Zebrafish as Versatile Model for Assessing Animal Venoms and Toxins: Current Applications and Future Prospects

Animal venoms and toxins hold promise as sources of novel drug candidates, therapeutic agents, and biomolecules. To fully harness their potential, it is crucial to develop reliable testing methods that provide a comprehensive understanding of their effects and mechanisms of action. However, traditional rodent assays encounter difficulties in mimicking venom-induced effects in human due to the impractical venom dosage levels. The search for reliable testing methods has led to the emergence of zebrafish (Danio rerio) as a versatile model organism for evaluating animal venoms and toxins. Zebrafish possess genetic similarities to humans, rapid development, transparency, and amenability to high-throughput assays, making it ideal for assessing the effects of animal venoms and toxins. This review highlights unique attributes of zebrafish and explores their applications in studying venom- and toxin-induced effects from various species, including snakes, jellyfish, cuttlefish, anemones, spiders, and cone snails. Through zebrafish-based research, intricate physiological responses, developmental alterations, and potential therapeutic interventions induced by venoms are revealed. Novel techniques such as CRISPR/Cas9 gene editing, optogenetics, and high-throughput screening hold great promise for advancing venom research. As zebrafish-based insights converge with findings from other models, the comprehensive understanding of venom-induced effects continues to expand, guiding the development of targeted interventions and promoting both scientific knowledge and practical applications.

Prediction of the interaction between Calloselasma rhodostoma venom-derived peptides and cancer-associated hub proteins: A computational study

The use of peptide drugs to treat cancer is gaining popularity because of their efficacy, fewer side effects, and several advantages over other properties. Identifying the peptides that interact with cancer proteins is crucial in drug discovery. Several approaches related to predicting peptide-protein interactions have been conducted. However, problems arise due to the high costs of resources and time and the smaller number of studies. This study predicts peptide-protein interactions using Random Forest, XGBoost, and SAE-DNN. Feature extraction is also performed on proteins and peptides using intrinsic disorder, amino acid sequences, physicochemical properties, position-specific assessment matrices, amino acid composition, and dipeptide composition. Results show that all algorithms perform equally well in predicting interactions between peptides derived from venoms and target proteins associated with cancer. However, XGBoost produces the best results with accuracy, precision, and area under the receiver operating characteristic curve of 0.859, 0.663, and 0.697, respectively. The enrichment analysis revealed that peptides from the Calloselasma rhodostoma venom targeted several proteins (ESR1, GOPC, and BRD4) related to cancer.

Seed Halopriming: A Promising Strategy to Induce Salt Tolerance in Indonesian Pigmented Rice

Unfavorable environmental conditions and climate change impose stress on plants, causing yield losses worldwide. The Indonesian pigmented rice (Oryza sativa L.) cultivars Cempo Ireng Pendek (black rice) and Merah Kalimantan Selatan (red rice) are becoming popular functional foods due to their high anthocyanin contents and have great potential for widespread cultivation. However, their ability to grow on marginal, high-salinity lands is limited. In this study, we investigated whether seed halopriming enhances salt tolerance in the two pigmented rice cultivars. The non-pigmented cultivars IR64, a salt-stress-sensitive cultivar, and INPARI 35, a salt tolerant, were used as control. We pre-treated seeds with a halopriming solution before germination and then exposed the plants to a salt stress of 150 mM NaCl at 21 days after germination using a hydroponic system in a greenhouse. Halopriming was able to mitigate the negative effects of salinity on plant growth, including suppressing reactive oxygen species accumulation, increasing the membrane stability index (up to two-fold), and maintaining photosynthetic pigment contents. Halopriming had different effects on the accumulation of proline, in different rice varieties: the proline content increased in IR64 and Cempo Ireng Pendek but decreased in INPARI 35 and Merah Kalimantan Selatan. Halopriming also had disparate effects in the expression of stress-related genes: OsMYB91 expression was positively correlated with salt treatment, whereas OsWRKY42 and OsWRKY70 expression was negatively correlated with this treatment. These findings highlighted the potential benefits of halopriming in salt-affected agro-ecosystems.

