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The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides. Genomic innovation in plant defense is explored by the authors who uncover the genome-wide hijacking of the albumin-1 gene family by biocidal cyclic peptides called cyclotides, and recruitment of asparaginyl endopeptidases for peptide cyclization. [ABSTRACT FROM AUTHOR]

The marker-assisted backcrossing (MAB) can help to transfer an interested allele at a target locus from a donor to a recipient line. Gynoecious is a pivotal trait of cucumber since commercial F1 hybrid seeds produced with gynoecious line as one of the parents are high-yield and affordable. This study aims to transfer the F locus encoded for gynoecious trait to Vietnamese domesticated cucumbers by marker-assisted backcrossing. Two monoecious cucumber lines, A1 (Ha Giang, Vietnam) A2 (Yen Bai, Vietnam), and two gynoecious cucumber lines, B1 (Plantgene, India) and B2 (Hue, Vietnam) were utilized as the starting materials. BCAT marker (located on the F locus) and 52 SSRs (spread across seven chromosomes and tightly linked with some crucial horticultural traits) were used as the foreground and background markers, respectively. With this, phenotype selection for fruit and leaf sizes was also applied. First, using phenotypic screening and foreground marker, A1 (Ha Giang, Vietnam) and B1 (Plantgene, India) were selected as donor and recurrent parents for backcrossing. Then, after two backcrosses followed by two self-pollinations, four gynoecious C cucumber lines were created. These C lines have leaf sizes slightly bigger than the recurrent parent. Importantly, their fruit length is the same or longer than A1 (Ha Giang, Vietnam). These new gynoecious lines could be used as material lines for producing commercial F1 hybrid seeds. [ABSTRACT FROM AUTHOR]

Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure–activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes. [ABSTRACT FROM AUTHOR]

Multiple sclerosis (MS) is a debilitating disease that requires prolonged treatment with often severe side effects. One experimental MS therapeutic currently under development is a single amino acid mutant of a plant peptide termed kalata B1, of the cyclotide family. Like all cyclotides, the therapeutic candidate [T20K]kB1 is highly stable as it contains a cyclic backbone that is cross-linked by three disulfide bonds in a knot-like structure. This stability is much sought after for peptide drugs, which despite exquisite selectivity for their targets, are prone to rapid degradation in human serum. In preliminary investigations, it was found that [T20K]kB1 retains oral activity in experimental autoimmune encephalomyelitis, a model of MS in mice, thus opening up opportunities for oral dosing of the peptide. Although [T20K]kB1 can be synthetically produced, a recombinant production system provides advantages, specifically for reduced scale-up costs and reductions in chemical waste. In this study, we demonstrate the capacity of the Australian native Nicotiana benthamiana plant to produce a structurally identical [T20K]kB1 to that of the synthetic peptide. By optimizing the co-expressed cyclizing enzyme, precursor peptide arrangements, and transgene regulatory regions, we demonstrate a [T20K]kB1 yield in crude peptide extracts of ~ 0.3 mg/g dry mass) in whole plants and close to 1.0 mg/g dry mass in isolated infiltrated leaves. With large-scale plant production facilities coming on-line across the world, the sustainable and cost-effective production of cyclotide-based therapeutics is now within reach. [ABSTRACT FROM AUTHOR]

Phytoremediation is one of the most powerful and viable solutions for developing countries to clean the soil and water bodies from metallic pollutants. Cyperus alternifolius Linn. (CAL), a tropical wetland plant, has been widely researched for removing harmful contaminants due to its hyperaccumulation ability. However, the waste biomass of phytoremediation processing may risk secondary environmental pollution. Thus, the preparation and application of biochar from metal-contaminated plants can be considered a new approach. In a 60-day experiment, CAL plants were irrigated with different concentrations of Zn(II) (200, 700, 1200, 1700, and 2200 mg·L−1), and then the plants were converted into biochar via the pyrolysis process. The characteristics of biochar including of surface composition and morphology, phase formation, and optical property were analyzed. The biochar enriched with Zn(II) at 1200 mg·L−1 had a bandgap value of 3.17 eV and consisted of carbon microparticles intermingled with ZnO and SiO2 nanoparticles. Furthermore, the adsorption and photocatalysis of the biochar were studied in the discolouration of methylene blue (MB), as a test reaction, with the maximum MB removal capacities of 55.2 mg·g−1. Such results will serve as the basis for new research aiming at the potential for reusing metal-contaminated plants to produce efficient depolluting biochar. [ABSTRACT FROM AUTHOR]

