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Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.

In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.

Jamaican cherry (Muntinga calabura Linn.) is tropical tree that is known to produce edible fruit with high nutritional and antioxidant properties. However, its use as functional food is still limited. Previous studies suggest that fermentation with probiotic bacteria could enhance the functional properties of non-dairy products, such as juices. In this study, we analyze the metabolite composition and activity of Jamaican cherry juice following fermentation with Lactobacillus plantarum FNCC 0027 in various substrate compositions. The metabolite profile after fermentation was analyzed using UPLC-HRMS-MS and several bioactive compounds were detected in the substrate following fermentation, including gallic acid, dihydrokaempferol, and 5,7-dihydroxyflavone. We also found that total phenolic content, antioxidant activities, and inhibition of diabetic-related enzymes were enhanced after fermentation using L. plantarum. The significance of its elevation depends on the substrate composition. Overall, our findings suggest that fermentation with L. plantarum FNCC 0027 can improve the functional activities of Jamaican cherry juice.

Background Cymbopogon is a member of the family Poaceae and has been explored for its phytochemicals and bioactivities. Although the antimicrobial activities of Cymbopogon spp . extracts have been extensively studied, comprehensive analyses are required to identify promising compounds for the treatment of antimicrobial resistance. Therefore, this study investigated the antioxidant and antimicrobial properties of Cymbopogon spp. ethanolic extracts in every single organ. Methods Ethanolic extracts were obtained from three Indonesian commercial species of Cymbopogon spp. , namely Cymbopogon citratus (L.) Rendle , Cymbopogon nardus (DC.) Spatf., and Cymbopogon winterianus Jowitt. The leaf, stem, and root extracts were evaluated via metabolite profiling using gas chromatography-mass spectrometry (GC–MS). In silico and in vitro analyses were used to evaluate the antioxidant and antimicrobial properties of the Cymbopogon spp. ethanolic extracts. In addition, bioactivity was measured using cytotoxicity assays. Antioxidant assays were performed using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2-azino-bis [3-ethylbenzothiazoline-6-sulfonic acid (ABTS) to determine toxicity to Huh7it-1 cells using a tetrazolium bromide (MTT) assay. Finally, the antimicrobial activity of these extracts was evaluated against Candida albicans , Bacillus subtilis , Staphylococcus aureus , and Escherichia coli using a well diffusion assay. Results GC–MS analysis revealed 53 metabolites. Of these, 2,5-bis(1,1-dimethylethyl)- phenol (27.87%), alpha-cadinol (26.76%), and 1,2-dimethoxy-4-(1-propenyl)-benzene (20.56%) were the predominant compounds. C. winterianus and C. nardus leaves exhibited the highest antioxidant activity against DPPH and ABTS, respectively. Contrastingly, the MTT assay showed low cytotoxicity. C. nardus leaf extract exhibited the highest antimicrobial activity against E. coli and S. aureus, whereas C. winterianus stem extract showed the highest activity against B. substilis . Furthermore, computational pathway analysis predicted that antimicrobial activity mechanisms were related to antioxidant activity. Conclusions These findings demonstrate that the leaves had strong antioxidant activity, whereas both the leaves and stems showed great antimicrobial activity. Furthermore, all Cymbopogon spp. ethanolic extracts showed low toxicity. These findings provide a foundation for future studies that assess the clinical safety of Cymbopogon spp. as novel drug candidates.

Violacein and its biosynthesis by-product deoxyviolacein are valuable natural pigments with different biological activities. Various efforts have been made to enhance violacein and deoxyviolacein production in microbes. However, the effect of different culture media, agitation, and fungal elicitation on biosynthesis in Janthinobacterium has not been evaluated. In this study, the effect of eight different culture media, agitation, and fungal elicitation by Agaricus bisporus on violacein and deoxviolacein production in Janthinobacterium agaricidamnosum DSM 9628 and Janthinobacterium lividum DSM 1552 were examined. The results showed that violacein and deoxviolacein are produced at high-levels when Janthinobacterium is cultivated in minimal media such as Davis minimal broth with glycerol (DMBgly), shipworm basal medium (SBM), and MM9 media. A 50-fold increase was observed in violacein production when Janthinobacterium was cultivated in these media compared to cultivation in Luria–Bertani (LB), nutrient broth (NB), and King’s B (KB). Agitation reduces violacein and deoxyviolacein production, while fungal elicitation decreases violacein but increases deoxyviolacein when Janthinobacterium is cultured in KB media, SBM, and modified SBM (MSBM). An antibacterial assay using various pathogenic bacteria showed that violacein and deoxyviolacein extracted from Janthinobacterium are effective against both Gram-positive and Gram-negative pathogens, confirming their functionality as antibacterial agents. The findings suggest that cultivation in minimal media and fungal elicitation might invoke a stress response, enhancing the production of violacein and deoxviolacein in Janthinobacterium.