Current Status and Complexity of Three Begomovirus Species in Pepper Plants in Lowlands and Highlands in Java Island, Indonesia

Three primary species from the Begomovirus genus, Pepper yellow leaf curl Indonesia virus (PepYLCIV), Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), and Tomato leaf curl New Delhi virus (ToLCNDV), are suspected of spreading throughout pepper production centers, and plants are infected by a single species or a combination of two or three species. This study was conducted to provide complete information about the symptoms, incidence and severity, whitefly biotypes, as well as the dominance status of the three Begomovirus species in pepper-producing areas in Java. A DNA analysis was carried out on leaf samples to identify Begomovirus species and biotypes of B. tabaci collected from 18 areas (16 districts) in lowlands (<400 m asl) and highlands (>700 m asl). The DNA analysis showed that B. tabaci biotype B was the most commonly detected in all locations compared to the A, AN, and Q biotypes. The incidence of begomovirus infection was at a high level, 93% and 88.78% in the lowlands and highlands, respectively. However, the severity of begomovirus infection was significantly higher in the lowlands (54.50%) than in the highlands (38.11%). A single infection of PepYLCIV was most dominant in all locations sampled and caused severe infection, followed by a mixed infection with TYLCKaV. Therefore, the current status of begomovirus infection, especially PepYLCIV, can provide advice to farmers using more tolerant and resistant varieties as well as a breeding strategy for resistant pepper varieties.

RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

BACKGROUND

Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown.

RESULTS

In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50% were up-regulated while the other half were down-regulated. Notably, approximately 37.5% of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways.

CONCLUSIONS

Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice.

Antioxidant and Anticancer Activity of Dillenia serrata Thunb Ethanol Extract Against MCF-7 Breast Cancer Cell Line

Women’s breast cancer incidence rate in Indonesia ranks number one with 12 per 100,000 cases, with luminal A as the dominant subtype. Currently, chemotherapeutic agents have limitations that lead to inefficiencies in therapy, therefore it is necessary to develop more effective and efficient chemopreventive agents. Plant secondary metabolites can provide pharmacological effects that can be used as chemoprevention agents. Secondary metabolites of D. serrata may have pharmacological effects as antioxidants and cytotoxic. This study aims to determine the antioxidant properties and cytotoxic activity of D. serrata ethanolic extract on the MCF-7 breast cancer cell line. The leaves of D. serrata were macerated, while the bark and root samples were refluxed with 96% ethanol as solvent. All extracts were evaporated with a rotary evaporator. Qualitative evaluation of the phytochemical content of leaf ethanolic extract, bark ethanolic extract, and root ethanolic extract was done using the standard tube test method. The antioxidant assay was carried out using the DPPH. The cytotoxic activity was determined in vitro using an MTT assay against the MCF-7 cell line with a series of concentrations from 12.5–400 μg/mL. Doxorubicin was the positive control treated at a 3.125–100 μg/mL concentration. The antioxidant activity showed that leaf extract had the highest antioxidant activity, followed by root and bark extract, with IC50 values of 95.66, 270.5, and 335.96 ppm, respectively. Leaf ethanolic extract and root ethanolic extract’s cytotoxic ability is considered moderate cytotoxic with IC50 values of 493.17 and 229.82 μg/mL, respectively. Amongst the ethanolic extract from the leaf, bark, and root of D. serrata, the leaf ethanolic extract has the best anti-oxidant activity and the bark ethanolic extract was the most cytotoxic one against MCF-7 cells.Keywords: Antioxidant, Cytotoxic, Dillenia serrata, MCF-7.

A Meta-Analysis of Latex Physiology Studies Reveals Limited Adoption and Difficulties to Interpret Some Latex Diagnosis Parameters in Hevea brasiliensis

