A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation.

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

Vermicompost Supply Enhances Fragrant-Rice Yield by Improving Soil Fertility and Eukaryotic Microbial Community Composition under Environmental Stress Conditions.

Heavy-metal contamination in agricultural soil, particularly of cadmium (Cd), poses serious threats to soil biodiversity, rice production, and food safety. Soil microbes improve soil fertility by regulating soil organic matter production, plant nutrient accumulation, and pollutant transformation. Addressing the impact of Cd toxicity on soil fungal community composition, soil health, and rice yield is urgently required for sustainable rice production. Vermicompost (VC) is an organic fertilizer that alleviates the toxic effects of Cd on soil microbial biodiversity and functionality and improves crop productivity sustainably. In the present study, we examined the effects of different doses of VC (i.e., 0, 3, and 6 tons ha-1) and levels of Cd stress (i.e., 0 and 25 mg Cd kg-1) on soil biochemical attributes, soil fungal community composition, and fragrant-rice grain yield. The results showed that the Cd toxicity significantly reduced soil fertility, eukaryotic microbial community composition and rice grain yield. However, the VC addition alleviated the Cd toxicity and significantly improved the soil fungal community; additionally, it enhanced the relative abundance of Ascomycota, Chlorophyta, Ciliophora, Basidiomycota, and Glomeromycta in Cd-contaminated soils. Moreover, the VC addition enhanced the soil's chemical attributes, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), and microbial biomass C and N, compared to non-VC treated soil under Cd toxicity conditions. Similarly, the VC application significantly increased rice grain yield and decreased the Cd uptake in rice. One possible explanation for the reduced Cd uptake in plants is that VC amendments influence the soil's biological properties, which ultimately reduces soil Cd bioavailability and subsequently influences the Cd uptake and accumulation in rice plants. RDA analysis determined that the leading fungal species were highly related to soil environmental attributes and microbial biomass C and N production. However, the relative abundance levels of Ascomycota, Basidiomycota, and Glomeromycta were strongly associated with soil environmental variables. Thus, the outcomes of this study reveal that the use of VC in Cd-contaminated soils could be useful for sustainable rice production and safe utilization of Cd-polluted soil.

Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system.

Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.

BioCoder: a benchmark for bioinformatics code generation with large language models.

SUMMARY: Pretrained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate LLMs in generating bioinformatics-specific code. BioCoder spans much of the field, covering cross-file dependencies, class declarations, and global variables. It incorporates 1026 Python functions and 1243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling, we show that the overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate various models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT-4. Furthermore, we fine-tuned one model (StarCoder), demonstrating that our training dataset can enhance the performance on our testing benchmark (by >15% in terms of Pass@K under certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (i) Successful models accommodate a long prompt (>2600 tokens) with full context, including functional dependencies. (ii) They contain domain-specific knowledge of bioinformatics, beyond just general coding capability. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on our benchmark (50% versus up to 25%). AVAILABILITY AND IMPLEMENTATION: All datasets, benchmark, Docker images, and scripts required for testing are available at: https://github.com/gersteinlab/biocoder and https://biocoder-benchmark.github.io/.

Multi-walled carbon nanotubes affect yield, antioxidant response, and rhizosphere microbial community of scented rice under combined cadmium-lead (Cd-Pb) stress.

Rice production is threatened by heavy metal stress. The use of multi-walled carbon nanotubes (MWCNTs) in agriculture has been reported in previous studies. We aimed to quantify the impact of MWCNTs on the growth and physiological characteristics of scented rice under cadmium (Cd) and lead (Pb) stresses. Therefore, a pot experiment was conducted, two scented rice varieties Yuxiangyouzhan and Xiangyaxiangzhan were used as materials grown under different concentrations of MWCNTs (0, 100, and 300 mg kg-1 recorded as CK, CNPs100, and CNPs300, respectively). The yield, antioxidant response, and rhizosphere microbial community of scented rice were studied. The results showed that compared with the CK treatment, the CNPs100 and CNPs300 treatments increased leaf dry weight by 17.95%-56.22% at the heading stage, and the H2O2 content in leaves decreased significantly by 36.64%-42.27% at the maturity stage. Under CNPs100 treatment, the grain yield of two scented rice varieties increased significantly by 17.54% and 27.40%, respectively. The MWCNTs regulated the distribution of the Cd and Pb in different plant tissues. The content of Cd (0.11-0.20 mg kg-1) and Pb (0.01-0.04 mg kg-1) in grain were at a safety level (<0.2 mg kg-1). Moreover, MWCNTs increased soil microbial community abundance and altered community composition structure under Cd-Pb stress, which in turn improved agronomic traits and quality of scented rice. Overall, this study suggested that the application of MWCNTs regulates the growth, yield, physiological response, and soil microbial community, the genotypes response effect of scented rice to MWCNTs is needed further studied.

MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations.

MOTIVATION: The current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models' versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain. RESULTS: We present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM's self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for learning, MolLM demonstrates robust molecular representation capabilities across four downstream tasks, including cross-modal molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks. AVAILABILITY AND IMPLEMENTATION: Our code, data, pre-trained model weights, and examples of using our model are all available at https://github.com/gersteinlab/MolLM. In particular, we provide Jupyter Notebooks offering step-by-step guidance on how to use MolLM to extract embeddings for both molecules and text.

Multiomics analysis reveals a substantial decrease in nanoplastics uptake and associated impacts by nano zinc oxide in fragrant rice (Oryza sativa L.).

Nanoplastics (NPs) have emerged as global environmental pollutants with concerning implications for sustainable agriculture. Understanding the underlying mechanisms of NPs toxicity and devising strategies to mitigate their impact is crucial for crop growth and development. Here, we investigated the nanoparticles of zinc oxide (nZnO) to mitigate the adverse effects of 80 nm NPs on fragrant rice. Our results showed that optimized nZnO (25 mg L-1) concentration rescued root length and structural deficits by improving oxidative stress response, antioxidant defense mechanism and balanced nutrient levels, compared to seedlings subjected only to NPs stress (50 mg L-1). Consequently, microscopy observations, Zeta potential and Fourier transform infrared (FTIR) results revealed that NPs were mainly accumulated on the initiation joints of secondary roots and between cortical cells that blocks the nutrients uptake, while the supplementation of nZnO led to the formation of aggregates with NPs, which effectively impedes the uptake of NPs by the roots of fragrant rice. Transcriptomic analysis identified a total of 3973, 3513 and 3380 differentially expressed genes (DEGs) in response to NPs, nZnO and NPs+nZnO, respectively, compared to the control. Moreover, DEGs were significantly enriched in multiple pathways including biosynthesis of secondary metabolite, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, carotenoid biosynthesis, plant-pathogen interactions, MAPK signaling pathway, starch and sucrose metabolism, and plant hormone signal transduction. These pathways could play a significant role in alleviating NPs toxicity and restoring fragrant rice roots. Furthermore, metabolomic analysis demonstrated that nZnO application restored 2-acetyl-1-pyrroline (2-AP) pathways genes expression, enzymatic activities, and the content of essential precursors related to 2-AP biosynthesis under NPs toxicity, which ultimately led to the restoration of 2-AP content in the leaves. In conclusion, this study shows that optimized nZnO application effectively alleviates NPs toxic effects and restores both root structure and aroma production in fragrant rice leaves. This research offers a sustainable and practical strategy to enhance crop production under NPs toxicity while emphasizing the pivotal role of essential micronutrient nanomaterials in agriculture.

Regulation of 2-Acetyl-1-pyrroline Content in Fragrant Rice under Different Temperatures at the Grain-Filling Stage.

2-Acetyl-1-pyrroline (2-AP) is a key volatile organic compound in fragrant rice aroma. However, the effects of temperature on 2-AP biosynthesis in fragrant rice and its regulation mechanism have been rarely reported. In the present study, three fragrant rice varieties were used as plant materials, and four temperature treatments during the grain-filling stage, i.e., (T1) 22/17 °C, (T2) 27/22 °C, (T3) 32/27 °C, and (T4) 37/32 °C, were adopted. The results showed that grain contents of 2-AP, proline, and γ-aminobutyric acid (GABA) significantly (P < 0.05) increased with decreased temperature, while the lowest and highest 2-AP contents were recorded in the T4 and T1 treatments, respectively. Higher pyrroline-5-carboxylic acid (P5C) content was recorded in low-temperature treatments (T1 and T2) than in high-temperature treatments (T3 and T4). The transcript levels of genes BADH2, PRODH, and OAT significantly (P < 0.05) decreased with decreased temperature. Lower transcript levels of genes P5CR, P5CS2, DAO2, DAO4, and DAO5 were recorded in low-temperature treatments (T1 and T2) than in high-temperature treatments (T3 and T4). In conclusion, low temperature increased 2-AP content and high temperature decreased 2-AP content in fragrant rice. We deduced that temperature regulated 2-AP biosynthesis through the metabolism of proline and GABA.

