Phenotypic and genetic dissection of the contents of important metallic elements in hybrid rice grown in cadmium-contaminated paddy fields.

Rice (Oryza sativa L.) is a staple food that feeds over half of the world's population, and the contents of metallic elements in rice grain play important roles in human nutrition. In this study, the contents of important metallic elements were determined by ICP-OES, and included cadmium (Cd), zinc (Zn), manganese (Mn), copper (Cu), iron (Fe), nickel (Ni), calcium (Ca), and magnesium (Mg) in brown rice, in the first node from the top (Node 1), in the second node from the top (Node 2), and in roots of 55 hybrids and their parental lines. The heritability of metallic element contents (MECs), the general combining ability (GCA) for MEC, and the correlation between MECs in different organs/tissues of hybrids were also analyzed. The results indicated that: (1) there was a positive correlation between the contents of Cd and Zn in nodes and roots, but a negative correlation between the contents of Cd and Zn in brown rice of the hybrids(2) the GCA for MECs can be used to evaluate the ability of the parental lines to improve the metal contents in brown rice of the hybrids(3) the contents of Cd, Zn, Ca, and Mg in brown rice were mainly affected by additive genetic effects(4) the restorer lines R2292 and R2265 can be used to cultivate hybrids with high Zn and low Cd contents in the brown rice.

Interfacial Supra-Assembly of Copolymer Nanoparticles Enables the Formation of Nanocomposite Crystals with a Tunable Internal Structure.

It is highly desirable but technically challenging to precisely control the spatial composition and internal structure of crystalline nanocomposite materials, especially in a one-pot synthetic route. Herein, we demonstrate a versatile pathway to tune the spatial distribution of guest species within a host inorganic crystal via an incorporation strategy. Specifically, well-defined block copolymer nanoparticles, poly(methacrylic acid)x-block-poly(styrene-alt-N-phenylmaleimide)y [PMAAx-P(St-alt-NMI)y], are synthesized by polymerization-induced self-assembly. Such anionic nanoparticles can supra-assemble onto the surface of larger cationic nanoparticles via an electrostatic interaction, forming colloidal nanocomposite particles (CNPs). Remarkably, such CNPs can be incorporated into calcite single crystals in a spatially controlled manner: the depth of CNPs incorporation into calcite is tunable. Systematic investigation indicates that this interesting phenomenon is governed by the colloidal stability of CNPs, which in turn is dictated by the PMAAx-P(St-alt-NMI)y adsorption density and calcium ion concentration. This study opens up a general and efficient route for the preparation of a wide range of crystalline nanocomposite materials with a controlled internal composition and structure.

Genomic analyses provide insights into the polyploidization-driven herbicide adaptation in Leptochloa weeds.

Polyploidy confers a selective advantage under stress conditions; however, whether polyploidization mediates enhanced herbicide adaptation remains largely unknown. Tetraploid Leptochloa chinensis is a notorious weed in the rice ecosystem, causing severe yield loss in rice. In China, L. chinensis has only one sister species, the diploid L. panicea, whose damage is rarely reported. To gain insights into the effects of polyploidization on herbicide adaptation, we first assembled a high-quality genome of L. panicea and identified genome structure variations with L. chinensis. Moreover, we identified herbicide-resistance genes specifically expanded in L. chinensis, which may confer a greater herbicide adaptability in L. chinensis. Analysis of gene retention and loss showed that five herbicide target-site genes and several herbicide nontarget-site resistance gene families were retained during polyploidization. Notably, we identified three pairs of polyploidization-retained genes including LcABCC8, LcCYP76C1 and LcCYP76C4 that may enhance herbicide resistance. More importantly, we found that both copies of LcCYP76C4 were under herbicide selection during the spread of L. chinensis in China. Furthermore, we identified another gene potentially involved in herbicide resistance, LcCYP709B2, which is also retained during polyploidization and under selection. This study provides insights into the genomic basis of the enhanced herbicide adaptability of Leptochloa weeds during polyploidization and provides guidance for the precise and efficient control of polyploidy weeds.

The Lesson Learned from the Unique Evolutionary Story of Avirulence Gene AvrPii of Magnaporthe oryzae.

