Non-targeted GC-MS metabolomics-based differences in Indica rice seeds of different varieties.

Rice seeds of different varieties exhibited distinct metabolic profiles in our study. We analyzed the metabolites in seeds of six rice varieties (CH, HM, NX, YX, HY, and MX) using non-targeted GC-MS. Our findings revealed that amino acids, sugars, and organic acids were predominant in all varieties, with significant differences observed in CH compared to the others. Specifically phenylalanine and glycine content differed notably in NX and YX, respectively. Additionally, 1,5-anhydroglucitol content in NX, and glutamate, aspartate, and lactulose in NX, YX, HM, HY, and MX were up-regulated. Due to the biological functions of these amino acids and sugars, these indicated that compared to CH, rice of NX were more conducive to metabolism of carbohydrate and fat, and healthy growth maintenance in the human body, but mightThese variations suggest that NX rice may be more beneficial for carbohydrate and fat metabolism and overall health maintenance compared to CH. However, it may not be suitable for diabetic patients. YX rice may not be an ideal glycine supplement, rice ofwhile HM, HY, and MX rice could serve as potential lactulose sources. Furthermore, NX and YX rice exhibited higher levels of main storage proteins compared to CH. This study offers valuable insights into the metabolic differences among various rice varieties.

Re-rolling treatment in the fermentation process improves the taste and liquor color qualities of black tea.

Fermentation is a vital process occurred under the premise of rolling affecting black tea quality. Theoretically, re-rolling during fermentation will remodel the biochemical conditions of tea leaves, and thus influence black tea quality. Herein, we studied the effect of re-rolling on black tea taste and liquor color. Sensory evaluation showed that re-rolling significantly weakened the astringency taste and improved the redness and luminance of liquor. With re-rolling, the color attributes of a* and L* and the contents of theaflavins and thearubigins were significantly improved. Metabolomics analysis showed that the contents of 110 non-volatile compounds were significantly different among black teas with different rolling treatments. In summary, re-rolling accelerated the oxidation of polyphenols into pigments, the hydrolysis of proteins into amino acids, and the metabolism of alkaloids, organic acids, glycosidically-bound volatiles, and lipids during the fermentation period. Our study provided a novel and simple way to improve black tea quality.

Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq.

BACKGROUND: Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. RESULTS: In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. CONCLUSION: Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.

Re-Rolling Treatment in the Fermentation Process Improves the Aroma Quality of Black Tea.

Aroma is a vital factor influencing tea quality and value. It is a challenge to produce a kind of black tea with a floral/fruity aroma, good taste, and without a green/grassy odor simultaneously using small- and medium-leaf tea species. In this study, the effect of re-rolling treatment on the aroma quality of small-leaf Congou black tea was investigated using the methods of the equivalent quantification of aroma and gas chromatography-mass spectrometry (GC-MS). Sensory evaluation showed that re-rolling treatment improved the aroma quality of Congou black tea by conferring upon it floral and fruity scents. In total, 179 volatile compounds were identified using GC-MS, of which 97 volatiles showed statistical differences (Tukey s-b(K), p < 0.05). Re-rolling treatment significantly reduced the levels of alcoholic fatty acid-derived volatiles (FADVs) and volatile terpenoid (VTs), but increased the levels of aldehydic and ester FADVs, most amino acid-derived volatiles (AADVs), carotenoid-derived volatiles (CDVs), alkene VTs, and some other important volatile compounds. Based on the odor characteristics and fold changes of differential volatile compounds, hexanoic acid, hexyl formate, cis-3-hexenyl hexanoate, (Z)-3-hexenyl benzoate, hexyl hexanoate, phenylacetaldehyde, benzyl alcohol, ß-ionone, α-ionone, dihydroactinidiolide, ipsenone, ß-farnesene, ß-octalactone, melonal, etc., were considered as the potential key odorants responsible for the floral and fruity scents of re-rolled black tea. In summary, this study provides a novel and simple processing technology to improve the aroma quality of small-leaf Congou black tea, and the results are beneficial to enriching tea aroma chemistry.

Free radical formation via BDE-209 thermolysis in the precalciner of a cement kiln: Simulation and DFT study.

