Supporting data-enhanced hybrid ordinary differential equation model for phosphate dynamics in municipal wastewater treatment.

A parallel hybrid ordinary differential equation (ODE) integrating the Activated Sludge Model No. 2d (ASM2d) and an artificial neural network (ANN) was developed to simulate biological phosphorus removal (BPR) with high accuracy and interpretability. Two novelties were introduced; first, the involved supporting data (i.e., phosphate-release activity) were incorporated as an input in the ANN. Second, the outputs of the ANN were selective. Three models were implemented using different ANN outputs, and all three outperformed ASM2d in phosphate estimation for anaerobic/aerobic sequencing batch reactor operation. In particular, the incorporation of four variables responsible for BPR into the ANN enabled the highest performance (R2 = 0.93) owing to the capture of increasing phosphate-accumulating organisms (PAOs). The ANN with the supporting data worked satisfactorily to compensate for ASM2d by adding proper PAOs, resulting in improvement in phosphate estimation. The novel parallel hybrid ODE can simulate BPR while maintaining physical meaning.

Comprehensive assessment of multiple biomarker mechanisms in the brackish water clam Corbicula japonica exposed to polystyrene microplastics using structural equation modeling.

Using structural equation modeling (SEM), we investigated multiple biomarker mechanisms in terms of biochemical and individual marker responses in the brackish water clam Corbicula japonica following acute exposure to polystyrene microplastic (PS-MP). This study is the first to comprehensively explore multiple biomarker responses in bivalves using SEM. The model revealed that PS-MP accumulation was an independent biomarker, exhibiting significant direct effects on superoxide dismutase (SOD) and catalase (CAT) among the biochemical markers. Although CAT generally interacts closely with SOD, no significant relationship was identified between them, indicating that CAT may have independently responded to PS-MP stress. Among individual markers, significant indirect effects were observed on clearance rate (CR), reflecting feeding activity and valve open rate, indicating excretion activity via SOD and CAT. Finally, the carbon-based scope for growth was significantly influenced by CR. SEM is efficient and useful for identifying significant direct and indirect pathway relationships and for uncovering uncommon relationships in unified multiple biomarker mechanisms in aquatic studies.

A simulation of acetate consumption and electricity generation in a single microbial fuel cell considering the diversity of nonelectrogenic bacteria.

To simulate acetate consumption and electricity generation in a cycle of a microbial fuel cell (MFC) treating synthetic acetate-based wastewater with low concentration, nonelectrogenic bacteria (NEB), which had no contribution in electricity generation, was incorporated with methanogen's kinetic parameters into a previous biofilm model proposed by Marcus et al. (Biotechnol Bioeng 98:1171-1182, 2007). However, the Coulombic efficiency was estimated to be 40.1%, whereas the experiment showed 13.6%, as the presence of NEB was obviously underestimated. Thus, the maximum NEB reaction rate (qmaxC) was temporarily calibrated, and a sensitivity analysis was then conducted. As a result, the growth parameters of NEB, the growth of the exoelectrogenic bacteria, and the biofilm detachment were identified as influential parameters. qmaxC and a half rate constant of NEB (KsC) were selected as potential calibration parameters. The two sets of calibrated parameters (0.342 mmol-acetate (Ac)/mg-volatile solids (VS)/d of qmaxC and 33.8 mg-carbon (C)/L of KsC; 0.274 mmol-Ac/mg-VS/d of qmaxC and 16.9 mg-C/L of KsC) showed a good agreement with the experimental results at 100 mg-C/L of initial acetate. However, the calibrated parameter values obviously differed from those in previous models. The calibrated model also showed good agreement with the experimental results at 50 and 200 mg-C/L of the initial acetate. In view of the different values of qmaxC and KsC from those of methanogenic bacteria in previous models and the previous findings on anode microbial community, which showed that NEB are not only methanogenic bacteria, we concluded that the diversity of NEB should be considered to simulate performances in a cycle of MFC treating low organic matter concentrations.

Machine learning estimation of biodegradable organic matter concentrations in municipal wastewater.

