Indonesian Journal of Biotechnology
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Elimination of ineffective inorganic salt component in medium for indole‐3‐acetic acid synthesis by Serratia plymuthica UBCF_13 and its effect on the growth of chili seedlings
No full textIndole‐3‐acetic acid (IAA) is an essential phytohormone that controls a variety of plant growth mechanisms. Bacteria can produce IAA to stimulate plant growth, with its production influenced by the culture conditions. Serratia plymuthica UBCF_13 is recognized as an IAA‐producing bacterium, exhibiting maximum IAA production in a yeast medium comprising yeast extract, sucrose, K2HPO4, MgSO4, NaCl, and CaCO3. However, prior studies optimizing individual inorganic salt components indicated minimal impact on IAA synthesis within this medium. This study aimed to eliminate the unnecessary inorganic salt components and the medium was then applied to investigate the IAA biosynthesis pathway and the plant growth‐promoting assay. The elimination assay consisted of yeast sucrose medium devoid of K2HPO4, MgSO4, NaCl, or CaCO3, and yeast sucrose medium containing only MgSO4 and CaCO3. Various indole compounds were then added to the revised medium composition to investigate the IAA biosynthesis pathway of UBCF_13 using high‐performance liquid chromatography (HPLC). Furthermore, the effect of UBCF_13 culture supernatant, cultivated in the new medium, on chili plant growth was evaluated. The highest IAA production (138.8 µg/mL) was observed in the yeast sucrose with CaCO3 and MgSO4 (elimination of K2HPO4 and NaCl). The presence of indole‐3‐acetamide (IAM) compound from the medium extracts, supplemented with multiple indole compounds, revealed that UBCF_13 may use the IAM pathway. The application of UBCF_13 supernatant enhanced the shoot, root length, fresh weight, and germination time of chili seeds by 37.7%, 49.3%, 204.3%, and 38.6%, respectively. This study demonstrated that eliminating K2HPO4 and NaCl provided a new culture medium composition conducive to IAA production by UBCF_13. Moreover, the UBCF_13 extract has the potential to promote plant growth
Omics strategies for crop improvement in response to climate change‐imposed abiotic stress
No full textGiven the current status of climate change and its impact on global food security, it is imperative to improve the abiotic stress tolerance of crop plants to enhance productivity. Traditional plant breeding methods have been widely employed to develop climate‐resilient crops; however, their success has been limited due to the lack of understanding of the complex relationships between genes and stress‐related phenotypes. The advent of modern genomics has enabled the expression analysis of stress genes in plants, as genome‐wide information is readily accessible and can be utilized to assign and validate the gene functions. This article highlights the potential applications and limitations of present‐day genomic technologies based on genome mapping, gain or loss‐of‐function analysis for identification of the role of a particular gene in abiotic stress response in plants. Such technologies are highly efficient in candidate gene identification; gene‐trait relationships establishment; functional elucidation of genes; and stress genes modification in crop plants. Modern high throughput genomic technologies offer wide scope for deciphering the complexities of genetic regulation of stress in plants; modulating stress responses; and developing stress tolerance in crop plants against drought, temperature, salinity, osmotic imbalance, herbicides and heavy metal toxicity
Performance of salt‐bridge microbial fuel cell (SB‐MFC) with various microorganism cultures on the generation of electricity from tofu wastewater
No full textA suitable wastewater treatment system is required due to the high organic compound content in tofu wastewater, which can harm the environment. Biological treatment methods are effective for treating tofu wastewater due to its characteristics. Microbial fuel cells (MFCs) represent one such biological treatment option, effectively removing organic contaminants while generating low‐power electricity through bioenergetic reactions. In MFCs, microorganisms are used as biocatalysts to degrade the organic compounds present in wastewater. This study aimed to assess the efficacy of Salt‐bridge microbial fuel cells (SB‐MFC) using various acclimatized microbe cultures for reducing organic compounds and generating energy from tofu wastewater. Tofu wastewater was sterilized prior to introduction into the reactor. Additional microbes, including the native microbe consortium from tofu wastewater, Escherichia coli, Saccharomycopsis fibuligera, and a mixed culture of E. coli and S. fibuligera, were then introduced as biocatalysts. Carbon electrodes were utilized as both the anode and cathode. The results indicate that the mixed culture of E. coli and S. fibuligera significantly reduced COD and BOD5 levels, with removal rates of 82.74% and 76.53%, respectively, after 48 h. Furthermore, the culture generated a voltage of 676 mV, a current of 2.53 mA, a power density of 428 mWatt/m2, and 4.789×10‐2 kWh of energy. This study contributes to the advancement of SB‐MFC by utilizing wastewater and a combination of bacteria and yeast as biocatalysts
Genetic polymorphism and frequency study at 15 short tandem repeat loci in the North and East Indian populations for use in personal identification and applications in India