To deeply understand the formation mechanism of polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) in the thermal disposal process of polybrominated diphenyl ether (PBDE)-containing waste, this paper studied the formation pathways of key intermediates (free radicals, FRs) in the formation process of PBDD/Fs. BDE-209, the most common PBDE in the environment, was selected as the object of study to analyze FR formation by simulating the key conditions such as temperature (850 °C) and Fe-based materials when PBDE-containing waste entering cement kiln precalciner. Electron paramagnetic resonance (EPR) spectroscopy and density functional theory (DFT) calculations were used to study the reaction. The result of simulation experiments revealed carbon-centered radicals, and DMPO-OH analysis further confirmed the generation of FRs. The findings confirmed previous calculations predicting the existence of radical intermediates during the formation of PBDD/Fs from BDE-209. DFT calculations revealed the existence of an inner ortho-position CBr bond in BDE-209. The priority order of the bond breaking of BDE-209 was ether bond, inner ortho-position CBr bond, and outside ortho-position CBr bond. BDE-209 can further form three kinds of FRs, namely, oxygen-centered radicals of single benzene rings, carbon-centered radicals of single benzene rings, and carbon-centered radicals of double benzene rings. The specific processes of FR formation were inferred: high-temperature homogeneous cleavage of chemical bonds, electron transfer, and chemisorption, where electron transfer and chemisorption may be more important pathways. The proposed inner ortho-position cleavage within BDE-209 provides new insights into the degradation of PBDEs and the formation of PBDD/Fs; the results regarding BDE-209 generation radicals further elucidate the synthesis mechanism of dioxins, which is important for controlling dioxin generation and emission during the treatment and disposal of waste containing PBDEs.

Effects of cadmium on the synthesis of active ingredients in Salvia miltiorrhiza.

Cadmium (Cd) could pose threats to human health by affecting Salvia miltiorrhiza (SM) safety. Cd enrichment trait and its effects on the active ingredient synthesis in SM remain unknown. Here we investigated the Cd concentration using ICP-MS-based method, physiologies (contents of malondialdehyde and proline, and activities of superoxide dismutase, peroxidase [POD], and catalase [CAT]), and LC-MS/MS-based metabolites of SM under 25, 50, and 100 mg kg-1 Cd stress. The results revealed that Cd concentrations, as it rose in soil, increased in roots and leaves of SM with transfer factors and bioconcentration factors below 1 in Cd-treated groups; POD and CAT activities and proline content increased and then declined. Amino acids and organic acids (especially d-glutamine [d-Gln], l-aspartic acid [l-Asp], l-phenylalanine [l-Phe], l-tyrosine [l-Tyr], geranylgeranyl-PP [GGPP], and rosmarinic acid [RA]) contributed more in discriminating SM roots of different groups. GGPP was negatively related to l-Tyr and l-Phe, and RA was positively related to d-Gln and l-Asp in SM. These results revealed that SM belonged to a non-Cd-hyperaccumulator with most Cd accumulated in roots, Cd could enhance phenolic acid synthesis via regulating amino acid metabolism and might inhibit tanshinone synthesis by declining the GGPP content, and proline, POD, and CAT played vital roles in resisting Cd stress. These provided new ideas and theoretical basis for further study on medical plants' response to heavy metals.

Physiological and Transcriptomic Analyses Reveal the Mechanisms of Compensatory Growth Ability for Early Rice after Low Temperature and Weak Light Stress.

"Late spring coldness" (T) is a frequent meteorological disaster in the spring in southern China, often causing severe yield losses of direct-seeded early rice. In this study, we investigated the mechanisms underlying the differences in the compensatory growth ability of different rice genotypes by focusing on agronomic traits, physiological indicators, and transcriptome. The results showed that there were significant differences in the compensatory growth recovery ability of different genotypes after a combination of four days of low temperature and weak light stress. Only the strong compensatory growth genotype B116 was able to grow rapidly and reduce soluble protein and H2O2 concentrations rapidly after stress. By analyzing enzyme activity as well as endogenous hormone concentration, we found that the high superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and high levels of abscisic acid (ABA) could reduce the damage of B116 during stress. Meanwhile, higher glutamine synthetase (GS) and nitrate reductase (NR) activity and higher levels of gibberellin A3(GA3), indoleacetic acid (IAA), and zeatin nucleoside (ZR) could enable B116 to grow rapidly after stress. The identified differentially expressed genes (DEGs) indicated that there were large differences in POD-related genes and gibberellin metabolism between B116 and B144 after stress; RT-PCR quantification also showed a trend consistent with RNA-seq, which may be an important reason for the differences in compensatory growth ability.

