HAYATI Journal of Biosciences
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Assessing Climate Factors and Cyanobacterial Abundance on Microcystins Prediction Using Artificial Neural Network: A Case Study in Malaysia’s Drinking Water Reservoir
No full textToxic cyanobacterial blooms often lead to contamination with cyanotoxins, particularly microcystins. This study aims to examine microcystins persistence in a selected public water supply system and predict their concentration at various points based on climate factors and cyanobacterial abundance. Using the Enzyme-Linked Immunosorbent Assay (ELISA) method, microcystins concentrations were quantified at various points of the water supply system, including the raw water intake, reservoir, water treatment plant outlet, and distribution system. The highest microcystins concentration was detected at the reservoir with a mean concentration of 2.63 μg/L. An artificial neural network (ANN) model was developed to predict microcystins concentration. Rainfall, temperature, chlorophyll-a, phycocyanin (BGA-PC), and mcyE gene copy numbers were used as inputs, while microcystins concentrations at various water sampling points served as outputs of the multilayer perceptron ANN. Using the Statistical Package for the Social Sciences (SPSS, ver. 29), three networks with scaled conjugate gradient, sigmoid functions, and one hidden layer with 4 to 13 neurons were trained and validated to determine the best configuration that fits the observed data. The result shows a satisfactory prediction at the reservoir (Point 2) with low values of error (root mean square error = 0.065) and high coefficient values (R2 = 0.894) between experimental and predicted values, which are below the maximum value of the actual concentrations. Phycocyanin (BGA-PC) and chlorophyll-a had the most positive effects in predicting microcystins concentrations. These results indicate that ANN modelling can be a reliable tool for predicting microcystins contamination in drinking water reservoir
Engineering of LysR-type Regulator DmlR in Burkholderia ubonensis CP01 to Enhance Its Antifungal Production against Ganoderma boninense
No full textThe utilization of an antifungal substance, occidiofungin and burkholdine, derived from Burkholderia ubonensis CP01 has displayed promising results in the management of basal stem rot caused by Ganoderma boninense. The study aims to further enhance the antifungal production of B. ubonensis CP01 through genetic modification. Through comparative genetic analysis, we identified the dmlR gene in B. ubonensis CP01, which is homologous to the scmR gene, a LysR-type transcriptional regulator (LTTR), in B. thailandensis. Deleting the dmlR gene in CP01 resulted in a complete loss of antifungal synthesis. In contrast, overexpression of this gene led to a substantial increase in antifungal production, as determined by an agar well diffusion assay. These findings suggest that dmlR acts as a positive regulator of antifungal gene expression in B. ubonensis CP01. RP-HPLC analysis revealed that the mutant strain overexpressing the dmlR gene (mutant WB12) produced a higher peak at the 24-25 minute elution time. Previous high-resolution mass spectrometry analysis by our group identified the compound at this peak as six analog compounds with monoisotopic masses similar to those of cyclic lipopeptides, including occidiofungin and burkholdine. The WB12 mutant exhibited approximately 15% higher concentrations of antifungal compounds than the wild type. Additionally, whole genome sequencing confirmed that the introduced dmlR gene had been integrated into the locus on chromosome 2 of B. ubonensis CP01. LTTRs play a pivotal role in regulating the production of antifungal agents in CP01. Furthermore, it highlights the potential for manipulating LTTRs to enhance the desirable characteristics of the Burkholderia genus in regard to the production of secondary metabolites
Isolation, Identification, Antimicrobial Activities, and Application of the Crude Pigmented Extract of Soil Actinobacteria in Handicraft and Painting