Latex diagnosis is widely adopted in natural rubber-producing countries to optimize the natural rubber production through a physiological-based latex-harvesting system management. This study is the first bibliographical searching and meta-analysis on the variation of latex physiological parameters i.e. sucrose, inorganic phosphorus, thiols, and total solid content. The study used information extracted from 158 scientific papers. Descriptive statistics, agglomerative hierarchical clustering, and principal component analysis were performed to characterize applications of latex diagnosis, how often parameters are used and interpreted as well as the variation of its parameter values. From 158 papers, latex diagnosis parameters were used in 114 agronomy, 22 in physiology, and 22 in breeding papers. The agglomerative hierarchical clustering analysis indicated that sucrose and inorganic phosphorus contents were clustered together and total solid and thiols contents were located in another cluster. The average values of the total solid content, sucrose, inorganic phosphorus and thiols were 43.9%, 9.4 mM, 16.5 mM, and 0.52 mM, respectively. The percentage of interpretation is 63.3% for sucrose, 54.4% for inorganic phosphorus, 47.5% for thiols, and 41.1% for the total solid content. The low interpretation of thiols and total solid contents question their relevance in latex diagnosis. The low adoption of latex diagnosis in breeding could hinder the selection of activities leads to a limitation of selection for long-term high yielding and stress-adapted clones.

Seed Halopriming Improves Salinity Tolerance of Some Rice Cultivars During Seedling Stage

BACKGROUND

Saline land in coastal areas has great potential for crop cultivation. Improving salt tolerance in rice is a key to expanding the available area for its growth and thus improving global food security. Seed priming with salt (halopriming) can enhance plant growth and decrease saline intolerance under salt stress conditions during the subsequent seedling stage. However, there is little known about rice defense mechanisms against salinity at seedling stages after seed halopriming treatment. This study focused on the effect of seed halopriming treatment on salinity tolerance in a susceptible cultivar, IR 64, a resistant cultivar, Pokkali, and two pigmented rice cultivars, Merah Kalimantan Selatan (Merah Kalsel) and Cempo Ireng Pendek (CI Pendek). We grew these cultivars in hydroponic culture, with and without halopriming at the seed stage, under either non-salt or salt stress conditions during the seedling stage.

RESULTS

The SES scoring assessment showed that the level of salinity tolerance in susceptible cultivar, IR 64, and moderate cultivar, Merah Kalsel, improved after seed halopriming treatment. Furthermore, seed halopriming improved the growth performance of IR 64 and Merah Kalsel rice seedlings. Quantitative PCR revealed that seed halopriming induced expression of the OsNHX1 and OsHKT1 genes in susceptible rice cultivar, IR 64 and Merah Kalsel thereby increasing the level of resistance to salinity. The expression levels of OsSOS1 and OsHKT1 genes in resistant cultivar, Pokkali, also increased but there was no affect on the level of salinity tolerance. On the contrary, seed halopriming decreased the expression level of OsSOS1 genes in pigmented rice cultivar, CI Pendek, but did not affect the level of salinity tolerance. The transporter gene expression induction significantly improved salinity tolerance in salinity-susceptible rice, IR 64, and moderately tolerant rice cultivar, Merah Kalsel. Induction of expression of the OsNHX1 and OsHKT1 genes in susceptible rice, IR 64, after halopriming seed treatment balances the osmotic pressure and prevents the accumulation of toxic concentrations of Na⁺, resulting in tolerance to salinity stress.

CONCLUSION

These results suggest that seed halopriming can improve salinity tolerance of salinity-susceptible and moderately tolerant rice cultivars.

Analysis of reduced and oxidized antioxidants in Hevea brasiliensis latex reveals new insights into the regulation of antioxidants in response to harvesting stress and tapping panel dryness

Latex diagnosis (LD) is applied to optimize the natural rubber production and prevent tapping panel dryness (TPD), a physiological syndrome affecting latex production in Hevea brasiliensis. The reduced thiol content (RSH) is one of the biochemical parameters associated with the risk of TPD. However, RSH is difficult to interpret because of the influence of the environment. In order to better understand the regulation of antioxidants and to better interpret RSH, a key parameter of LD, this study analysed in latex both oxidised and reduced forms of ascorbic acid (AsA) and glutathione, and their cofactors as well as other latex diagnosis parameters in response to harvesting stress (tapping and ethephon stimulation) and TPD occurrence. The content of antioxidants in latex had a high variability among five rubber clones. The concentration in AsA was about ten times higher than GSH in laticifer, GSH accounting for about 50% of RSH. For short-term harvesting stress, RSH increased with tapping frequency and ethephon stimulation. TPD is associated with high latex viscosity and bursting of lysosomal particles called lutoids, as well as for several rubber clones with lower RSH and GSH contents. These results suggest that a high level of RSH shows the capacity of laticifer metabolism to cope with harvesting stress, while a drop in RSH is the sign of long stress related to lower metabolic activity and TPD occurrence. RSH remains an essential physiological parameter to prevent TPD when associated with reference data under low and high harvesting stress. This study paves the way to understand the role of AsA and GSH, and carry out genetic studies of antioxidants.