Blast, caused by Magnaporthe oryzae, is one of the most destructive diseases affecting rice production. Understanding population dynamics of the pathogen's avirulence genes is pre-required for breeding and then deploying new cultivars carrying promising resistance genes. The divergence and population structure of AvrPii was dissected in the populations of southern (Guangdong, Hunan, and Guizhou) and northern (Jilin, Liaoning, and Heilongjiang) China, via population genetic and evolutionary approaches. The evolutionary divergence between a known haplotype AvrPii-J and a novel one AvrPii-C was demonstrated by haplotype-specific amplicon-based sequencing and genetic transformation. The different avirulent performances of a set of seven haplotype-chimeric mutants suggested that the integrity of the full-length gene structures is crucial to express functionality of individual haplotypes. All the four combinations of phenotypes/genotypes were detected in the three southern populations, and only two in the northern three, suggesting that genic diversity in the southern region was higher than those in the northern one. The population structure of the AvrPii family was shaped by balancing, purifying, and positive selection pressures in the Chinese populations. The AvrPii-J was recognized as the wild type that emerged before rice domestication. Considering higher frequencies of avirulent isolates were detected in Hunan, Guizhou, and Liaoning, the cognate resistance gene Pii could be continuously used as a basic and critical resistance resource in such regions. The unique population structures of the AvrPii family found in China have significant implications for understanding how the AvrPii family has kept an artful balance and purity among its members (haplotypes) those keenly interact with Pii under gene-for-gene relationships. The lesson learned from case studies on the AvrPii family is that much attention should be paid to haplotype divergence of target gene.

Multi-omics analyses reveal the crosstalk between the circadian clock and the response to herbicide application in Oryza sativa.

Plants have evolved circadian clock systems that enable biological processes to occur in tandem with periodic changes in the environment. However, it is largely unknown whether crosstalk occurs between the circadian clock and the response to herbicide in rice. We identified 19 conserved rhythmic metabolites which were response to pesticide application and their metabolic abundance peaked mainly at ZT2 or ZT14-ZT18. We found a series of glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 response genes were expressed following stable circadian rhythms. In order to determine the patterns of their temporal expression, co-expression network analysis was done on 10,467 genes that were periodically expressed throughout a 24-hour period. Next, we identified 4,031 potential direct target genes of OsCCA1 in using DAP-seq data for OsCCA1. Of these, 339, 22, 53, 53 and 63 genes showed a response to glyphosate, s-Metolachlor, fenclorim, metcamifen and GA3 application, respectively. And they were mainly phased from dusk to midnight. Interestingly, we identified significant OsCCA1 binding peaks in the promoter regions of four herbicide resistance genes, including OsCYP81A12, OsCYP81E22, OsCYP76C2, and OsCYP76C4. Finally, we found that herbicide application could affects the expression of some of the central oscillator genes of the rice circadian clock. Here, we used multi-omics data to reveal the crosstalk between the circadian clock and herbicide response processes at the epigenomics, transcriptome, and metabolome levels in rice. This work will serve as a theoretical guide for identifying rhythmic herbicide targets, leading to the creation of new herbicides or the breeding of crops resistant to herbicides.

New Framework for Dynamic Water Environmental Capacity Estimation Integrating the Hydro-Environmental Model and Load-Duration Curve Method-A Case Study in Data-Scarce Luanhe River Basin.

A better understanding of river capacity for contaminants (i.e., water environmental capacity, WEC) is essential for the reasonable utilization of water resources, providing government's with guidance about sewage discharge management, and allocating investments for pollutant reduction. This paper applied a new framework integrating a modified hydro-environmental model, Soil and Water Assessment Tool (SWAT) model, and load-duration curve (LDC) method for the dynamic estimation of the NH3-N WEC of the data-scarce Luanhe River basin in China. The impact mechanisms of hydrological and temperature conditions on WEC are discussed. We found that 77% of the WEC was concentrated in 40% hydrological guarantee flow rates. While the increasing flow velocity promoted the pollutant decay rate, it shortened its traveling time in streams, eventually reducing the river WEC. The results suggest that the integrated framework combined the merits of the traditional LDC method and the mechanism model. Thus, the integrated framework dynamically presents the WEC's spatiotemporal distribution under different hydrological regimes with fewer data. It can also be applied in multi-segment rivers to help managers identify hot spots for fragile water environmental regions and periods at the basin scale.

Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields.

Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance.

BACKGROUND: Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use. RESULTS: In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR). CONCLUSIONS: This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

Colorimetric detection of blood glucose based on GOx@ZIF-8@Fe-polydopamine cascade reaction.

