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Amaranthus tricolor is an important vegetable, and its quality is affected by salt stress. Cation/proton antiporters (CPA) contribute to plant development and tolerance to salt stress. In this study, 35 CPA genes were identified from a genome database for A. tricolor, including 9 NHX, 5 KEA, and 21 CPA2 genes. Furthermore, in A. tricolor, the expression levels of most AtrNHX genes were higher at a low salinity level (50 or 100 mM NaCl) than in the control or 200 mM NaCl treatment. Levels of most AtrNHX genes were elevated in the stem. Moreover, AtrNHX8 was homologous to AtNHX4, which is involved in the regulation of sodium homeostasis and salt stress response. After AtrNHX8 overexpression in Arabidopsis thaliana, seed germination was better, and the flowering time was earlier than that of wild-type plants. Additionally, the overexpression of AtrNHX8 in A. thaliana improved salt tolerance. These results reveal the roles of AtrNHX genes under salt stress and provide valuable information on this gene family in amaranth. [ABSTRACT FROM AUTHOR]

Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50–200 mmol·L−1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L−1, while it was promoted at 50 mmol·L−1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L−1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene. [ABSTRACT FROM AUTHOR]

It has been widely observed that there exists no universal best Multi-Objective Evolutionary Algorithm (MOEA) dominating all other MOEAs on all possible Multi-Objective Optimization Problems (MOPs). In this work, we advocate using the Parallel Algorithm Portfolio (PAP), which runs multiple MOEAs independently in parallel and gets the best out of them, to combine the advantages of different MOEAs. Since the manual construction of PAPs is non-trivial and tedious, we propose to automatically construct high-performance PAPs for solving MOPs. Specifically, we first propose a variant of PAPs, namely MOEAs/PAP, which can better determine the output solution set for MOPs than conventional PAPs. Then, we present an automatic construction approach for MOEAs/PAP with a novel performance metric for evaluating the performance of MOEAs across multiple MOPs. Finally, we use the proposed approach to construct an MOEAs/PAP based on a training set of MOPs and an algorithm configuration space defined by several variants of NSGA-II. Experimental results show that the automatically constructed MOEAs/PAP can even rival the state-of-the-art multi-operator-based MOEAs designed by human experts, demonstrating the huge potential of the automatic construction of PAPs in multi-objective optimization. [ABSTRACT FROM AUTHOR]

Amaranth plants contain abundant betalains and flavonoids. Anthocyanins are important flavonoids; however, they cannot coexist in the same plant with betalains. Blue light influences metabolite synthesis and hypocotyl elongation; accordingly, analyses of its effects on betalain and flavonoid biosynthesis in Amaranthus tricolor may provide insight into the distribution of these plant pigments. We analyzed the betalain and flavonoid content and transcriptome profiles in amaranth hypocotyls under blue light and dark conditions. Furthermore, we analyzed the expression patterns of key genes related to betalains and flavonoids. Amaranth hypocotyls were shorter and redder and showed higher betalain and flavonoid content under blue light than in dark conditions. Key genes involved in the synthesis of betalains and flavonoids were upregulated under blue light. The gene encoding DELLA was also upregulated. These results suggest that blue light favors the synthesis of both betalains and flavonoids via the suppression of bioactive gibberellin and the promotion of DELLA protein accumulation, which also suppresses hypocotyl elongation. The metabolite profiles differed between plants under blue light and dark conditions. These findings improve our understanding of the environmental cues and molecular mechanisms underlying pigment variation in Amaranthus. [ABSTRACT FROM AUTHOR]

Traditional solvers for tackling combinatorial optimization (CO) problems are usually designed by human experts. Recently, there has been a surge of interest in utilizing deep learning, especially deep reinforcement learning, to automatically learn effective solvers for CO. The resultant new paradigm is termed neural combinatorial optimization (NCO). However, the advantages and disadvantages of NCO relative to other approaches have not been empirically or theoretically well studied. This work presents a comprehensive comparative study of NCO solvers and alternative solvers. Specifically, taking the traveling salesman problem as the testbed problem, the performance of the solvers is assessed in five aspects, i.e., effectiveness, efficiency, stability, scalability, and generalization ability. Our results show that the solvers learned by NCO approaches, in general, still fall short of traditional solvers in nearly all these aspects. A potential benefit of NCO solvers would be their superior time and energy efficiency for small-size problem instances when sufficient training instances are available. Hopefully, this work would help with a better understanding of the strengths and weaknesses of NCO and provide a comprehensive evaluation protocol for further benchmarking NCO approaches in comparison to other approaches. [ABSTRACT FROM AUTHOR]