Identification and characterization of drought-tolerant local pigmented rice from Indonesia

Water is essential to support life. Because limited water availability may affect their life cycles, plants have developed multiple responses to drought stress. Plant physiological and metabolic changes during drought may reflect changes that occur at the level of gene expression. In this study, we investigated the variation in drought-mitigating strategies employed by pigmented rice (Oryza sativa) varieties and the genes involved in their possible drought tolerance. We screened 21 local pigmented rice cultivars from Indonesia for increased drought tolerance using the fraction transpirable soil water method to exert precise control of the drought stress imposed on plants. We then determined the expression of OsDREB1A, OsNAC6, OsNHX1, OsCuZnSOD2, OsOSCAT2, and OsCAT3 in plants grown under well-watered conditions and under moderate or severe drought stress. Among the pigmented rice cultivars, Merah Pari Eja had the greatest drought tolerance, while the red rice Inpari 24 had the highest mortality rate (60%). We also included the white rice cultivar Putih Payo, which is fully sensitive to drought (with 100% mortality under the conditions used) as a negative control. Gene expression profiling revealed a general upregulation of drought-related genes in Merah Pari Eja and a downregulation of such genes in the other two cultivars. Measurements of antioxidant enzyme activity, leaf damage, free radicals, chlorophyll, and anthocyanin contents provided further evidence that Merah Pari Eja is more drought tolerant than the other two cultivars. We conclude that OsDREB1A, OsNAC6, OsNHX1, OsCuZnSOD2, OsOSCAT2 and OsCAT3 expression patterns can reveal plants that have increased drought tolerance.

Metabolite profile of two Allium cepa L. aggregatum group cultivars by Nuclear Magnetic Resonance

Abstract. Basundari FRA, Sulistyaningsih E, Murti RH, Nuringtyas TR. 2021. Metabolite profile of two Allium cepa L. aggregatum group cultivars by Nuclear Magnetic Resonance. Biodiversitas 22: 3127-3135. Shallot, an Allium species with high economic value, is widely cultivated in Indonesia. The species includes numerous cultivars with unique characteristics, such as harvesting time, yield, taste, odor, and bulb color. Tuk Tuk and Trisula, the cultivars used in this experiment, have different bulb colors. Tuk Tuk’s bulb color is light red, while that of Trisula is dark red. This color difference may be attributed to variations in the metabolite contents of the shallot bulbs. The present experiment aimed to reveal differences in the metabolite contents of the two shallot cultivars by using Nuclear Magnetic Resonance (NMR) and then determine the specific metabolites contributing to these differences. Bulbs of Tuk Tuk and Trisula were planted in the field under the same conditions and then collected. The bulb samples were powdered, freeze-dried, and subjected to a two-phase extraction method with CDCl3 and D2O as solvents to separate the nonpolar metabolites from polar ones. The extracts were analyzed by 1H-NMR, and the spectra collected were analyzed using MNOVA software and Metaboanalyst.ca. A total of 23 metabolites were successfully identified and characterized in this experiment. The contents of eight of these metabolites, namely, sucrose, glutamine, citric acid, choline, methiin, propiin, threonine, and formic acid, were significantly higher in Trisula than in Tuk Tuk. These differences may be correlated with variations in the color intensity, pungency, and other traits of the cultivars. The results demonstrate that NMR metabolite profiling could effectively differentiate metabolite profile variations among shallot cultivars.