No full textA total of 21 actinobacterial strains were isolated from soils in Thailand. The selected strains were applied for pigment extraction before handicraft and painting application. Based on the color tones, 4 actinobacterial strains, namely B3 (yellow), B8 (violet), F4 (brown), and F9 (pink), were selected. Their antimicrobial activities against pathogenic bacteria and molds, including Escherichia coli PSRU-01, Staphylococcus aureus PSRU-01, Colletotrichum sp. NPJM -01, and Fusarium sp. PSRU-01 were tested using the agar well and the poisoned food techniques. Phylogenetic identification was analyzed on the basis of partial 16S rDNA sequence comparison for species delineation. They closed Streptomyces tendae 99.73% (B3), Streptomyces muensis 99.52% (B8), Streptomyces ardesiacus 99.38% (F4), and Streptomyces iakyrus 99.59% (F9). These strains were evaluated for their potential as colorants in handicraft clay and painting colors. Streptomyces pigment may be a naturally produced and eco-friendly alternative for handicraft and painting applications
Bacterial Community in Apis cerana and Heterotrigona itama Honey Using a Metabarcoding Approach
No full textHoney is a healthy, natural product with high nutritional value that is converted from sugar in nectar by bacteria in the honey stomach of the bees. Several beneficial bacteria in honey produce bioactive compounds, such as Lactobacillus in Apis mellifera honey, which synthesizes lactic acid, bacteriocins, and enzymes. Here, we employed the metabarcoding technique using the 16S rRNA gene to identify the bacterial community in honey from A. cerana and Heterotrigona itama collected in Sukabumi Regency, West Java, Indonesia. Genomic DNA from both honey samples was isolated using the ZymoBIOMICSTM DNA miniprep kit before sequencing with the Oxford Nanopore Technologies (ONT) platform. Our studies showed that the most dominant bacteria in the honey of A. cerana and H. itama were Paenibacillus glucanolyticus and Limosilactobacillus, respectively. In both types of honey, Gram-positive and Gram-negative bacteria were also detected, as well as lactic acid bacteria, including Acetilactobacillus jinshanensis and Limosilactobacillus. We also found Actinobacteria in A. cerana and H. itama honey. This genomic data showed that A. cerana honey has a higher bacterial diversity than H. itama. Our finding is the first genomic study of bacterial diversity found in the honey of A. cerana and H. itama that live sympatrically in a bee farm
Phytochemistry Profile and Antioxidant Activity of Dumortiera hirsuta (Sw.) Nees from Gumitir, East Java
No full textDumortiera hirsuta, a thalloid liverwort, predominantly grows on the ground floor of coffee plantations in Gumitir, Jember District, East Java, and is known for its rich phytochemical content. This study aimed to comprehensively profile the volatile and non-volatile compounds present in the methanol extract of D. hirsuta and evaluate its antioxidant activity. The thallus was macerated using 96% methanol (1:10 ratio), followed by analysis using Gas Chromatography–Mass Spectrometry (GC–MS) and Liquid Chromatography–Mass Spectrometry Quadrupole Time-of-Flight (LC–MS QTOF). GC–MS identified 37 volatile compounds, with terpenes (29%), phenols (21%), and fatty acids (13%) as dominant classes. Several potent antioxidant sesquiterpenoids, including caryophyllene, guaiene, and aromadendrene derivatives, were notably abundant, along with unique compounds such as phytol, benzoic acid, pyrocatechol, and furanones. LC–MS analysis detected 15 non-volatile secondary metabolites, predominantly flavonoids (e.g., kaempferol-3-O-β-D-glucuronide, luteolin, leucocyanidin), phenolics (sesamol, euparin), and terpenoids (brefeldin A, E-p-coumaric acid), of which nine are well-documented for their antioxidant properties. These compounds were identified with high accuracy (mass error ±4 ppm) across positive and negative ion modes. Antioxidant potential was confirmed through the DPPH radical scavenging assay, which yielded a moderate IC₅₀ value of 101.13 ppm and a strong dose-response correlation (R² = 0.9526). The favourable microclimatic conditions of Mount Gumitir likely contributed to the phytochemical richness observed. Collectively, these findings highlight D. hirsuta as a chemically diverse bryophyte with promising antioxidant constituents, supporting its potential application in pharmacological development and natural antioxidant sourcing
Morphological and Genetic Variation of Filopaludina javanica (von dem Busch, 1844) (Gastropoda: Viviparidae) from Madura Island, Indonesia