This study investigates whether a novel estimation method based on machine learning can feasibly predict the readily biodegradable chemical oxygen demand (RB-COD) and slowly biodegradable COD (SB-COD) in municipal wastewater from the oxidation-reduction potential (ORP) data of anoxic batch experiments. Anoxic batch experiments were conducted with highly mixed liquor volatile suspended solids under different RB-COD and SB-COD conditions. As the RB-COD increased, the ORP breakpoint appeared earlier, and fermentation occurred in the interior of the activated sludge, even under anoxic conditions. Therefore, the ORP decline rates before and after the breakpoint were significantly correlated with the RB-COD and SB-COD, respectively (p < 0.05). The two biodegradable CODs were estimated separately using six machine learning models: an artificial neural network (ANN), support vector regression (SVR), an ANN-based AdaBoost, a SVR-based AdaBoost, decision tree, and random forest. Against the ORP dataset, the RB-COD and SB-COD estimation correlation coefficients of SVR-based AdaBoost were 0.96 and 0.88, respectively. To identify which ORP data are useful for estimations, the ORP decline rates before and after the breakpoint were separately input as datasets to the estimation methods. All six machine learning models successfully estimated the two biodegradable CODs simultaneously with accuracies of ≥0.80 from only ORP time-series data. Sensitivity analysis using the Shapley additive explanation method demonstrated that the ORP decline rates before and after the breakpoint obviously contributed to the estimation of RB-COD and SB-COD, respectively, indicating that acquiring the ORP data with various decline rates before and after the breakpoint improved the estimations of RB-COD and SB-COD, respectively. This novel estimation method for RB-COD and SB-COD can assist the rapid control of biological wastewater treatment when the biodegradable organic matter concentration dynamically changes in influent wastewater.

Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number.

In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.

Molecular characterization of two isoforms of a farnesyl pyrophosphate synthase gene in wheat and their roles in sesquiterpene synthesis and inducible defence against aphid infestation.

Aphids are important pests of wheat (Triticum aestivum) that affect crop production globally. Herbivore-induced emission of sesquiterpenes can repel pests, and farnesyl pyrophosphate synthase (FPS) is a key enzyme involved in sesquiterpene biosynthesis. However, fps orthologues in wheat and their functional roles in sesquiterpene synthesis and defence against aphid infestation are unknown. Here, two fps isoforms, Tafps1 and Tafps2, were identified in wheat. Quantitative real-time polymerase chain reaction (qRT-PCR) and in vitro catalytic activity analyses were conducted to investigate expression patterns and activity. Heterologous expression of these isoforms in Arabidopsis thaliana, virus-induced gene silencing (VIGS) in wheat and aphid behavioural assays were performed to understand the functional roles of these two isoforms. We demonstrated that Tafps1 and Tafps2 played different roles in induced responses to aphid infestation and in sesquiterpene synthesis. Heterologous expression in A. thaliana resulted in repulsion of the peach aphid (Myzus persicae). Wheat plants with these two isoforms transiently silenced were significantly attractive to grain aphid (Sitobion avenae). Our results provide new insights into induced defence against aphid herbivory in wheat, in particular, the different roles of the two Tafps isoforms in both sesquiterpene biosynthesis and defence against aphid infestation.

A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses.

Drought and salinity are the primary factors limiting wheat production worldwide. It has been shown that a rice stress-responsive transcription factor encoded by the rice NAC1 gene (SNAC1) plays an important role in drought stress tolerance. Therefore, we introduced the SNAC1 gene under the control of a maize ubiquitin promoter into an elite Chinese wheat variety Yangmai12. Plants expressing SNAC1 displayed significantly enhanced tolerance to drought and salinity in multiple generations, and contained higher levels of water and chlorophyll in their leaves, as compared to wild type. In addition, the fresh and dry weights of the roots of these plants were also increased, and the plants had increased sensitivities to abscisic acid (ABA), which inhibited root and shoot growth. Furthermore, quantitative real-time polymerase chain reactions revealed that the expressions of genes involved in abiotic stress/ABA signaling, such as wheat 1-phosphatidylinositol-3-phosphate-5-kinase, sucrose phosphate synthase, type 2C protein phosphatases and regulatory components of ABA receptor, were effectively regulated by the alien SNAC1 gene. These results indicated high and functional expression of the rice SNAC1 gene in wheat. And our study provided a promising approach to improve the tolerances of wheat cultivars to drought and salinity through genetic engineering.

TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat.

The cytokinin oxidase/dehydrogenase (CKX) gene plays a principal role in controlling cytokinin levels and has been shown to be a major quantitative trait locus (QTL) affecting grain number in rice. However, the function and evaluation of the haplotypes of the wheat CKX gene have yet to be illustrated. In this study, TaCKX6-D1, a wheat ortholog of rice OsCKX2, was cloned and its haplotype variants were determined to be significantly associated with the 1000-grain weight on the basis of linkage mapping, association analysis and gene expression analysis. Five TaCKX6-D1 haplotypes, designated a-e, were identified. An indel marker was developed to identify haplotype a, which was associated with higher grain weight. Haplotype a showed decreased expression relative to haplotype b in seeds at 8 d after pollination. Sequence variations among modern cultivars, landraces and wild species suggest a significant domestication signature at the TaCKX6-D1 locus in Chinese wheat germplasm. TaCKX6-D1 may serve as a useful gene for the breeding of high-yielding wheat. A strategy for allele mining and utilization of TaCKX6-D1 was proposed. Our study also sheds light on the mechanisms of grain development and domestication of wheat, as well as the functional divergence of orthologs in comparative genomics.

Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use- and yield-related traits in bread wheat.

Glutamine synthetase (GS) plays a key role in the growth, nitrogen (N) use and yield potential of cereal crops. Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N-use efficiency and yield. We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform (GS2) genes located on chromosomes 2A, 2B and 2D in bread wheat. By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2-A1 (a and b), TaGS2-B1 (a-f) and TaGS2-D1 (a and b), respectively. By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes (A1b, B1a, B1b, D1a) were revealed. These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration. Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N-use efficiency.

The characterization and geographical distribution of the genes responsible for vernalization requirement in Chinese bread wheat.

The frequency and distribution of the major vernalization requirement genes and their effects on growth habits were studied. Of the 551 bread wheat genotypes tested, seven allelic combinations of the three Vrn-1 genes were found to be responsible for the spring habit, three for the facultative habit and one for the winter habit. The three Vrn-1 genes behaved additively with the dominant allele of Vrn-A1 exerting the strongest effect. The allele combinations of the facultative genotypes and the discovery of spring genotypes with "winter" allele of Vrn-1 implied the presence of as yet unidentified alleles/genes for vernalization response. The dominant alleles of the three Vrn-1 genes were found in all ten ecological regions where wheat is cultivated in China, with Vrn-D1 as the most common allele in nine and Vrn-A1 in one. The combination of vrn-A1vrn-B1Vrn-D1 was the predominant genotype in seven of the regions. Compared with landraces, improved varieties contain a higher proportion of the spring type. This was attributed by a higher frequency of the dominant Vrn-A1 and Vrn-B1 alleles in the latter. Correlations between Vrn-1 allelic constitutions and heading date, spike length, plant type as well as cold tolerance were established.

Evolutionary and functional study of the CDPK gene family in wheat (Triticum aestivum L.).

Calcium-dependent protein kinases (CDPKs) are crucial sensors of calcium concentration changes in plant cells under diverse endogenous and environmental stimuli. We identified 20 CDPK genes from bread wheat and performed a comprehensive study on their structural, functional and evolutionary characteristics. Full-length cDNA sequences of 14 CDPKs were obtained using various approaches. Wheat CDPKs were found to be similar to their counterparts in rice in genomic structure, GC content, subcellular localization, and subgroup classification. Divergence time estimation of wheat CDPK gene pairs and wheat-rice orthologs suggested that most duplicated genes already existed in the common ancestor of wheat and rice. The number of CDPKs in diploid wheat genome was estimated to be at least 26, a number close to that in rice, Arabidopsis, and poplar. However, polymorphism among EST sequences uncovered transcripts of all three homoeologous alleles for 13 out of 20 CDPKs. Thus, the hexaploid wheat should have 2-3 fold more CDPK genes expressing in their cells than the diploid species. Wheat CDPK genes were found to respond to various biotic and abiotic stimuli, including cold, hydrogen peroxide (H(2)O(2)), salt, drought, powdery mildew (Blumeria graminis tritici, Bgt), as well as phytohormones abscisic acid (ABA) and gibberellic acid (GA). Each CDPK gene often responded to multiple treatments, suggesting that wheat CDPKs are converging points for multiple signal transduction pathways. The current work represents the first comprehensive study of CDPK genes in bread wheat and provides a foundation for further functional study of this important gene family in Triticeae.

[Comparison of methods to construct a full-length cDNA library].

The use of full-length cDNA libraries is an effective tool to obtain complete gene information in a high-efficiency, high-throughput manner, especially in organisms with huge genomes that are not amenable to whole genome sequencing. In this review, we outlined several methods of full-length cDNA library construction and compared their advantages and disadvantages based on their respective principles. Drawing on our own experience, we described the Cap-trapper method in detail, with an emphasis on its application in wheat full-length cDNA library construction as well as the determination of the ratio of full-length cDNA in a library.

[Construction of a full-length cDNA library of Aegilops speltoides Tausch with optimized cap-trapper method].

To discover new genes in a throughput manner,the cap-trapper method published previously was optimized for raising the efficiency in the construction of full-length cDNA library. Using the optimized protocol,we successfully constructed a full-length cDNA library of Aegilops speltoides,which contained 3.0 x 10(6) clones and more than 99% of plaques were recombinant phages. Sequence analysis results indicated that more than 89% of the clones were full-length.