resistant to bacterial wilt disease
No full textBacterial wilt caused by Ralstonia solanacearum is one of the most important bacterial diseases in potato production. This study aimed to obtain the transgenic potato (Solanum tuberosum L.) cultivar IPB CP3, containing LYZ‐C gene encoding for lysozyme type C, resistant to bacterial disease caused by R. solanacearum. Genetic transformation using Agrobacterium tumefaciens LBA4404 to 124 internode explants resulted in the transformation efficiency of about 47.58% with a regeneration efficiency of approximately 30.51%. Gene integration analysis showed that 16 clones were confirmed as transgenic clones containing the LYZ‐C gene. Analysis of resistance to R. solanacearum of three transgenic clones showed that all three transgenic clones were more resistant than a non‐transgenic one. This result showed that the LYZ‐C gene integrated in the genome of transgenic potato increased the resistance of potato plants to R. solanacearum. We obtained two transgenic clones considered resistant to bacterial wilt disease
Detection of species substitution in raw, cooked, and processed meats utilizing multiplex-PCR assay
No full textThe rise of beef consumption in Indonesia opens an opportunity for “rogue” suppliers to mix beef with other meat species that are relatively cheaper, such as pork, chicken, etc. The aim of this study was to identify pig and chicken meat in raw, cooked, and processed meat products using multiplex-PCR of mitochondrial DNA Cytochrome b gene, which is maternally inherited and widely used for forensic studies. A total of 90 samples-33 raw meats, 33 cooked meats, and 24 meatballs-were used in this study. Each sample was extracted to obtain the DNA genome and this was then amplified using multiplex-PCR. The PCR products were visualized using 2% agarose gel electrophoresis. The results showed that species contained in raw, cooked, and processed meat samples could be identified as indicated by DNA bands at 398, 274, 227, and 157 bp for pig, cattle, chicken, and goat species respectively. This study concluded that species substitution in raw, cooked, and processed meats could be detected using the Cytochrome b gene as a genetic marker through multiplex-PCR assay
Reaction kinetics of lactic acid fermentation from bitter cassava (Manihot glaziovii) starch by Lactobacillus casei
No full textOne of the utilizations of bitter cassava is modified cassava flour (Mocaf) production using the fermentation process by Lactobacillus casei. The Mocaf has potential as the future of food security products. It has a characteristic property similar to wheat flour. Lactic acid was also produced as a by‐product during fermentation. After 40 h of fermentation, the proximate composition content of Mocaf was lactic acid content of 0.000928 g/L, hydrogen cyanide levels of 0.02 ppm, starch content of 59.13%, amylose content of 12.98% and amylopectin content of 46.15%. In the scaling‐up process from a laboratory scale to a pilot and industrial scale, modeling is needed. There are five equation models used to describe the kinetic reactions of lactic acid from bitter cassava starch: Monod, Moser, Powell, Blackman, and Product Inhibitor. Each parameter was being searched by a fitting curve using sigmaplot 12.0. The best result in terms of the highest R2 (0.65913) was obtained in the Powell equation with the value of µmax of 1.668/h, Ks of 123.4 g/L, and maintenance rate (m) of 4.672. The kinetic data obtained can be used to design biochemical reactors for industrial scale Mocaf flour production
Anammox biofilm process using sugarcane bagasse as an organic carrier
No full textThe anaerobic ammonium oxidation (anammox) biofilm process commonly uses various inorganic carriers to enhance nitrogen removal under anaerobic conditions. This study aims to analyze the performance of nitrogen removal in anammox process using sugarcane bagasse as an organic carrier. The experiment was carried out by using an up‐flow anaerobic sludge blanket (UASB) reactor for treating artificial wastewater at room temperature. The reactor was fed with ammonium and nitrite with the concentrations of 70‐150 mg–N/L and variations in the hydraulic retention time of 24 and 12 h. The granular anammox belongs to the genus Candidatus Brocadia sinica that was added as an inoculum of the reactor operation. The experimental stoichiometric of anammox for ΔNO2‐–N: ΔNH4+–N and ΔNO3‐: ΔNH4+ were 1.24 and 0.18, respectively, which is similar to anammox stoichiometry. The maximum Nitrogen Removal Rate (NRR) has achieved 0.29 kg–N/m3.d at Nitrogen Loading Rate (NLR) 0.6 kg–N/m3.d. The highest ammonium conversion efficiency (ACE) and nitrogen removal efficiency (NRE) were 88% and 85%, respectively. Based on this results, it indicated that sugarcane bagasse as organic carriers could increase the amount of total nitrogen removal by provided of denitrification process but inhibited the anammox process at a certain COD concentration
Analysis using top‐k skyline query of protein‐protein interaction reveals alpha‐synuclein as the most important protein in Parkinson’s disease
No full textParkinson’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
No full textProteases 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
Comparative lactic acid bacteria (LAB) profiles during dadih fermentation with spontaneous and back-slopping methods, as identified by terminal-restriction fragment length polymorphism (T-RFLP)
No full textThe diversity of lactic acid bacteria (LAB) present during the manufacture of traditional fermented buffalo milk from West Sumatra, known as dadih, was studied via a culture-independent approach using terminal-restriction fragment length polymorphism (T-RFLP) to compare the dynamic diversity in back-slopping and spontaneous fermentation methods. Total LAB and pH were measured in freshly prepared buffalo milk and in \textit{dadih} fermented for 24 and 48 hours. The results indicated significant differences between the fermentation methods, with higher total LAB, and greater phylotype richness and relative abundance being identified in the back-slopping method. Terminal fragment lengths (TRFs) of 68 and 310 bp were common to both techniques, similar to those of Lactobacillus fermentum, Fructobacillus pseudoficulneus, Leuconostoc citreum, Leuconostoc kimchii, and Leuconostoc sp. The changes in phylotype number (species number) and relative abundances of LAB communities identified are expected to produce data needed to formulate the best fermentation process for dadih manufacturing. A 24-hour back-slopping fermentation method is recommended, as fermentation time of longer than 24 hours reduced viable LAB significantly. Our results also indicated that the T-RFLP technique is not only clearly sensitive enough and adequate for segregating LAB diversity in both fermentation methods, but that it also provides good information regarding the structure of microbial communities and their composition change during the fermentation process
Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions
No full textObservation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results