Untargeted LC-MS/MS-Based Metabolomic Profiling for the Edible and Medicinal Plant Salvia miltiorrhiza Under Different Levels of Cadmium Stress.

Salvia miltiorrhiza, a medicinal and edible plant, has been extensively applied to treat cardiovascular diseases and chronic hepatitis. Cadmium (Cd) affects the quality of S. miltiorrhiza, posing serious threats to human health. To reveal the metabolic mechanisms of S. miltiorrhiza's resistance to Cd stress, metabolite changes in S. miltiorrhiza roots treated with 0 (CK), 25 (T1), 50 (T2) and 100 (T3) mg kg-1 Cd by liquid chromatography coupled to mass spectrometry (LC-MS/MS) were investigated. A total of 305 metabolites were identified, and most of them were amino acids, organic acids and fatty acids, which contributed to the discrimination of CK from the Cd-treated groups. Among them, S. miltiorrhiza mainly upregulated o-tyrosine, chorismate and eudesmic acid in resistance to 25 mg kg-1 Cd; DL-tryptophan, L-aspartic acid, L-proline and chorismite in resistance to 50 mg kg-1 Cd; and L-proline, L-serine, L-histidine, eudesmic acid, and rosmarinic acid in resistance to 100 mg kg-1 Cd. It mainly downregulated unsaturated fatty acids (e.g., oleic acid, linoleic acid) in resistance to 25, 50, and 100 mg kg-1 Cd and upregulated saturated fatty acids (especially stearic acid) in resistance to 100 mg kg-1 Cd. Biosynthesis of unsaturated fatty acids, isoquinoline alkaloid, betalain, aminoacyl-tRNA, and tyrosine metabolism were the significantly enriched metabolic pathways and the most important pathways involved in the Cd resistance of S. miltiorrhiza. These data elucidated the crucial metabolic mechanisms involved in S. miltiorrhiza Cd resistance and the crucial metabolites that could be used to improve resistance to Cd stress in medicinal plant breeding.

Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice.

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn't any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.

qTGW12a, a naturally varying QTL, regulates grain weight in rice.

KEY MESSAGE: A stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation. Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality. Therefore, the discovery and identification of rice grain size genes can provide pathways for the cultivation of high-yielding varieties. In the present work, 45,607 SNP markers were used to construct a high-density genetic map of rice recombinant inbred lines, and hence a total of 14 quantitative trait loci (QTLs) were detected based on the phenotypic data of grain weight, grain length and grain width under four different environments. qTGW12a and qGL12 are newly detected QTLs related to grain weight, and are located between 22.43 Mb and 22.45 Mb on chromosome 12. Gene annotation shows that the QTL region contains the LOC_Os12g36660 annotated gene, which encodes the multidrug and toxic compound extrusion (MATE) transporter. Mutations in exons and the splice site were responsible for the changes in grain type and weight. Gene knockout experiments were used to verify these results. Hence, these results provide a basis for the cloning of qTGW12a. This discovery provides new insights for studying the genetic mechanism of rice grain morphology, and reveals a promising gene to ultimately increase rice yield.

Research on Hazardous Waste Removal Management: Identification of the Hazardous Characteristics of Fluid Catalytic Cracking Spent Catalysts.

Fluid catalytic cracking (FCC) spent catalysts are the most common catalysts produced by the petroleum refining industry in China. The National Hazardous Waste List (2016 edition) lists FCC spent catalysts as hazardous waste, but this listing is very controversial in the petroleum refining industry. This study collects samples of waste catalysts from seven domestic catalytic cracking units without antimony-based passivation agents and identifies their hazardous characteristics. FCC spent catalysts do not have the characteristics of flammability, corrosiveness, reactivity, or infectivity. Based on our analysis of the components and production process of the FCC spent catalysts, we focused on the hazardous characteristic of toxicity. Our results show that the leaching toxicity of the heavy metal pollutants nickel, copper, lead, and zinc in the FCC spent catalyst samples did not exceed the hazardous waste identification standards. Assuming that the standards for antimony and vanadium leachate are 100 times higher than that of the surface water and groundwater environmental quality standards, the leaching concentration of antimony and vanadium in the FCC spent catalyst of the G set of installations exceeds the standard, which may affect the environmental quality of surface water or groundwater. The quantities of toxic substances in all spent FCC catalysts, except those from G2, does not exceed the standard. The acute toxicity of FCC spent catalysts in all installations does not exceed the standard. Therefore, we exclude "waste catalysts from catalytic cracking units without antimony-based passivating agent passivation nickel agent" from the "National Hazardous Waste List."