No full textFilopaludina javanica (von dem Busch, 1844) is a freshwater gastropod species in the Viviparidae family. Filopaludina javanica is widely distributed in freshwater waters in Java (including Madura), Sulawesi, Sumatra, Borneo, Papua, Thailand, and Vietnam. The morphological, morphometric, and molecular characterization studies of F. javanica based on the COI gene originating from Madura Island are still quite limited. Therefore, this study aims to determine the morphological variations, morphometry, and molecular characters of F. javanica in Bangkalan, Madura. The samples used are the Taxonomy Laboratory collection from Madura Island, followed by morphological observations, morphometry, and analysis of DNA: isolation, amplification, electrophoresis, and COI gene sequencing. Morphological and morphometric variations in F. javanica from Madura Island showed seven types of morphological variations. Principal Component Analysis (PCA) scatterplot results showed morphometric clustering of F. javanica based on morphological type. Identification of F. javanica using BLAST and comparison with the GenBank database revealed five nucleotide base variations, with an overall genetic distance of 0.031. Therefore, the phylogenetic tree shows that F. javanica from Madura Island belongs to the same clade as F. javanica from Sarawak, West Java, and North Kalimantan
Genome-wide Analysis of CONSTANS-like (CqCOL) Transcription Factors in Quinoa (Chenopodium quinoa): Structural Diversity, Phylogeny, and Stress-Responsive Expression
Full text linkQuinoa (Chenopodium quinoa) is an ancient grain renowned for its remarkable nutritional value and remarkable adaptability to diverse environmental conditions, making it a valuable crop for enhancing food security. Understanding the molecular mechanisms triggering its development and stress responses is crucial for crop improvement. This study conducted a comprehensive analysis of the CONSTANS-like (CqCOL) transcription factors in quinoa, which play a pivotal role in photoperiodic flowering regulation. We identified and characterized 20 CqCOL genes, analyzing their physicochemical properties, phylogenetic relationships, gene structures, and promoter regions. Our findings revealed significant diversity among the CqCOL proteins and suggested potential functional specialization within the family. Promoter analysis uncovered various stress-responsive and phytohormone-responsive cis-regulatory elements, revealing that CqCOL genes may be associated with stress adaptation and hormonal signaling pathways. Transcriptomic analyses under different conditions supported these insights, highlighting the importance of CqCOL genes in quinoa\u27s developmental processes and stress responses. Specifically, most CqCOL genes exhibited stable expression under heat stress, except CqCOL02 and CqCOL12, which were induced in roots by 1.85- and 1.91-fold, respectively. Under normal conditions, CqCOL01, CqCOL11, and CqCOL18 showed organ-specific expression, particularly in flowers and leaves, with no expression detected in roots. This study enhances our understanding of the CqCOL transcription factor family. It provides a foundation for future functional studies and breeding strategies aimed at improving stress tolerance and optimizing flowering time in quinoa
Tannase Activity Optimization and Antibiotic Resistance Profiling of Bacteria Isolated from Goat Feces and Ruminal Fluid
Full text linkTannase is a vital enzyme produced by microorganisms in the rumen and gastrointestinal tracts of animals, capable of converting tannins—a common anti-nutritional factor in feeds. This study optimized physicochemical conditions of pH, temperature, substrate concentration, and incubation time for evaluating crude tannase activity in tannin-degrading bacteria (TDB) isolated from ruminal fluid (TDB17: Lysinibacillus macroides (KR780381), TDB18: Acinetobacter nosocomialis [MH084921], TDB23: Acinetobacter nosocomialis [MT540255]), and goat feces (TDB24: Acinetobacter nosocomialis [MT540255]). Among these, TDB23: A. nosocomialis (MT540255) demonstrated the highest tannase activity, reaching 96.83 U/ml under optimized conditions. Interestingly, TDB17: L. macroides (KR780381) and TDB24: A. nosocomialis (MT540255) exhibited thermostable tannase across