HAYATI Journal of Biosciences
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Dynamic Changes of Gut Microbiome in Borneo Earless Monitor Lizard Across Different Diets
Get PDFThe Borneo earless monitor lizard (Lanthanotus borneensis) is one of the endemic animals of Indonesia. In 2019, the IUCN listed L. borneensis as an ‘endangered’ species. The declining population of the L. borneensis is a major concern for conservation efforts. One of the efforts to conserve endangered wild animals is to know the gut microbiome profile and the relationship between the host and the bacterial community in the body, which is associated with an influence on health. This research aims to determine the gut microbiome profile of animals with metagenomic analysis using Next-Generation Sequencing (NGS). This research was carried out by providing three feed types: earthworms, shrimp, and fish. Sample feces was collected by cloacal swabs and the DNA was sequenced using the Illumina NGS technique in the V4 16S rRNA region to examine the gut microbiome. The results of the metagenomic analysis showed differences in bacterial abundance in each feed treatment. The L. borneensis treated with earthworms and fish were dominated at the phylum level by Proteobacteria and Bacteriodota, while in shrimp, the phyla were Proteobacteria and Firmicutes. Index Shanon, Simpson, and the rarefaction curve also showed the highest bacterial diversity found in the fish treatment. This study can be used as a reference in designing suitable feed formulations for effective captive breeding for the conservation of L. borneensi
Anti-Inflammatory Activity of Phyllanthus niruri L. Leaf Extract: In Vitro Study on RAW 264.7 Macrophage Cells and In Silico Analysis
Get PDFPhyllanthus niruri L. is a medicinal plant recognized for its wide range of therapeutic benefits, particularly its anti-inflammatory properties. This research focused on assessing the impact of P. niruri leaf extract on pro-inflammatory cytokines in vitro using RAW 264.7 macrophage cells, analyze its phytochemical composition, and validate its potential anti-inflammatory mechanisms through molecular docking studies. The extract was analyzed for its phytochemical composition using LC-MS, revealing the presence of sesquiterpene glycosides, flavonoid glycosides, and tannins among the identified compounds. Cell viability tests showed that the extract was not toxic to the cells at concentrations up to 50 µg/ml. Treatment with the extract significantly reduced the levels of pro-inflammatory cytokines TNF-α and IL-1β in LPS-induced RAW 264.7 cells, with the most effective concentration being 50 µg/ml. Molecular docking studies further supported the anti-inflammatory potential of the extract by demonstrating its ability to inhibit COX-2 and TNF-alpha. These findings suggest that P. niruri leaf extract has promising anti-inflammatory properties and needs further investigation as a potential treatment for inflammatory diseases. The in silico study provided insights into the molecular interactions between the extract\u27s compounds and inflammatory targets, supporting its anti-inflammatory mechanism of action
In Silico Study, Design, and Expression of an Intranasal Dual Chimeric Vaccine for Indonesian-Based Norovirus GII-2 and Hepatitis B
Get PDFHepatitis B virus (HBV) remains an important healthcare challenge, leading to liver diseases like cirrhosis and cancer. In response, we created a prophylactic and therapeutic HBV vaccine by integrating HBcAg and HBsAg from HBV genotype B into Norovirus (NoV) GII.2 P domain (PdomGII.2-HBV) for enhanced intranasal delivery. This vaccine also aimed to simultaneously prevent NoV infection, which causes gastroenteritis. Since the selected HBV epitopes have undergone extensive research and are tailored to the Indonesian population, this study focused on identifying NoV epitopes and assessing T cell epitopes coverage of the PdomGII.2-HBV for the Indonesian population. Following that, we expressed the PdomGII.2-HBV protein using Escherichia coli BL21(DE3) and employed a gentle solubilization technique for protein purification. Our in-silico analysis identified two B cell epitopes, along with 15 CD4+T cell epitopes and 35 CD8+T cell epitopes within the GII.2 P domain. These T cell epitopes cover 100% of the Javanese-Sundanese population\u27s HLA allele variations, which constituted the largest demographic group in Indonesia. Subsequently, we successfully purified the presumed PdomGII.2-HBV protein, revealing a molecular weight of 39.5 kDa. Following the successful expression and purification of the presumed PdomGII.2-HBV protein, it is evident that this vaccine design has significant potential, warranting further study
LC-HRMS-Based Metabolomics for Profiling the Metabolites in Different Plant Parts of Centella asiatica
Get PDFCentella asiatica, or pegagan in Indonesia, is a perennial plant used in Indonesian traditional medicine (jamu) and functional food with many biological activities. Those biological activities come from the bioactive metabolites present in C. asiatica. Differences in metabolite pathways in each part of the plant affect the accumulation of metabolites contained, thus impacting its biological activity. Therefore, this study aims to identify and evaluate differences in the distribution of metabolites in each part of C. asiatica, namely leaves, stems, stolons, and roots. Each plant part was extracted using methanol and sonicated for 30 minutes. The metabolites in the samples were separated and detected using UHPLC-Q-Orbitrap HRMS. Differences in the distribution of metabolites in each part of the plant were evaluated using chemometrics analysis. UHPLC-Q-Orbitrap HRMS analysis could positively identify 37 metabolites, most of which belong to the phenylpropanoid, triterpenoid, triterpenoid saponin, and flavonoid groups. Principal component analysis was able to clearly distinguish each part of the plant using the peak intensity of the overall chromatogram and the peak area of the identified metabolites. The different biosynthetic pathways of metabolites in plants could cause a difference in the distribution of metabolites in each plant
Antagonistic Effects of Bacterial Rhizosphere of Oil Palm in Biocontrol of Basal Stem Rot Disease (Ganoderma boninense Pat.)
