Indonesian Journal of Biotechnology
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Ethanolic extract of sappan wood (Caesalpinia sappan L.) inhibits MCF-7 and MCF-7/HER2 mammospheres' formation: an in vitro and bioinformatic study
No full textOne of the mechanisms of cancer cell resistance toward chemotherapy is through cancer stem cells (CSCs), which are characterized by excessive activation of regulator proteins such as human epidermal receptor 2 (HER2). Sappan wood (Caesalpinia sappan L.) contains brazilin and brazilein that exhibit cytotoxic effects on several cancer cell lines. We aimed to explore the potency of the ethanolic extract of sappan (EES) in CSCs through bioinformatic analyses and by using a three-dimensional (3D) breast cancer stem cells (BCSCs) for in vitro assay with two different models (i.e., BCSCs and HER2-BCSCs) in order to identify the potential therapeutic targets of genes (PTTGs). Bioinformatic analyses identified PTTGs, which were further analyzed by gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, protein-protein interaction (PPI) networks, and hub protein selection. Mammospheres were cultured under conditioned media. The cytotoxic effects of EES were then measured by direct counting and based on the mammosphere-forming potential (MFP). Bioinformatic analysis disclosed PIK3CA and TP53 as PTTGs in BCSCs and HER2-BCSCs, respectively. In addition, the KEGG pathway analyses also demonstrated that PTTGs could regulate the ERBB pathway. EES thus demonstrated cytotoxicity and inhibited the formation of mammospheres. Collectively, EES exhibited excellent potential for further development as an inhibitor of cancer stem cells in breast cancer
Performance of CO1 and ITS2 nested PCR in molecular identification of ordinary scabies (Sarcoptes scabiei var. hominis)
No full textScabies 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
Analyzing the biosynthetic potential of antimicrobial-producing actinobacteria originating from Indonesia
No full textWe investigated the biosynthetic potential of soil-associated actinobacteria originating from Indonesia, identified as Streptomyces luridus and as Streptomyces luteosporeus. Antimicrobial assays indicated inhibitory activity by both strains against the pathogen Pseudomonas aeruginosa, with S. luteosporeus particularly inhibiting the growth of Bacillus subtilis. PCR-amplification, cloning, and sequencing of ketosynthase (KS) domains of type I modular polyketide (PKS-I) and adenylation (AD) domains of non-ribosomal peptide synthetase (NRPS) indicated the diversity of KS and AD domains derived from both Indonesian Streptomyces. Further phylogenetic analysis showed that KS domains from the subclass cis-AT PKS can be classified as being a part of a loading module or an extension module, along with their predicted substrate specificity. The results suggest that both strains are a potential source of novel biosynthetic pathways. This genetic analysis approach can be used as a fast guide to obtain insight into natural product biosynthetic gene diversity in microorganisms
Biodesulfurization of the mixture of dibenzothiophene and its alkylated derivatives by Sphingomonas subarctica T7b
No full textOrganosulfur compounds classified as dibenzothiophenes (DBTs) and their derivatives are contained in petroleum. When used as fuel, these substances release SOx emissions, thus contributing to air pollution, acid rain, and climate change. Therefore, it is necessary to reduce the content of these organic sulfur compounds in fuels and one way to achieve this is through bacterial desulfurization. This study reports the biodesulfurization process of a mixture of DBT, 4-hexyl DBT, 4,6-dibutyl DBT, and various organosulfur compounds in light gas oil (LGO). The experiment was conducted by treating 1 mL of aromatic organosulfur compounds with 100 mg/L in \textit{n}-tetradecane or 1 mL LGO with 5 mL mineral salts in sulfur-free medium, incubated at 27 °C for 5 days with shaking at 273 rpm. Gas chromatography analyses revealed that the growing Sphingomonas subarctica T7b cells desulfurized and converted 88.29% of DBT to 2-hydroxybiphenyl as a metabolite while a mixture of DBT and 4,6-dibutyl DBT was desulfurized at 86.40\% and 7.00%, respectively. Furthermore, the mixture of DBT, 4-hexyl DBT, and 4,6-dibutyl DBT had a desulfurization percentage of 84.40%, 41.00%, and 6.66%, respectively, after five days of incubation. The compounds were observed to desulfurize slightly better as single compounds compared to when mixed with other aromatic sulfur compounds
Optimization of solid‐state fermentation condition for crude protein enrichment of rice bran using Rhizopus oryzae in tray bioreactor
No full textEnhancement of crude protein content in rice bran with the solid‐state fermentation method in tray bioreactor using Rhizopus oryzae FNCC 6011 has been investigated. This research aimed to optimize the fermentation condition using the response surface methodology (RSM). The central composite design (CCD) with three independent variables, including substrate thickness (1 to 3 cm), fermentation temperature (28 to 32 °C), and nutrient concentration of KH2PO4 (2 to 6 g/L) used to determine the crude protein enrichment. The quadratic model has successfully described the effect of variable interactions on responses very well as indicated by the F value and p‐value are 11.20 and 0.0041, respectively. The multiple correlation coefficients (R2) of 0.9438 indicated that 94.38% of the model data has approached the actual data with a deviation of 5.62%. The interaction between the variable substrate thickness and the fermentation temperature is the most influential variable on the crude protein enrichment of rice bran, indicated by the highest F value of 24.08 and the lowest p‐value of 0.0027. The highest protein increase of 62.51% was obtained at 2 cm substrate thickness, fermentation temperature of 30 °C, and KH2PO4 concentration of 4 g/L
The potential of mesenchymal stem‐cell secretome for regeneration of intervertebral disc: A review article