Background and aims: Extreme climate events, including flooding and prolonged drought, may establish long-lasting (legacy) effects on soil abiotic and biotic properties, potentially influencing soil N-cycling, microbial communities, and plant productivity. Nitrogen (N) fertilizer often stimulates plant growth, but it remains unknown whether N addition can alleviate the impact of legacy drought or waterlogging events on crops. Our aim was to assess the interactive effects of legacy extreme climate events and N-addition on these processes.Methods: Using cotton as a model system, soils previously exposed to waterlogging and prolonged drought were used to examine potential legacy impacts of extreme climate on soil N process rates, abundance and structure of associated microbial communities, and cotton growth and productivity under different levels of N fertilizer application (0, 100, 200 and 300 kg N/ha).Results: The deleterious legacy effects of prolonged drought on plant productivity were due to negative impacts on microbial abundance and community structure, and soil nutrient availability, thereby negatively influencing the rate of nitrification, and consequently plant available N. The legacy impacts of prolonged drought persisted throughout the experiment despite fertiliser applications of up to 300 kg of N/ha. The only observed legacy impacts of waterlogging were low NO3− levels in soils without N-addition and shifts in the abundance and structure of the N2O-reducing community.Conclusions: There were strong legacy impacts of prolonged drought, but minor legacy impacts of waterlogging, on soils and crop yields which could not be fully counteracted by the high rates of N fertilizer application. This study provides critical knowledge contributing to the development of adaptation and soil N management strategies to minimize the loss of farm productivity, within the context of increased frequencies and intensities of extreme weather events. [ABSTRACT FROM AUTHOR]

Background and aims: Waterlogging may affect soil nitrification rates, resulting in changes in plant-available nitrogen (N), and hence potentially influencing crop productivity. Because nitrification is a microbially-driven process and ammonia-oxidizing communities regulate soil nitrification rates, the aim of this study was to investigate the mechanistic response of ammonia-oxidizing communities and nitrification rates to waterlogging.Methods: A field study was conducted by experimentally imposing two short-term waterlogging events when cotton plants were at the early- and late-flowering stages. Soil physicochemical properties, nitrification rates, and ammonia-oxidizing community abundance and structure in response to waterlogging were examined.Results: Soil nitrate (NO3−) content, potential nitrification rates (PNR) and the abundance of ammonia-oxidizing communities significantly decreased upon waterlogging. Shifts in ammonia-oxidizing community structure were also observed. Both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) responded to waterlogging. PNR was significantly correlated with the abundance and structure of both AOB and AOA.Conclusions: Waterlogging had strong negative effects on soil nitrification rates by altering the ammonia-oxidizing community abundance and structure, resulting in reduced soil N availability. Decreased plant-available N is likely to negatively affect primary productivity. [ABSTRACT FROM AUTHOR]

Mining association rules plays an important role in data mining and knowledge discovery since it can reveal strong associations between items in databases. Nevertheless, an important problem with traditional association rule mining methods is that they can generate a huge amount of association rules depending on how parameters are set. However, users are often only interested in finding the strongest rules, and do not want to go through a large amount of rules or wait for these rules to be generated. To address those needs, algorithms have been proposed to mine the top-k association rules in databases, where users can directly set a parameter k to obtain the k most frequent rules. However, a major issue with these techniques is that they remain very costly in terms of execution time and memory. To address this issue, this paper presents a novel algorithm named ETARM (Efficient Top-k Association Rule Miner) to efficiently find the complete set of top-k association rules. The proposed algorithm integrates two novel candidate pruning properties to more effectively reduce the search space. These properties are applied during the candidate selection process to identify items that should not be used to expand a rule based on its confidence, to reduce the number of candidates. An extensive experimental evaluation on six standard benchmark datasets show that the proposed approach outperforms the state-of-the-art TopKRules algorithm both in terms of runtime and memory usage. [ABSTRACT FROM AUTHOR]