Get PDFBasal stem rot disease caused by Ganoderma boninense is a major problem for oil palm cultivation. The research was conducted to obtain biocontrol agents from rhizosphere of oil palm to control the disease as part of sustainable pest management in oil palm plantation. Rhizosphere bacteria were isolated from rhizospheres of healthy oil palm trees. Isolation of bacteria was done using serial dilution method. The isolated bacteria were then tested for its antifungal activity against G. boninense in vitro using dual culture assay. The ability of the bacteria to produce antifungal compound was also determined by culturing the bacteria on ISP2 liquid media. Once the bacterial cells were removed, the crude metabolites were then tested against G. boninense using agar well diffusion and toothpick colonization. The result showed that several isolates demonstrated strong antifungal activity against G. boninense. Some isolates were also able to degrade chitin and to solubilize phosphate. Furthermore, the crude metabolites produced by the rhizosphere bacteria demonstrated the ability to inhibit the growth of G. boninense in the agar diffusion method. Colonization of the G. boninense on toothpick following soaking in the crude metabolites was also inhibited. The isolated rhizosphere bacteria (BARK7 and BARK15 in which identified as Burkholderia sp.) showed promising ability to be developed as biocontrol agent for basal stem rot disease of oil palm
Genetic Characterization of Sumatran Mirah Chicken Based on Mitochondrial D-loop Region Sequence
Get PDFMirah chickens are Indonesian indigenous chickens that originate from Simalungun Regency, North Sumatera Province of Indonesia. The study aimed to determine the genetic characterization of Mirah chicken based on the mitochondrial D-loop region (838 bp). Twenty Mirah cocks from Simalungun Regency of Indonesia were used in the present study. The results showed that fourteen haplotypes were found in the studies of birds based on sixteen mutation sites. Therefore, these haplotype and nucleotide diversities in the partial D-loop region of the Mirah chicken were classified as high. The Median-joining tree revealed that the Mirah chickens were classified in a similar cluster with the Red jungle fowl (Gallus gallus). Ten haplotypes of birds were close to G. g. bankiva, and four haplotypes of birds were close to G. g. gallus. In conclusion, Mirah chickens had the genetic introgression from two sub-species of Red junglefowl, i.e., G.g. gallus and G.g. bankiva. Hence, the pure breeding program for Mirah chickens is important to conserve their genetic resources from extinction
Quantile Normalization for High Throughput Circulating MicroRNA Expression Study using TaqMan® Low Density Array Panels: Supporting Evidence
Get PDFIn searching for new biomarkers, high throughput technique has been widely used by researchers, including for gene expression study. However, the reliability and accuracy of results from high throughput study critically depends on appropriate data management, including normalization methods. Data driven normalization has been introduced as a normalization method for high throughput gene expression study. Thus, this study was conducted to evaluate the performance of various data driven and reference genes normalization methods using a high throughput circulating microRNA expression dataset. A quantification cycle (Cq) dataset generated from a high throughput circulating microRNA study was used to test the normalization methods using HTqPCR package in R software. The normalized Cq generated from different methods were compared descriptively using box plot analysis and coefficient of variance. The box plot analysis showed that quantile normalization produced more homogenous Cq distribution, lesser outliers and reduced coefficient of variance as compared to other normalization methods in screening and validation phases. The overview on quantile normalized Cq showed consistency in its level of expression before and after 2-∆∆Cq calculation indicating the reliability of quantile normalized Cq. Quantile normalization is suggested to be used in high throughput miRNA expression study due to its performance in homogenizing the data, reduce outliers and coefficient of variance
Lysinibacillus sphaericus Isolated from Palm Oil Waste Land as Lipase Producer
Get PDFIn this research, lipolyic bacteria have been isolated from palm oil waste land for the production of lipase. Species of potential lipolytic bacteria were identified based on their morphology and sequences of 16 rRNA gene. Enzymes are produced by growing bacteria in a medium with various vegetable oils and nitrogen sources. The enzyme produced by the bacteria measured its lipolytic activity against the substrate para-nitrophenylpalmitate. The lipolytic bacteria was recognized as Lysinibacillus sphaericus L49a based on morphological and phylogenetic analysis. Mineral media with different vegetable oils as carbon sources, and different nitrogen sources were suitable for growth and production of lipase enzymes of L. sphaericus L49a. Culltivation of L. sphaericus L49a in medium containing ammonium sulfate and olive oil produced lipase with the highest lipolytic activity
Antimicrobial Activities and Painting Application of Pigmented-Producing Actinobacteria Isolated from Rhizospheric Soils of Mosses (Taxithelium nepalense (Schwägr.) Broth. and Barbula indica (Hook.) Spreng.)