Ultrasonic seed treatment improved seed germination, growth, and yield of rice by modulating associated physio-biochemical mechanisms.

Ultrasonic seed (US) treatment could alter seed germination mechanism, however, US induced alterations in morph-physiological attributes and yield of fragrant rice were rarely reported. In the present study, the seeds of three fragrant rice cultivars viz., Xiangyaxiangzhan, Meixiangzhan 2, Ruanhuayou 6100 and one non-fragrant rice viz., Wufengyou 615 were exposed to ultrasonic waves at 20-40 kHz for 1.5 min (T) whereas the seeds without exposure were taken as control (CK). Results showed that US treatment caused minor cracks on seed surface while improved seed germination rate (1.79 %-11.09 %) and 3-indoleacetic acid (IAA) (3.36 %-46.91 %). Furthermore, peroxidase (POD) activity and methionine sulfoxide reductase activity was increased by 29.15 %-74.13 % and 11.26 %-20.87 %, respectively; however, methionine sulfoxide reductase related protein repairing gene MSRA4 was down-regulated by 17.93 % -41.04 % under T, compared to CK. Besides, US treatment also improved soluble protein in flag leaf (0.92 %-40.79 %), photosynthesis (3.37 %-16.46 %), biomass (5.17 %-31.87 %), as well as 2-acetyl-1-pyrroline content (4.77 %-15.48 %) in rice grains. In addition, multivariate analysis showed that the dry weight at the maturity stage were significantly related to the POD, glutathione reductase (GR) activity, IAA, and abscisic acid (ABA) content while germination rate was positively related to the GR activity, ABA content, and yield, but which were negatively related to the IAA and gibberellic acid content.

Effects of paclobutrazol seed priming on seedling quality, photosynthesis, and physiological characteristics of fragrant rice.

BACKGROUND: Paclobutrazol is widely used in the agricultural field. This study investigated the effects of seed priming with different concentrations of paclobutrazol on seedling quality, 2-acetyl-1-pyrroline (2-AP, a key aroma component of fragrant rice) biosynthesis, and related physiological and biochemical indicators in fragrant rice seedlings. RESULTS: The experiment is being conducted at the College of Agriculture, South China Agricultural University. In the experiment, three concentrations of paclobutrazol (Pac 1: 20 mg·L-1; Pac 2: 40 mg·L-1; Pac 3: 80 mg·L-1) were used to initiate the treatment of fragrant rice seeds, while water treatment was used as a control (CK). The results showed that compared with CK, paclobutrazol treatment reduced plant height, increased stem diameter, and increased fresh and dry weight of aromatic rice seedlings. Moreover, paclobutrazol treatment also increased the seedlings' photosynthetic pigment content and net photosynthetic rate. CONCLUSIONS: This study demonstrates that paclobutrazol primarily increases the content of proline by reducing the content of glutamate and down-regulating the expression of P5CS2, thereby promoting the conversion of proline to the aromatic substance 2-AP. Under the appropriate concentration of paclobutrazol (40 mg·L-1~80 mg·L-1), the seedling quality, stress resistance, and aroma of fragrant rice can be improved.

Substation of vermicompost mitigates Cd toxicity, improves rice yields and restores bacterial community in a Cd-contaminated soil in Southern China.