No full textLow back pain is a crucial public health problem that is commonly associated with intervertebral disc de‐ generation and has vast socio‐economic impact worldwide. Current treatments for disc degeneration are conservative, non‐surgical, or surgical interventions, and there is no current clinical therapy aimed at directly reversing the degeneration. Given the limited capacity of intervertebral disc (IVD) cells to self‐repair, treatment aiming to regenerate IVDs is a topic of interest and mesenchymal stem cells (MSCs) have been identified as having potential in this regeneration. Recent studies have revealed that the benefits of MSC therapy could result from the molecules the cells secrete and that play principal roles in regulating essential biologic processes, rather than from the implanted cells themselves. Therefore, the objective of this study is to review the potential use of the MSC secretome to regenerate IVDs. Current evidence shows that the secretome may regenerate IVDs by modulating the gene expressions of nucleus pulposus cells (upregulation of keratin 19 and downregulation of matrix metalloproteinase 12 and matrix Gla protein) and stimulating IVD progenitor cells to repair the degenerated disc
Plant growth‐promoting activity of endophytic bacteria from sweet sorghum (Sorghum bicolor (L.) Moench)
No full textApplication 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
Distinguishing resistances of transgenic sugarcane generated from RNA interference and pathogen‐derived resistance approaches to combating sugarcane mosaic virus
No full textSugarcane mosaic virus (SCMV) is a causative agent that reduces growth and productivity in sugarcane. Pathogen‐derived resistance (PDR) and RNA interference (RNAi) are the most common approaches to generating resis‐ tance against plant viruses. Two types of transgenic sugarcane have been obtained by PDR and RNAi methods using a gene‐encoding coat protein (CP) of SCMV (SCMVCp). This research aimed to distinguish resistance of the two transgenic sugarcanes in combating SCMV through artificial viral inoculation. The experiment was conducted using transgenic sugar‐ cane lines validated by PCR analysis. Insertion of gene‐encoding CP in the transgenic lines was confirmed by amplification of 702 bp of DNA fragment of SCMVCp. After viral inoculation, mosaic symptoms appeared earlier, at 21 days post inoculation (dpi) in PDR transgenic lines, but was at 26 dpi in RNAi transgenic lines. Symptom observation showed that 77.8% and 50% of the inoculated plants developed mosaic symptoms in PDR and RNAi transgenic lines, respectively. RT‐PCR analysis revealed that the nuclear inclusion protein b (Nib) gene of SCMV was amplified in the symptomatic leaves in plants classified as susceptible lines. Immunoblot analysis confirmed presence of viral CP with a molecular size of 37 kDa in the susceptible lines. Collectively, these results indicated that the RNAi approach targeting the gene for CP effectively produces more resistance against the SCMV infection in transgenic sugarcane compared to the PDR approach
Characterization of recombinant Bacillus halodurans CM1 xylanase produced by Pichia pastoris KM71 and its potential application in bleaching process of bagasse pulp
No full textThermoalkalophilic xylanases promise potential application in pulp biobleaching to reduce the use of toxic chlorinated chemical agents, which are harmful to the environment. In this study, a thermoalkalophilic endoxylanase gene (bhxyn3) originating from Indonesian indigenous Bacillus halodurans CM1 was cloned into yeast expression vector pPICZα A and expressed in Pichia pastoris KM71 under the control of AOX1 promoter. Recombinant P. pastoris expressed the highest final level of xylanase (146 U/mL) on BMGY medium after five days of cultivation. Optimization of xylanase production on a small scale was carried out by varying the methanol concentrations and the optimal xylanase production by the recombinant P. pastoris was observed in the culture with 2% (v/v) methanol after four days of the induction phase. The recombinant xylanase (BHxyn3E) was thermotolerant and alkalophilic, with an optimal temperature at around 55‐65 °C and under pH 8.0. The enzyme activity was slightly induced by K+, Fe2+, and MoO42‐. Enzymatic bleaching of bagasse pulp with no prior pH adjustment (pH 9) using BHxyn3E at 200 U/g oven dried pulp increased the lightness index (L*) and changed substantially the color a index (a*); however, the treatments did not change the whiteness index in a significant way. Therefore, further optimization and assessment such as adjustment of incubation temperature and pH in biobleaching were needed to reduce the use of harmful chemical agents in industrial applications
Antiviral activities of curcumin and 6‐gingerol against infection of four dengue virus serotypes in A549 human cell line in vitro
No full textDengue virus (DENV) is the most geographically widespread arbovirus causing dengue disease epidemics in tropical and subtropical regions. Nature provides abundant plants as a source for lead molecules against various diseases including DENV infection. We investigated the antiviral effect of curcumin and 6‐gingerol, the major active constituent of turmeric (Curcuma longa Linn.) and ginger (Zingiber officinale Roscoe), respectively, against all four serotypes of DENV infecting human lung epithelial carcinoma (A549) cell line in vitro. Both compounds generated cell cytotoxicity to A549 cells at CC50 values of 108 µM for curcumin and 210 µM for 6‐gingerol. The compound curcumin showed antiviral properties as described by IC50 of 20.60, 13.95, 25.54, and 12.35 µM, while 6‐gingerol of 14.70, 14.17, 78.76, and 112.84 µM for DENV‐1, ‐2, ‐3, and ‐4, respectively. Different levels of antiviral properties were observed between DENV serotypes. Our findings suggest that the antiviral assay of compounds against DENV should be performed to all four serotypes and not limited to a particular serotype. In conclusion, curcumin and 6‐gingerol exhibit antiviral properties against DENV infection and could provide a new therapeutic approach for dengue disease treatment strategies