Zeolitic imidazolate framework-8 (ZIF-8) has become one of the most typical examples of nanostructures for multi-enzyme immobilization due to its economical, mild and easy synthesis process. However, ZIF-8 nanocrystals are easily decomposed under acidic conditions. To solve this problem, the Fe-polydopamine (Fe-PDA) was bonded with ZIF-8 surface to form ZIF-8@Fe-PDA hybrid shell with good stability. Based on this, we developed glucose oxidase@ZIF-8@Fe-PDA (GOx@ZIF-8@Fe-PDA) integrated nanozymes (INAzymes) with cascade reactions via a mild and environmentally friendly method. In order to synthesize the INAzymes, GOx was first embedded in ZIF-8 by coprecipitation (GOx@ZIF-8), and then GOx@ZIF-8 was bonded with Fe-PDA, which acted as a peroxidase mimic. The ZIF-8@Fe-PDA hybrid shell protected the INAzymes nanostructure from degradation under acidic conditions, which results in good chemical stability of the GOx@ZIF-8@Fe-PDA. In the INAzymes system, glucose is converted to gluconic acid by GOx in the presence of oxygen to produce H2O2 as an intermediate. The H2O2 reacts rapidly with Fe-PDA to generate OH, which oxidizes 3,3',5,5'-tetramethylbenzidine (TMB). The UV absorbance of oxidized TMB is directly proportional to the glucose concentration, and has a good linear relationship in the range of 5.0-100.0 µM glucose with detection limit of 1.1 µM. The INAzymes system has been successfully applied to rapid colorimetric detection of blood glucose levels. The INAzymes system exhibits high catalytic activity, excellent sensitivity, and enhanced chemical stability, playing great promise in clinical diagnosis and biosensing.

A bifunctional metal organic framework of type Fe(III)-BTC for cascade (enzymatic and enzyme-mimicking) colorimetric determination of glucose.

A metal organic framework (MOF) of type Fe(III)-BTC (where BTC is 1,3,5-benzenetricarboxylic acid) was utilized to construct an integrated system for cascade colorimetric determination of glucose. The MOF performs a dual function in acting (a) as a peroxidase (POx) mimic, and (b) as a solid support for immobilization of glucose oxidase (GOx). The MOF was prepared by a one-pot method. Glucose is consumed while H2O2 is produced during the enzymatic oxidation by GOx. In the presence of H2O2, the POx mimic catalytically oxidizes 3,3',5,5'-tetramethylbenzidine (TMB) to form a blue-green product. The absorbance of oxidized TMB (measured at 652 nm) increases linearly in the 5.0-100 µM glucose concentration range, and the detection limit is 2.4 µM. The GOx@Fe-BTC MOF was successfully applied to the determination of glucose in serum. Graphical abstract Schematic presentation of a bifunctional metal organic framework of type Fe-BTC for cascade (enzymatic and enzyme-mimicking) colorimetric determination of glucose. The Fe-BTC performs a dual function in acting as both a peroxidase mimic and support for immobilizing glucose oxidase. Using the integrated enzyme, a colorimetric method was successfully applied to one-step detection of glucose in human serum.

Polymorphism rs3819102 in thymidylate synthase and environmental factors: effects on lung cancer in Chinese population.

PURPOSE: Lung cancer is the leading cause of cancer death worldwide, and the predominant risk factor for its development is smoking. Thymidylate synthase (TYMS) is a key enzyme in DNA synthesis that catalyzes the conversion of deoxyuridine monophosphate to dTMP. Rs931794, a single nucleotide polymorphism located in the TYMS gene, was suggested to be associated with cancer risk. METHODS: To analyze the interaction between rs3819102 and environmental factors on the risk of lung cancer in a Chinese population, single nucleotide polymorphismscan was used to genotype this polymorphism in 974 lung cancer cases and 1005 control subjects. RESULTS: The frequencies of TT, CT, and CC genotypes of TYMS rs3819102 were 61.8%, 32.9%, and 5.3% in controls, and 53.8%, 38.4%, and 7.8% in cases, respectively. Compared with the TT genotype, the CT (odds ratio [OR], 1.380; 95% confidence interval [CI], 1.131-1.683), and CC (OR, 1.786; 95% CI, 1.213-2.644) genotypes were associated with an increased risk of lung cancer after adjustment for age, gender, smoking status, and family history. The C allele of rs3819102 is the risk allele for lung carcinogenesis in a dominant model (OR, 1.435; 95% CI, 1.188-1.735). In a stratified analysis, the risk effects of both the CT and CC genotypes of rs3819102 were more evident in subgroups of smokers and people without a family history of cancer. CONCLUSION: The rs3819102 polymorphism in TYMS might increase susceptibility to environmental factors and contribute to the risk of lung cancer. The C allele is a risk allele in lung carcinogenesis.

The Race Structure of the Rice Blast Pathogen Across Southern and Northeastern China.