a temperature between 20°C and 80°C, with sustained activity in the range of 60.15-50.34 U/ml and 29.93-28.98 U/ml, respectively. Additionally, the antibiotic resistance profile of these TDB and the synergistic effects of its crude tannase were evaluated using a disc diffusion assay. All TDBs were susceptible to meropenem, tigecycline, gentamicin, streptomycin, and chloramphenicol but resistant to penicillin G, cephalothin, cefoxitin, and vancomycin. Notably, A. nosocomialis (TDB18, TDB23, and TDB24) demonstrated sensitivity to sulfamethoxazole, while L. macroides (TDB17) exhibited resistance. Moreover, the crude tannase synergistically enhanced the antibacterial activity of antibiotics (p<0.05) against both Gram-positive and Gram-negative bacteria
Effectiveness of Biolarvicides of Imperata cylindrica, Saccharum spotaneum and Andropogon aciculatus on Aedes aegypti larval Mortality and Egg-laying Ability in Adults
Full text linkVector-borne disease such as Dengue Hemorrghagic (DHF), transmitted by Aedes aegypti and Aedes albopictus, remain a significant public health concern in Indonesia. Controlling these disease often involves insectides; however, the negative impact of chemical insecticides have prompted interest in organic alternatives derived from plants. Certain weeds, including cogon grass (Imperata cylindrica), wild sugarcane (Saccharum spontaneoum), and needle grass (Andropogon aciculatus), have shown potential as botanical insecticides. Research findings showed that weed root extracts significantly affect larval mortality rate of Ae. Aegypti. At 1000 ppm, larval mortality was significantly higher compared to 100 ppm and the control, while treatments of 1 ppm and 10 ppm showed similar results to the control. Probit analysis revealed that I. cylindrica root extract achieved an LC50 of 974.99 ppm within 24 hours, indicating it could kill 50% of Ae. Aegypti larvae. Within 48 hours, the LC50 dropped to 889.20 ppm. Toxicity tests further revealed significant differences in Ae. Aegypti egg-laying abilities when treated with extracts. Analysis of variance yielded p-values of 0.000 for egg hatching within 72 and 96 hours, highlighting significant differences across samples. These findings suggest the extracts influence mosquito reproduction, warranting further studies to assess the quality of egg hatched from larvae exposed to these treatments. The potential of botanical insecticides derived from weeds represents a promising step toward sustainable mosquito control in the fight against vector-borne diseases
Molecular Evidence Points to Strong Resemblance in the Parasitoid Species of Rice and Cogongrass Gall Midges, Platygaster spp. (Hymenoptera: Platygasteridae)
Full text linkThe rice gall midge, Orseolia oryzae, and the cogongrass gall midge, O. javanica, cause gall formation on rice and cogongrass (alang-alang) (Imperata cylindrica). Two different species parasitize these two gall midges but closely related platygasterids, Platygaster oryzae on the rice gall midge and P. orseoliae on the cogongrass gall midge. Both the gall midges and their parasitoids are often found in the adjacent area, raising a question about the relationship between the two gall midges and their parasitoids. This research aims to study the molecular identity of the rice and cogongrass gall midges, along with their platygasterid parasitoids, based on partial sequences of the mtCOI gene. Samples were collected from rice and cogongrass in the adjacent area in Cianjur, West Java Province, and a rice field with no cogongrass in Bogor, West Java Province. Successful DNA amplification was achieved using universal primers for mtCOI. Nucleotide sequencing analysis revealed that the rice gall from Bogor and Cianjur shared 100% similarity and 93.2-99.3% similarity with the rice gall from other countries. Notably, the parasitoids P. oryzae collected from rice in Bogor and Cianjur shared 97.2% similarity with P. orseoliae collected from cogongrass in Cianjur. These findings suggest that the platygaster parasitoids associated with the rice gall and the cogongrass gall midges are identical, serving as potential natural enemies for both pests. This study represents the first molecular identification report of rice and cogongrass gall midges and their platygasterid parasitoids from Java Island, Indonesia