Cadmium (Cd) contamination in agricultural soil is a global concern for soil health and food sustainability because it can cause Cd accumulation in cereal grains. An in-situ stabilizing technology (using organic amendments) has been widely used for Cd remediation in arable lands. Therefore, the current study examined the influence of vermicompost (VC) on soil biochemical traits, bacterial community diversity and composition, Cd uptake and accumulation in rice plants and grain yield in a Cd-contaminated soil during the late growing season in 2022. Different doses of VC (i.e., V1 = 0 t ha-1, V2 = 3 t ha-1 and V3 = 6 t ha-1) and two concentrations of Cd (i.e., Cd1 = 0 and Cd2 = 50 mg Cd Kg-1 were used. We performed high-throughput sequencing of 16S ribosomal RNA gene amplicons to characterize soil bacterial communities. The addition of VC considerably affected the diversity and composition of the soil bacterial community; and increased the relative abundance of phyla Chloroflexi, Proteobacteria, Acidobacteriota, Plantomycetota, Gemmatimonadota, Patescibacteria and Firmicute. In addition, VC application, particularly High VC treatment, exhibited the highest bacterial diversity and richness (i.e., Simpson, Shannon, ACE, and Chao 1 indexes) of all treatments. Similarly, the VC application increased the soil chemical traits, including soil pH, soil organic carbon (SOC), available nitrogen (AN), total nitrogen (TN), total potassium (TK), total phosphorous (TP) and enzyme activities (i.e., acid phosphatase, catalase, urease and invertase) compared to non-VC treated soil under Cd stress. The average increase in SOC, TN, AN, TK and TP were 5.75%, 41.15%, 18.51%, 12.31%, 25.45% and 29.67%, respectively, in the High VC treatment (Pos-Cd + VC3) compared with Cd stressed soil. Redundancy analysis revealed that the leading bacterial phyla were associated with SOC, AN, TN, TP and pH, although the relative abundance of Firmicutes, Proteobacteria, Bacteroidata, and Acidobacteria on a phylum basis and Actinobacteria, Gammaproteobacteria and Myxococcia on a class basis, were highly correlated with soil environmental factors. Moreover, the VC application counteracted the adverse effects of Cd on plants and significantly reduced the Cd uptake and accumulation in rice organs, such as roots, stem + leaves and grain under Cd stress conditions. Similarly, applying VC significantly increased the fragrant rice grain yield and yield traits under Cd toxicity. The correlation analysis showed that the increased soil quantities traits were crucial in obtaining high rice grain yield. Generally, the findings of this research demonstrate that the application of VC in paddy fields could be useful for growers in Southern China by sustainably enhancing soil functionality and crop production.

Impact and mitigation of lead, cadmium and micro/nano plastics in fragrant rice.

Heavy metals (HMs) and micro(nano)plastics (MNPs), represent a significant risk to global food supply as well as a potential risk to humankind. Over 50% of the worldwide population eat rice every day, and rice aroma is a significant qualitative trait that is highly valued by consumers and fetches premium prices in the global market. Despite the huge commercial importance of fragrant rice, limited studies were directed to investigate the influence of HMs and MNPs on yield related traits and 2-Acetyl-1-pyrroline (2-AP) compound, mainly responsible for aroma production in fragrant rice. In this review, we found that the interaction of HMs and MNPs in fragrant rice is complex and accumulation of HMs and MNPs was higher in root as compared to the grains. Nutrients and phytohormones mediated mitigation of HMs and MNPs were most effective sustainable strategies. In addition, monitoring the checkpoints of 2-AP biosynthesis and its interaction with HMs and MNPs is challenging. Finally, we explained the potential challenges that fragrant rice faces considering the continuous rise in environmental pollutants and discussed the future avenues of research to improve fragrant rice's yield and qualitative traits.

Nitric oxide confers cadmium tolerance in fragrant rice by modulating physio-biochemical processes, yield attributes, and grain quality traits.

Cadmium (Cd) stress causes serious disruptions in plant metabolism, physio-biochemical processes, crop yield, and quality characters. Nitric oxide (NO) improves the quality features and nutritional contents of fruit plants. However, how NO confers Cd toxicity in fragrant rice plants, is sparse. Hence, the present study investigated the effects of 50 µM NO donor sodium nitroprusside (SNP) on physio-biochemical processes, plant growth attributes, grain yield, and quality traits of fragrant rice under Cd stress (100 mg kg-1 soil). The results revealed that Cd stress diminished rice plant growth, impaired photosynthetic apparatus and antioxidant defense system, and deteriorated the grain quality traits. However, foliar application of SNP mitigated Cd stress by improving plant growth and gas exchange attributes. Higher electrolyte leakage (EL) was accompanied with elevated levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) under Cd stress; however, exogenous application of SNP reduced them. The activities and relative expression levels of enzymatic antioxidants; superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) and non-enzymatic antioxidants, glutathione (GSH) contents were reduced by Cd stress, while SNP application regulated their activity and transcript abundances. SNP application improved fragrant rice grain yield and 2-acetyl-1-pyrroline content by 57.68 % and 75.54 % respectively, which is concomitant with higher biomass accumulation, photosynthetic efficiency, photosynthetic pigment contents, and an improved antioxidant defense system. Collectively, our results concluded that SNP application regulated the fragrant rice plant physio-biochemical processes, yield traits and grain quality characters under Cd-affected soil.