Get PDFIn the survey of biodiversity of actinobacteria associated with mosses (Taxithelium nepalense (Schwägr.) Broth. and Barbula indica (Hook.) Spreng.), certain strains of pigment producing actinobacteria were isolated and purified on SCA and incubated at 30°C for 1 week. Based on deep-shade color of actinobacterial pigments, 4 strains were collected and used for painting color preparation. To evaluate the antimicrobial activities, the crude extracts were prepared from 4 actinobacterial strains and tested with Escherichia coli PSRU-01 and Staphylococcus aureus PSRU-01. The results indicated that the crude extracts of C7, C13, C15 and D13 could not inhibit growth of E. coli PSRU-01, but S. aureus PSRU-01 was inhibited. Two fungal testers, including Colletotrichum sp. PSRU-01 and Fusarium sp. PSRU-01, were completely inhibited by the crude pigment extracts of C13, C15 and D13. Based on phylogenetic results, the actinobacterial strains were closely related to Streptomyces californicus (C7, 100% identity), Streptomyces bungoensis (C13, 99.8% similarity), Streptomyces humi (C15, 99.9% similarity), and Streptomyces rectiverticillatus (D13, 99.8% similarity). They also shared phenotypic characteristics with Streptomyces. The cultivated cells of actinobacteria on broken-milled rice were used for pigment extraction and followed by determination of the extracted pigments for mixing with acrylic color in the shade violet, green, orange and pink colors. Application of actinobacterial pigments in painting is the first report and it is an innovative utilization of actinobacterial pigments in non-scientific field in Thailand
Aromatherapeutic Antibacterials: Comparative Study of 40 Essential Oils and Their Biofilm Inhibition in Pseudomonas aeruginosa ATCC9027
Get PDFGrowing evidence suggests that biofilm formation in Pseudomonas aeruginosa (PA) results from quorum sensing, reducing bacterial sensitivity to antibiotics and fostering the development of antibiotic-resistant strains. Addressing the need for a compound that can inhibit quorum sensing signals to mitigate biofilm formation in PA, this study screened 40 essential oils for their potential as quorum sensing inhibitors against PA ATCC9027. Utilizing the agar well diffusion assay, the antibacterial activity of these essential oils was compared with levofloxacin, revealing that 25 out of 40 essential oils exhibited antibacterial activity against PA ATCC9027. The highest antibacterial activity was exhibited by essential oils from Cinnamomum burmannii (Cinnamon Bark Oil), Cananga odorata (Ylang-ylang Oil), and Eucalyptus globulus (Eucalyptus Oil), confirmed by respective MIC values of 0.09765% (v/v), 0.390625% (v/v), and 1.5625% (v/v), and MBC values of 0.09765% (v/v), > 1.5625% (v/v), and > 1.5625% (v/v). Growth curve inhibition assay followed by crystal violet biofilm formation assay revealed that only Ylang-ylang Oil exhibited biofilm formation inhibition at 1/4 MIC concentration. Docking analysis of compounds from these essential oils against quorum sensing enzymes (LasR, PqsR, and QscR) revealed that Ylang-ylang Oil compounds exhibited the highest binding affinity. In conclusion, among the 40 essential oils tested, 25 show potential as antibacterials against PA ATCC9027, with Ylang-ylang Oil standing out as a promising candidate for quorum sensing inhibitor development. The use and development of quorum sensing inhibitors from Ylang-ylang Oil compounds are expected to reduce the burden of antibiotic resistance, especially in Pseudomonas aeruginosa