No full textAllele frequency is a crucial factor in estimating the weight of evidence (WoE) for an individual’s involvement in a DNA sample. To determine the allele and genotype frequencies within the populations of the northern and eastern states of India, 15 short tandem repeats (STRs) were used, including Penta E, CSF1PO, D18S51, D7S820, D21S11, TH01, D3S1358, Vwa, FGA, TPOX, D8S1179, D16S539, D13S317, Penta D, and D5S818. The study involved 509 randomly selected individuals, analyzed using the PowerPlex 16 System Kit. Various statistical parameters of forensic significance were calculated using Forensic Statistic Analysis Toolbox (FORSTAT) software, including the typical paternity index (TPI), power of exclusion (PE), matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), and observed (Hobs) and expected heterozygosities (Hexp). The analysis revealed a maximum allele frequency of 0.4282 at TPOX, with a minimum frequency of 0.0009 observed at different loci. FGA was found to be the most polymorphic loci among the 15 loci analyzed in the North and East Indian populations. Furthermore, no divergence from the Hardy‐Weinberg equilibrium (HWE) was observed. The results serve as a valuable source of information for establishing a DNA database for North and East Indian populations, providing essential information for population genetics studies and forensic casework in India
Metagenomic analysis of bacterial diversity in pigeon pea after soaking in water
No full textThis study investigated the diversity of bacterial community in the samples of pigeon pea (Cajanus cajan L. Millsp.) soaked in water for 12 h and 24 h. The detection of certain bacterial species in the samples that can be isolated and potentially be used as starter cultures in the development of pigeon pea‐based functional foods is the importance of this study. For bacterial identification, the V1–V9 regions on the 16S ribosomal RNA gene were amplified using 27F and 1492R primers under specific polymerase chain reaction conditions. Genomic DNA (130 ng) was sequenced on the R9.4 flow cell by Oxford Nanopore Technologies using a GridION sequencer. Library preparations were conducted using a Native Barcoding Kit 24 V14 (SQK‐NBD114.24). Primary data were acquired using MinKNOW version 22.05.7. A total of 13 bacterial families and 89 genera were identified in the pigeon pea sample soaked for 12 h, and 26 families and 90 genera were identified in the pigeon pea soaked for 24 h. The values of five diversity indices showed that the sample soaked in water for 24 h had richer bacterial abundance and diversity than for 12 h. Shannon and Simpson values revealed the higher bacterial diversity in the samples collected at 24 h than in those collected at 12 h. Species observation and abundance‐based coverage estimators (ACE) values demonstrated that the samples collected at 24 h harbored higher bac‐ terial richness than those collected at 12 h. Bacterial communities during soaking of the pigeon pea were dominated by the family Enterobacteriaceae and genus Enterobacter. The presence of bacterial genera like Lacticaseibacillus, Lentilactobacillus, and Secundilactobacillus is interesting because of their importance as starter cultures for fermented plant‐based milk product
Detection and quantification of splicing variants of Hd3a gene in oil palm
No full textAlternative splicing is a complex process that contributes to the generation of diverse mRNA and protein isoforms, including in oil palm (Elaeis guineensis). Despite their importance, many functions of alternative splicing genes remain poorly characterized. This study aims to investigate splicing variants of gene encoding Heading date 3a in E. guineensis (EgHd3a) using the GenBank database and ClustalW algorithm. To ensure the data accuracy and reliability of design isoform‐ specific primers, special emphasis is given to primer design techniques and validation using polymerase chain reaction (PCR) and quantitative real‐time (qRT)‐PCR analysis. The designed primers demonstrated high specificity and discrimination between mRNA specimens. Nucleotide variations at the 3’‐end influenced the specificity of primers with the addition of GC composition. Furthermore, qRT‐PCR analysis revealed a strong correlation between Ct values and gene concentration for the isoforms which indicates a reliable amplification of EgHd3a. Although two isoforms, Hd3a‐X2 and Hd3a‐X3, showed slightly higher than acceptable PCR efficiency values, caution is advised to prevent non‐specific amplification. Despite the challenge posed by the limitation of primer positioning due to alternative splicing, the chosen primer proved optimal for analysis. This study highlights the importance of considering alternative splicing in gene quantification experiments and provides insights into the critical steps, methods, and quality control measures necessary for accurately detecting alternative splicing events, contributing to understanding this complex biological process
Development of a dimer‐based screening system that targets PhoR, a sensor kinase of the two‐component regulatory system, in Mycobacterium tuberculosis