Since automatic algorithm configuration methods have been very effective, recently there is increasing research interest in utilizing them for automatic solver construction, resulting in several notable approaches. For these approaches, a basic assumption is that the given training set could sufficiently represent the target use cases such that the constructed solvers can generalize well. However, such an assumption does not always hold in practice since in some cases, we might only have scarce and biased training data. This article studies effective construction approaches for the parallel algorithm portfolios that are less affected in these cases. Unlike previous approaches, the proposed approach simultaneously considers instance generation and portfolio construction in an adversarial process, in which the aim of the former is to generate instances that are challenging for the current portfolio, while the aim of the latter is to find a new component solver for the portfolio to better solve the newly generated instances. Applied to two widely studied problem domains, that is, the Boolean satisfiability problems (SAT) and the traveling salesman problems (TSPs), the proposed approach identified parallel portfolios with much better generalization than the ones generated by the existing approaches when the training data were scarce and biased. Moreover, it was further demonstrated that the generated portfolios could even rival the state-of-the-art manually designed parallel solvers. [ABSTRACT FROM AUTHOR]

Amaranth is rich in betalain. Both betalain metabolites and plant growth are affected by external factors. However, studies of amaranth seedling growth and betalain metabolism are limited by a lack of appropriate reference genes for qRT-PCR analyses. We selected 13 candidate reference genes from the amaranth transcriptome database and tested their expression stability under various environmental conditions and plant growth regulators. Five methods were used for the analysis: geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder. The most stable reference genes were SAND and RAN1 for light quality, SAND and EIF5a for photoperiod, Actin-7 and TuA for temperature, SAND and Actin-7 for different tissue, SAND and EIF5a for NaCl, SAND and 60S RPL for GA3, 28S rRNA and 18S rRNA for 6-BA, 18S rRNA and 60S RPL for 2,4-D, EIF5a and 28S rRNA for ABA, Actin-11 and SKIP35 for SA, 28S rRNA and Actin-7 for MeJA, SAND and EIF5a for all samples. To further verify the reliability of the reference genes identified in this study, the expression levels of CYP76AD1 were studied in amaranth. This is the first systematic analysis aimed at the selection of reference genes for qRT-PCR in A. tricolor under different culture conditions. [ABSTRACT FROM AUTHOR]

This work aims to explore the feasibility of using type D botulinum toxin as a novel, environmentally friendly biological rodenticide for the population control of rodents in plateau pastoral area. The toxin is subjected to toxin component, DNA sequencing, and bioinformatic analyses. The lethal median dose (LD50) values of intragastrically and orally administred type D botulinum toxin in wild plateau pikas, plateau zokors, and Microtus fuscus are calculated through Horn's method and the improved Karber method. The ability of the toxin to prevent and control rodent damage is assessed through plot experiments. The safety of type D botulinum toxin toward nontarget animals, such as yaks, Tibetan sheep, dogs, vultures, and birds, is also tested. Results show that the toxin is encoded by a type D botulinum neurotoxin gene. The DNA and amino acid sequences of the full neurotoxin gene comprise 3831 base pairs and 1276 amino acid residues, respectively. The nucleic acid and protein sequences of the toxin exhibits 99% homology with those of a known type D botulinum neurotoxin gene, and the composition of the functional domain of the toxin is consistent with that of type D botulinum neurotoxin. For plateau pikas and plateau zokors, the LD50 values of intragastrically administered type D botulinum toxin is 6810 and 5840 MLD/kg weight, respectively, and those of orally administered type D botulinum are 1.231and 1.319 g/kg weight, respectively. The natural enemies of rodents are strongly resistant to type D botulinum toxin. Experimental results indicate that type D botulinum toxin can be used as a new biological rodenticide for the prevention and control of rodent damage in plateau pastoral area. [ABSTRACT FROM AUTHOR]