Optimization of liquid fertilizer management improves grain yield, biomass accumulation, and nutrient uptake of late-season indica fragrant rice.

BACKGROUND: The use of liquid fertilizer is an effective measure to increase rice yield and nitrogen use efficiency. There has been a lack of information regarding the effects on the grain yield, biomass accumulation, and nutrient uptake in late-season indica fragrant rice of split fertilizer application and of nitrogen management in liquid fertilizer application. RESULTS: A 2-year field experiment was carried out during 2019 and 2020 with two fragrant rice cultivars grown under differing fertilizer management treatments. Results showed that the fertilization treatments affected the grain yield, yield components, biomass accumulation, and nutrient accumulation significantly. The mean nitrogen recovery efficiency with liquid fertilizer management was greater than in a control treatment corresponding to a practice commonly used by farmers (H2). The effects of nitrogen metabolism enzymes in the leaves of both rice cultivars were stronger with liquid fertilizer treatments than with H2. Grain yield was positively associated with the effective panicle number, spikelets per panicle, dry matter accumulation, N and K accumulation, and the nitrogen metabolism enzymes. CONCLUSIONS: Optimized liquid fertilizer management increases biomass accumulation, nitrogen utilization efficiency, and nitrogen metabolism. It stabilizes yields and increases the economic benefits of late-season indica fragrant rice. © 2023 Society of Chemical Industry.

Foliar spray of La2O3 nanoparticles regulates the growth, antioxidant parameters, and nitrogen metabolism of fragrant rice seedlings in wet and dry nurseries.

Nanoparticles (NPs) have been widely used in agriculture, and lanthanum oxide nanoparticles (La2O3) NPs can regulate plant growth. La2O3 NPs treatment was hypothesized to affect the accumulation and distribution of substances in rice seedlings under wet and dry nursery conditions. The objective of the present study was to ascertain the effects of La2O3 NPs foliar spray on the morphology and physiology of fragrant rice seedlings under wet and dry nursery conditions. Seedlings of two fragrant rice cultivars, namely 'Xiangyaxiangzhan' and 'Yuxiangyouzhan,' were grown under wet and dry nursery conditions with La2O3 NPs treatments at three concentrations (CK, La2O3 NPs 0 mg L-1; T1, La2O3 NPs 20 mg L-1; and T2, La2O3 NPs 40 mg L-1). The results showed that the seedling-raising method was significantly associated with La2O3 NPs application (P < 0.05), affecting the leaf area of both cultivars. Changes in plant morphological parameters, such as dry weight and root-shoot ratio, were the reasons for the differences in cultivars in response to La2O3 NPs application. Changes were also observed in the plant morphological and physiological parameters of leaf area, specific leaf area, chlorophyll contents, antioxidant properties, and activities of nitrogen metabolism enzymes. The relationship between morphological and physiological processes in fragrant rice was investigated to test the hypothesis. In both wet and dry nursery methods, the T2 concentration of La2O3 NPs was beneficial for rice seedlings and significantly increased their leaf area due to changes in morphological and physiological parameters. Therefore, the results of this study provide a theoretical basis for expanding the research on La2O3 NPs application in rice, as well as relevant references for strengthening rice seedlings in the nursery, which has a positive effect on the grain yield improvement in fragrant rice.

Exogenous TiO2 Nanoparticles Alleviate Cd Toxicity by Reducing Cd Uptake and Regulating Plant Physiological Activity and Antioxidant Defense Systems in Rice (Oryza sativa L.).