No full textThe PhoR‐PhoP two‐component regulatory system, which is responsible for regulating the virulence of Mycobacterium tuberculosis, presents a promising target for the development of novel tuberculosis drugs. Disrupting the interaction of PhoR‐PhoP proteins has the potential to decrease the virulence of the bacterium, rendering it more vulnerable to immune system clearance. A dimer‐based screening system was developed to screen for inhibitors of PhoR dimerization. The coding sequence for the cytoplasmic domain of PhoR (cytoPhoR) was combined with the DNA‐binding domain of the AraC repressor coding sequence. These sequences were positioned upstream of the emerald green fluorescent protein (EmGFP), which serves as a reporter gene. and controlled by the araC promoter. The in silico investigation examined the modeling of the fusion AraC_cytoPhoR and its binding to the promoter. The plasmid construct generated, namely pAraC_PhoRMTB, was synthesized and confirmed using DNA sequencing. The confirmed plasmid was then transformed into Escherichia coli BL21(DE3). Both SDS PAGE and fluorescence analysis indicated that the transformed culture expressed the AraC‐cytoPhoR fusion protein and displayed lower relative fluorescence in comparison to the transformed culture consisting solely of the AraC DNA‐binding domain coding sequence. This reduction in fluorescence suggests that the dimer‐based screening system effectively monitors the inhibition of dimerization of cytoPhoR. These analysis findings indicate that the system is now ready for use in the screening of PhoR dimerization inhibitors
A comprehensive study of potential Arthrospira platensis cultivated in various manure‐based media for biodiesel feedstock
No full textArthrospira platensis has emerged as a promising biodiesel feedstock due to its rapid growth and substantial biomass. In efforts to reduce production costs, researchers have explored alternative media derived from livestock waste to modify conventional mediums for Arthrospira platensis cultivation. The experimental design of this research employed a Completely Randomized Design, with treatments comprising inorganic fertilizer (A), chicken manure (B), cow manure (C), and goat manure (D). The livestock manures were macerated for seven days before being utilized as A. platensis medium. The results revealed significant (p < 0.05) impacts of different media on peak growth values and biomass production, reaching 2.03 ± 0.06 g/L and 1.76 ± 0.05 g/ L, respectively for chicken manure. The highest peak lipid content was observed in A. platensis cultured in goat manure medium. This study recommends goat manure as the preferred medium for mass cultivation of A. platensis. Mass cultivation in goat manure medium yielded 1.53 kg of dried biomass, with a lipid content of 1.91% and a biodiesel yield of 1.65%. The predominant fatty acid in this biodiesel was heneicosane, constituting 26.4% of the total area
The effect of non‐contact electro capacitive cancer therapy on DMBA‐induced rat breast tumor angiogenesis
No full textAlternating Current‐Electric Field (AC‐EF) generated by non‐contact Electro Capacitive Cancer Therapy (ECCT) can inhibit breast tumor growth. However, its effect on breast tumor angiogenesis remains unclear. Since angiogenesis is involved in normal physiology and tumors, it is crucial to investigate the effect of ECCT on normal and breast tumor angiogenesis. Samples consisting of rat breast normal tissue and breast tumors were obtained from the biobank, with tumors induced by 7,12‐dimethylbenz (α) anthracene (DMBA) at 20 mg/kg BW 10 times over five weeks. Meanwhile, ECCT exposure of 150 kHz and 18 Vpp was conducted for 21 days at 10 hours/day. The qPCR method was used for gene expression analysis, while immunohistochemistry used antibody anti‐Vegfr2 that was used to detect Vegfr2 protein expression. Data were analyzed using one‐way ANOVA and t‐tests performed with GraphPad Prism ver.9.5.1 software. The results revealed no impact of ECCT exposure on normal breast tissue angiogenesis. Interestingly, there was a significant increase in the number of blood vessels following the upregulation of Vascular Endothelial Growth Factor Receptor‐2 (Vegfr2) as opposed to its primary signal, Vascular Endothelial Growth Factor‐A (Vegfa). Furthermore, gene expression of Hypoxia Inducible Factor‐1α (Hif1α) and Specificity Protein‐1 (Sp1) was similar to that of the control group, suggesting that Vegfr2‐dependent angiogenesis regulates ECCT‐treated breast tumor angiogenesis
Specific PCR primers for rapid detection of five rat and mouse species in Java, Indonesia
No full textIdentifying rat and mouse species quickly, affordably, and accurately is crucial for effective population management, as well as for eradication or conservation purposes. However, the sheer diversity of these species poses a challenge. To address this, a molecular approach has been developed, involving the amplification of a short genetic marker from materials commonly left by the animal, such as hairs and feces. Recent available PCR primers were not suitable for the surveillance of large sample sizes. As a solution, this study designed and validated a PCR primer set capable of detecting five species of rats and mice (Mus musculus, Rattus tanezumi, Bandicota indica, Rattus tiomanicus, and Rattus argentiventer) commonly found in Java, Indonesia. The specific primers were derived from the cytochrome c oxidase subunit 1 (COI) gene, designed using the SP‐Designer V7.0 application, and validated using both in silico and in vitro methods. The validation results demonstrated that all five pairs of primers were highly specific, generated correct amplicons, and successfully detected the five distinct species present in a Javan mongoose feces sample. These findings are significantly important as they enable the effective detection of rat and mouse species and potentially provide valuable ecological insights from the field