Metabolomic Response of Tomatoes (Solanum lycopersicum L.) against Bacterial Wilt (Ralstonia solanacearum) Using 1H-NMR Spectroscopy

Ralstonia solanacearum is the pathogen responsible for wilting, yield losses, and death in tomato plants. The use of resistant cultivars has been proven as the most appropriate solution to controlling this pathogen. Therefore, further study of host-plant resistance mechanisms in tomatoes is urgently needed. ¹H-NMR (nuclear magnetic resonance) spectroscopy combined with multivariate data analysis has been used to identify the biochemical compounds that play a crucial role in the defense mechanisms of tomato against bacterial wilt. Eleven metabolites consisting of amino acids, sugars and organic acids were identified and presented at different concentrations in each cultivar. Leucine and valine were determined as distinguishable metabolites of resistant and susceptible cultivars. Permata and Hawaii 7996 as resistant cultivars had a significant decrease of valine after inoculation about 1.5-2 times compared to the susceptible cultivar (GM2). Meanwhile, the resistant cultivars had a higher level of leucine, about 1.3-1.5 times compared to the susceptible ones. Synthesis of leucine and valine are linked as a member of the pyruvate family. Therefore, the decrease in valine may be related to the higher need for leucine to form the leucine-rich receptor, which plays a role in the plant's immune system against the bacterial wilt.

Metabolomics Approach for the Analysis of Resistance of Four Tomato Genotypes (Solanum Lycopersicum L.) to Root-Knot Nematodes (Meloidogyne Incognita)

Metabolomics allows the identification of biochemical markers that have important roles in plant resistance to pests and diseases by which breeders can select plants based on differences in these compounds. This study examines the range of compounds associated with plant defense against nematodes. Resistant tomato genotypes, GM2 and F1 (GM2 × Hawai 7996), and susceptible genotypes, Gondol Putih and Gondol Hijau, were used in this study. Peroxidase activity was measured colorimetrically using a spectrophotometer. ¹H-NMR (nuclear magnetic resonance) spectroscopy combined with orthogonal projections to latent structures discriminant analysis was used to analyze the metabolites involved in the tomato-nematode interactions. Identified signals were semi-quantitatively calculated by scaling the intensity of the ¹H-NMR to the signals of an internal standard (trimethyl silyl-3-propionic acid) at 0.00 ppm. Resistant plants showed a higher peroxidase activity than susceptible plants. Chemical compounds that differentiated between susceptible and resistant plants were glucose and caffeic acid. Resistant tomatoes were observed to have seven times higher level of glucose than susceptible plants. Glucose is the primary metabolite that acts in the signaling pathways in plant defense mechanisms. Caffeic acid is one of the phenolic compounds alleged to have a negative effect on the nematode.

Investigation of the chemomarkers correlated with flower colour in different organs of Catharanthus roseus using NMR-based metabolomics

INTRODUCTION

Flower colour is a complex phenomenon that involves a wide range of secondary metabolites of flowers, for example phenolics and carotenoids as well as co-pigments. Biosynthesis of these metabolites, though, occurs through complicated pathways in many other plant organs. The analysis of the metabolic profile of leaves, stems and roots, for example, therefore may allow the identification of chemomarkers related to the final expression of flower colour.

OBJECTIVE

To investigate the metabolic profile of leaves, stems, roots and flowers of Catharanthus roseus and the possible correlation with four flower colours (orange, pink, purple and red).

METHODS

(1) H-NMR and multivariate data analysis were used to characterise the metabolites in the organs.

RESULTS

The results showed that flower colour is characterised by a special pattern of metabolites such as anthocyanins, flavonoids, organic acids and sugars. The leaves, stems and roots also exhibit differences in their metabolic profiles according to the flower colour. Plants with orange flowers featured a relatively high level of kaempferol analogues in all organs except roots. Red-flowered plants showed a high level of malic acid, fumaric acid and asparagine in both flowers and leaves, and purple and pink flowering plants exhibited high levels of sucrose, glucose and 2,3-dihydroxy benzoic acid. High concentrations of quercetin analogues were detected in flowers and leaves of purple-flowered plants.

CONCLUSIONS

There is a correlation between the metabolites specifically associated to the expression of different flower colours and the metabolite profile of other plant organs and it is therefore possible to predict the flower colours by detecting specific metabolites in leaves, stems or roots. This may have interesting application in the plant breeding industry.