Cadmium (Cd) is a potentially hazardous element with significant biological toxicity, negatively affecting plant growth and physio-biochemical metabolism. Thus, it is necessary to examine practical and eco-friendly approaches to reduce Cd toxicity. Titanium dioxide nanoparticles (TiO2-NPs) are growth regulators that help in nutrient uptake and improve plant defense systems against abiotic and biological stress. A pot experiment was performed in the late rice-growing season (July-November) 2022 to explore the role of TiO2-NPs in relieving Cd toxicity on leaf physiological activity, biochemical attributes, and plant antioxidant defense systems of two different fragrant rice cultivars, i.e., Xiangyaxiangzhan (XGZ) and Meixiangzhan-2 (MXZ-2). Both cultivars were cultivated under normal and Cd-stress conditions. Different doses of TiO2-NPs with and without Cd-stress conditions were studied. The treatment combinations were: Cd-, 0 mg/kg CdCl2·2.5 H2O; Cd+, 50 mg/kg CdCl2·2.5 H2O; Cd + NP1, 50 mg/kg Cd + 50 TiO2-NPs mg/L; Cd + NP2, 50 mg/kg Cd + 100 TiO2-NPs mg/L; Cd + NP3, 50 mg/kg Cd + 200 TiO2-NPs mg/L; Cd + NP4, 50 mg/kg Cd + 400 TiO2-NPs mg/L. Our results showed that the Cd stress significantly (p < 0.05) decreased leaf photosynthetic efficiency, stomatal traits, antioxidant enzyme activities, and the expression of their encoding genes and protein content. Moreover, Cd toxicity destabilized plant metabolism owing to greater accretion of hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels at vegetative and reproductive stages. However, TiO2-NPs application improved leaf photosynthetic efficacy, stomatal traits, and protein and antioxidant enzyme activities under Cd toxicity. Application of TiO2-NPs decreased the uptake and accumulation of Cd in plants and levels of H2O2 and MDA, thereby helping to relieve Cd-induced peroxidation damage of leaf membrane lipids by enhancing the activities of different enzymes like ascorbate peroxidase (APX), catalase (CAT), peroxidase (POS), and superoxide dismutase (SOD). Average increases in SOD, APX, CAT, and POS activities of 120.5 and 110.4%, 116.2 and 123.4%, 41.4 and 43.8%, and 36.6 and 34.2% in MXZ-2 and XGZ, respectively, were noted in Cd + NP3 treatment across the growth stages as compared with Cd-stressed plants without NPs. Moreover, the correlation analysis revealed that the leaf net photosynthetic rate is strongly associated with leaf proline and soluble protein content, suggesting that a higher net photosynthetic rate results in higher leaf proline and soluble protein content. Of the treatments, the Cd + NP3 (50 mg/kg Cd + 200 mg/L TiO2-NPs) performed the best for both fragrant rice cultivars under Cd toxicity. Our results showed that TiO2-NPs strengthened rice metabolism through an enhanced antioxidant defense system across the growth stages, thereby improving plant physiological activity and biochemical characteristics under Cd toxicity.

Effects of contrasting tillage managements on the vertical distribution of plant- and microbial-derived carbon in rice paddy.

Soil microbial necromass is considered a persistent component of soil organic carbon (SOC), constituting the final product of the microbial carbon pump (MCP). However, the mechanisms involved in the effects of tillage and rice residue managements on the vertical distribution of microbial necromass and plant residues in rice paddy soils remain unclear, limiting knowledge of SOC sequestration mechanisms. Therefore, we estimated microbial- and plant-derived C by biomarker amino sugars (AS) and lignin phenols (VSC) at the 0-30 cm soil depth, as well as their relationships with SOC contents and mineralization in a rice paddy soil under contrasting tillage practices, namely no-tillage (NT), reduced tillage (RT), and conventional tillage (CT). The results showed that the SOC contents in the rice paddy soil were positively correlated with soil AS and VSC contents. The NT resulted in significantly higher (P < 0.05) AS (expressed as per kilogram soil) at the 0-10 cm and 10-30 cm soil depths by 45-48 % than RT and CT. However, microbial-derived C contents and SOC mineralization were not significantly changed by NT. In contrast, the plant-derived C contents in the total SOC decreased significantly under the NT scenario, suggesting the consumption of plant-derived C even with more rice residue inputs (at the 0-10 cm soil depth). In summary, 5-year short-term NT management with more rice residue mulch on the soil surface in rice paddy maintained a low plant-derived C content (at a sampling date before rice transplanting), suggesting a different mode of C sequestration, except for the protection of plant-derived C under anaerobic conditions.

Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics.

Rice is a staple food for more than half of the world's population, and rice fragrance is a key quality attribute which is highly desired by consumers and attracts premium prices in the international market. There are around 200 volatile compounds involved in rice fragrance, but 2-acetyl-1-pyrroline (2-AP) has been considered a master regulator of aroma in fragrant rice. Consequently, efforts were made to increase the 2-AP contents in the grain by managing agronomical practices or by using modern functional genomic tools, which successfully converted nonfragrant cultivars to fragrant rice. Furthermore, environmental factors were also reported to influence the 2-AP contents. However, a comprehensive analysis of 2-AP biosynthesis in response to agro-management practices, environmental factors, and the application of functional genomic tools for fragrant rice production was missing. In this Review, we summarize how micro/macronutrients, cultivation practices, amino acid precursors, growth regulators, and environmental factors, such as drought, salinity, light, and temperature, influence the 2-AP biosynthesis to modulate the aroma of fragrant rice. Furthermore, we also summarized the successful conversion of nonfragrant rice cultivars to fragrant rice using modern gene editing tools, such as RNAi, TALENS, and CRISPR-Cas9. Finally, we discussed and highlighted the future perspective and challenges related to the aroma of fragrant rice.

Trans-Zeatin induce regulation the biosynthesis of 2-acetyl-1-pyrroline in fragrant rice (Oryza sativa L.) seedlings.

BACKGROUND: In plants, cytokinin is activated into trans-zeatin to fight abiotic stresses. However, the mechanism of the effect of trans-zeatin on 2-acetyl-1-pyrroline (2-AP) biosynthesis in fragrant rice has yet to be studied. The present study was conducted to explore the effects of exogenous trans-zeatin on enzymes activities, genes expression, and precursors involved in 2-AP biosynthesis and 2-AP contents as well as the seedling quality of a fragrant rice cultivar viz., Meixiangzhan2. Four concentrations of trans-zeatin solutions at 20, 40, and 80 µmol L- 1 (ZT1, ZT2, and ZT3) were sprayed onto rice seedlings. RESULTS: Compared to the control, trans-zeatin treatments showed significantly higher 2-AP contents of fragrant rice seedlings. Increased plant height and stem width were observed due to trans-zeatin treatments. The trans-zeatin application increased 1-pyrroline, methylglyoxal, proline, and P5C contents, enhanced P5CS and OAT activities, and reduced glutamic acid contents. In addition, expressions of ProDH, P5CS2, and DAO4 were comparatively higher under trans-zeatin treatments than CK in fragrant rice seedlings. CONCLUSIONS: Overall, up-regulation of P5C, 1-pyrroline, and proline and down-regulation of glutamic acid under appropriate trans-zeatin concentrations (20 and 40 µmol L- 1) resulted in enhanced 2-AP biosynthesis in fragrant rice seedlings and 20-40 µmol L- 1 was considered as the suggested concentrations of trans-zeatin application in fragrant rice seedling.

CRISPR-Cas9-mediated editing of BADH2 gene triggered fragrance revolution in rice.

Fragrance is one of the most important quality traits for breeding in rice. The natural aroma substance 2-acetyl-1-pyrroline (2-AP) is a key fragrance compound among over 200 volatiles identified in fragrant rice. In addition to rice, there are other plant species that contain a germplasm that naturally produces a fragrant aroma. These other plant species all have lower activity levels of the enzyme BETAINE ALDEHYDE DEHYDROGENASE 2 (BADH2). Therefore, improving fragrance efficiency has been a focus of intensive research. Recent studies have engineered BADH2 gene, which is responsible for fragrance trait in non-fragrant cultivars of rice, using CRISPR-Cas9. Although engineering rice BADH2 can be useful for upregulating 2-AP, there are still a lot of restrictions on how it can be applied in practice. In this review article, we discuss the recent developments in BADH2 editing and propose potential future strategies to effectively target BADH2 for transcriptional regulation, with the goal of producing a better fragrance.