Generalization, i.e., the ability of solving problem instances that are not available during the system design and development phase, is a critical goal for intelligent systems. A typical way to achieve good generalization is to learn a model from vast data. In the context of heuristic search, such a paradigm could be implemented as configuring the parameters of a parallel algorithm portfolio (PAP) based on a set of “training” problem instances, which is often referred to as PAP construction. However, compared to the traditional machine learning, PAP construction often suffers from the lack of training instances, and the obtained PAPs may fail to generalize well. This article proposes a novel competitive co-evolution scheme, named co-evolution of parameterized search (CEPS), as a remedy to this challenge. By co-evolving a configuration population and an instance population, CEPS is capable of obtaining generalizable PAPs with few training instances. The advantage of CEPS in improving generalization is analytically shown in this article. Two concrete algorithms, namely, CEPS-TSP and CEPS-VRPSPDTW, are presented for the traveling salesman problem (TSP) and the vehicle routing problem with simultaneous pickup–delivery and time windows (VRPSPDTW), respectively. The experimental results show that CEPS has led to better generalization, and even managed to find new best-known solutions for some instances. [ABSTRACT FROM AUTHOR]

Amaranth plants are rich in betalains. Additionally, the molecular structure and metabolic pathway of betalains are different in amaranth than in beet. To date, only a few studies have examined the regulatory roles of microRNAs (miRNAs) in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 239 miRNAs including 198 known and 41 novel miRNAs. 493 target genes for the 239 miRNAs were detected in an amaranth transcriptome database. The validation of the expression of 20 miRNAs and nine target genes in a quantitative real-time polymerase chain reaction assay revealed the miRNAs and target genes that were differentially expressed in the two leaf sectors. The miRNAs involved in betalain metabolism in amaranth plants were identified by Illumina sequencing platform. The data presented herein may provide insights into the regulation molecular mechanisms for betalain biosynthesis in amaranth and other plant species. [ABSTRACT FROM AUTHOR]

Amaranth plants contain large amounts of betalains, including betaxanthins and betacyanins. Amaranthin is a betacyanin, and its molecular structure and associated metabolic pathway differ from those of betanin in beet plants. The chlorophyll, carotenoid, betalain, and flavonoid contents in amaranth leaves were analyzed. The abundance of betalain, betacyanin, and betaxanthin was 2–5-fold higher in the red leaf sectors than in the green leaf sectors. Moreover, a transcriptome database was constructed for the red and green sectors of amaranth leaves harvested from 30-day-old seedlings. 22 unigenes were selected to analyze the expression profiles in the two leaf sectors. The RNA-sequencing data indicated that many unigenes are involved in betalain metabolic pathways. The potential relationships between diverse metabolic pathways and betalain metabolism were analyzed. The validation of the expression of 22 selected unigenes in a qRT-PCR assay revealed the genes that were differentially expressed in the two leaf sectors. Betalains were biosynthesized in specific tissues of the red sectors of amaranth leaves. Almost all of the genes related to betalain metabolism were identified in the transcriptome database, and the expression profiles were different between the red sectors and green sectors in the leaf. Amaranth plants consist of diverse metabolic pathways, and the betalain metabolic pathway is linked to a group of other metabolic pathways. [ABSTRACT FROM AUTHOR]

Recently, the design of group sparse regularization has drawn much attention in group sparse signal recovery problem. Two of the most popular group sparsity-inducing regularization models are $$\ell _{1,2}$$ and $$\ell _{1,\infty }$$ regularization. Nevertheless, they do not promote the intra-group sparsity. For example, Huang and Zhang (Ann Stat 38:1978-2004, 2010) claimed that the $$\ell _{1,2}$$ regularization is superior to the $$\ell _1$$ regularization only for strongly group sparse signals. This means the sparsity of intra-group is useless for $$\ell _{1,2}$$ regularization. Our experiments show that recovering signals with intra-group sparse needs more measurements than those without, by the $$\ell _{1,\infty }$$ regularization. In this paper, we propose a novel group sparsity-inducing regularization defined as a mixture of the $$\ell _{1/2}$$ norm and the $$\ell _{1}$$ norm, referred to as $$\ell _{1/2,1}$$ regularization, which can overcome these shortcomings of $$\ell _{1,2}$$ and $$\ell _{1,\infty }$$ regularization. We define a new null space property for $$\ell _{1/2,1}$$ regularization and apply it to establish a recoverability theory for both intra-group and inter-group sparse signals. In addition, we introduce an iteratively reweighted algorithm to solve this model and analyze its convergence. Comprehensive experiments on simulated data show that the proposed $$\ell _{1/2,1}$$ regularization is superior to $$\ell _{1,2}$$ and $$\ell _{1,\infty }$$ regularization. [ABSTRACT FROM AUTHOR]

Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in Am. tricolor growth and development, but the results were somewhat similar to Arabidopsis. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate in vitro plantlet growth and flowering in Am. tricolor, the process appears to be highly complex in this species. [ABSTRACT FROM AUTHOR]