Antibiotic resistance is a global public health concern that has been exacerbated by the overuse and misuse of antibiotics, leading to the emergence of resistant bacteria. The gut microbiota, often influenced by antibiotic usage, plays a crucial role in overall health. Therefore, this study aimed to investigate the prevalence of antibiotic resistant genes in the gut microbiota of Indonesian coastal and highland populations, as well as to identify vancomycin-resistant bacteria and their resistant genes. Stool samples were collected from 22 individuals residing in Pacet, Mojokerto, and Kenjeran, Surabaya Indonesia in 2022. The read count of antibiotic resistant genes was analyzed in the collected samples, and the bacterium concentration was counted by plating on the antibiotic-containing agar plate. Vancomycin-resistant strains were further isolated, and the presence of vancomycin-resistant genes was detected using a multiplex polymerase chain reaction (PCR). The antibiotic resistant genes for tetracycline, aminoglycosides, macrolides, beta-lactams, and vancomycin were found in high frequency in all stool samples (100%) of the gut microbiota. Meanwhile, those meant for chloramphenicol and sulfonamides were found in 86% and 16% of the samples, respectively. Notably, vancomycin-resistant genes were found in 16 intrinsically resistant Gram-negative bacterial strains. Among the detected vancomycin-resistant genes, was the most prevalent (27.3%), while was the least prevalent (4.5%). The presence of multiple vancomycin resistance genes in intrinsically resistant Gram-negative bacterial strains demonstrated the importance of the gut microbiota as a reservoir and hub for the horizontal transfer of antibiotic resistant genes.

Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.

The objective of our research was to the evaluated biological activities of G. procumbens leaves methanol extract (GLME) for the hepatoprotective against cadmium (Cd) toxicity in mice. Research was performed using twenty five healthy male mice, which were grouped into five treatments: P1 (control), P2 (Cd-100mg/L), P3 (GLME-100mg/L+Cd-100mg/L), P4 (GLME-200mg/L+Cd-100mg/L), P5 (GLME-300mg/L+Cd-100mg/L). The results showed GLME contain phenolic and flavonoids compound by total phenolic content (TPC) and total flavonoid content (TFC) assay, they were strongly correlated with antioxidant activities. In this study, it was also known that Cd exposure increasing malondialdehyde (MDA) level and decreasing of superoxide dismutase (SOD) and catalase (CAT) activities in liver homogenates compared to control significantly. This is in line with a decreased in the number of normal cells and slightly an increased in damage cells in the histological hepatic cells. Administration of GLME can prevent liver cell damage due to Cd treatment by increasing the number of histological normal cells and the activities of SOD and CAT enzyme and reducing the level of MDA in liver homogenates. The best treatment of GLME was 100mg/L.

Approximately 381 million tons of plastic are produced globally every year, and the majority of it ends up as pollutants. In the environment, plastic waste is fragmented into microplastic particles less than 5 mm in size; owing to their small size, durability, and abundance, they can easily be dispersed, incorporated into the food chains, and enter the human body. The extent of microplastic exposure in the human body has become a major concern in many countries, including in Indonesia, the second largest plastic waste contributor in the world. Here, we report the detection of microplastics in human stools collected from a fisherman community in the coastal area of Surabaya, Indonesia. Microplastics were found in more than 50% of samples analyzed with a concentration ranging from 3.33 to 13.99 µg of microplastic per gram of feces (µg/g). HDPE was observed as the most prevalent type of microplastic, with an average concentration of 9.195 µg/g in positive samples. Different types of microplastics were also detected in seafood, staple foods, drinking water, table salts, and toothpaste, which were regularly used and consumed by the study participants. Results from this preliminary study indicate widespread contamination of microplastic in the human body and in consumables associated with the coastal populations of Indonesia.