BACKGROUND: Rice blast, caused by the ascomycete Magnaporthe oryzae (Mo), imposes a major constraint on rice productivity. Managing the disease through the deployment of host resistance requires a close understanding of race structure of the pathogen population. RESULTS: The host/pathogen interaction between isolates sampled from four Mo populations collected across the rice-producing regions of China was tested using two established panels of differential cultivars. The clearest picture was obtained from the Chinese cultivar panel, for which the frequency of the various races, the race diversity index, the specific race isolate frequency, and the frequency of the three predominant races gave a consistent result, from which it was concluded that the pathogen population present in the southern production region was more diverse than that in the northeastern region. The four blast resistance genes Pi1, Pik, Pik-m, and Piz all still remain effective in the southern China rice production area, as does Pi1 in the northeastern region. The effectiveness of Pita, Pik-p, Piz, and Pib is restricted to single provinces. The distinctive resistance profile shown by the Chinese differential cultivar set implied the presence of at least five as yet unidentified blast resistance genes. CONCLUSIONS: The Chinese differential cultivar set proved to be more informative than the Japanese one for characterizing the race structure of the rice blast pathogen in China. A number of well characterized host resistance genes, in addition to some as yet uncharacterized ones, remain effective across the major rice production regions in China.

Expression and purification of human TAT-p53 fusion protein in Pichia pastoris and its influence on HepG2 cell apoptosis.

P53 is an attractive target in molecular cancer therapeutics because of its critical role in regulating cell cycle arrest and apoptosis. The limitations in the development of p53-based cancer therapeutic strategy include its inefficient transmission through cell membrane of tumor cells and low protein yields in the expression system. In the present study, p53 was fused with HIV TAT protein, which can cross cell membranes, and expressed by Pichia pastoris. Stable production of Tat-p53 was achieved. After being transduced with Tat-p53 protein, the growth of cancer cell line, HepG2, was inhibited by increased apoptosis in culture. This expression system could thus be utilized to produce human Tat-p53 fusion protein.

Characterization and fine mapping of the rice blast resistance gene Pia.

Blast, caused by Magnaporthe oryzae, is one of the most widespread and destructive diseases of rice. Breeding durable resistant cultivars (cvs) can be achieved by pyramiding of various resistance (R) genes. Pia, carried by cv. Aichi Asahi, was evaluated against 612 isolates of M. oryzae collected from 10 Chinese provinces. The Pia gene expresses weak resistance in all the provinces except for Jiangsu. Genomic position-ready marker-based linkage analysis was carried out in a mapping population consisting of 800 F(2) plants derived from a cross of Aichi Asahi×Kasalath. The locus was defined in an interval of approximately 90 kb, flanked by markers A16 and A21. Four candidate genes (Pia-1, Pia-2, Pia-3, and Pia-4), all having the R gene conserved structure, were predicted in the interval using the cv. Nipponbare genomic sequence. Four candidate resistance gene (CRG) markers (A17, A25, A26, and A27), derived from the four candidates, were subjected to genotyping with the recombinants detected at the flanking markers. The first three markers completely co-segregated with the Pia locus, and the fourth was absent in the Aichi Asahi genome and disordered with the Pia locus and its flanking markers, indicating that the fourth candidate gene, Pia-4, could be excluded. Co-segregation marker-based genotyping of the three sets of differentials with known R gene genotypes revealed that the genotype of A26 (Pia-3) perfectly matched the R gene genotype of Pia, indicating that Pia-3 is the strongest candidate gene for Pia.

Ceramide from sphingomyelin hydrolysis differentially mediates mitogen-activated protein kinases (MAPKs) activation following cerebral ischemia in rat hippocampal CA1 subregion.

OBJECTIVE: To explore the role that ceramide plays in the activation of mitogen-activated protein kinases (MAPKs) during cerebral ischemia and reperfusion. METHODS: Rats were subjected to ischemia by the four-vessel occlusion (4-VO) method. The sphingomyelinase inhibitor TPCK was administered to the CA1 subregion of the rat hippocampus before inducing ischemia. Western blot was used to examine the activity of extracellular-signal regulated kinase (ERK) and c-Jun N-terminal protein kinase (JNK) using antibodies against ERK, JNK and diphosphorylated ERK and JNK. RESULTS: At 1h reperfusion post-ischemia, JNK reached its peak activity while ERK was undergoing a sharp inactivation (P < 0.05). The level of diphosphorylated JNK was significantly reduced but the sharp inactivation of ERK was visibly reversed (P < 0.05) by the sphingomyelinase inhibitor. CONCLUSION: The ceramide signaling pathway is up-regulated through sphingomyelin hydrolysis in brain ischemia, promoting JNK activation and suppressing ERK activation, culminating in the ischemic lesion.