Genome-wide identification and comprehensive analysis of NAC family genes involved in fruit development in kiwifruit (Actinidia).

BACKGROUND: NAC transcription factors (TFs) are plant-specific proteins encoded by a large gene family. They play important roles in diverse biological processes, such as plant growth and development, leaf senescence, and responses to biotic or abiotic stresses. Functions of a number of NAC TFs have been identified mainly in model plants. However, very few studies on NAC TFs have been conducted in the fruit tree of kiwifruit. RESULTS: Genome-wide NAC genes were identified and their phylogeny, genomic structure, chromosomal location, synteny relationships, protein properties and conserved motifs were analyzed. In addition, the fruit developmental process was evaluated in a new kiwifruit cultivar of Actinidia eriantha 'Ganlu 1'. And expressions for all those NAC genes were analyzed by quantitative real-time PCR method in fruits of 'Ganlu 1' during its developmental process. Our research identified 142 NAC TFs which could be phylogenetically divided into 23 protein subfamilies. The genomic structures of those NAC genes indicated that their exons were between one and ten. Analysis of chromosomal locations suggested that 116 out of 142 NACs distributed on all the 29 kiwifruit chromosomes. In addition, genome-wide gene expression analysis showed that expressions of 125 out of 142 NAC genes could be detected in fruit samples. CONCLUSION: Our comprehensive study provides novel information on NAC genes and expression patterns in kiwifruit fruit. This research would be helpful for future functional identification of NAC genes involved in kiwifruit fruit development.

Distribution and toxicity of polycyclic aromatic hydrocarbons during CaO-assisted hydrothermal carbonization of sewage sludge.

Hydrothermal carbonization (HTC) of sewage sludge (SS) with and without calcium oxide (CaO) introduction was conducted at 160-240 °C, and the yield and distribution of polycyclic aromatic hydrocarbons (PAHs) were evaluated for the first time. PAHs (2972.99 µg/kg) and toxic equivalent quantity (TEQ) (373.09 µg/kg) yields in SS decreased by 13.61% and 14.65%, respectively, after treatment at 160 °C and substantially increased as temperatures increased. More PAHs were distributed in the hydrochar than in the aqueous products. Hydrochar yields decreased linearly with temperature, thus increasing PAH concentration in hydrochar; 6221.98 µg/kg of PAHs in hydrocar at 240 °C exceeded agricultural use standard limits. PAH and TEQ yields at 200 °C decreased by 5.55-15.98% and 2.88-3.54%, respectively, when 3-9% CaO was added, which could be ascribed to CaO inhibition in the free radical reaction for PAH generation. Additionally, 6% CaO addition substantially weakened the acceleration effect of high temperatures on PAH formation; the decrease of PAH yield at 240 °C was 22.14%, which is higher than that at other temperatures. Consequently, the PAH concentration in hydrochar declined by 2.33-22.37%. PAH content in hydrochar obtained from CaO-assisted HTC of SS fell within agriculture use standard limit and exhibits potential for use as a soil conditioner. However, condition with a CaO amount of 15% would significantly increase TEQ yields. Considering both PAH and TEQ yields and the ecological risks of PAHs in hydrochar derived from HTC of SS, the appropriate reaction conditions were found to be 200 °C with 3-6% added CaO.

Prevalent intron retention fine-tunes gene expression and contributes to cellular senescence.

Intron retention (IR) is the least well-understood alternative splicing type in animals, and its prevalence and function in physiological and pathological processes have long been underestimated. Cellular senescence contributes to individual aging and age-related diseases and can also serve as an important cancer prevention mechanism. Dynamic IR events have been observed in senescence models and aged tissues; however, whether and how IR impacts senescence remain unclear. Through analyzing polyA+ RNA-seq data from human replicative senescence models, we found IR was prevalent and dynamically regulated during senescence and IR changes negatively correlated with expression alteration of corresponding genes. We discovered that knocking down (KD) splicing factor U2AF1, which showed higher binding density to retained introns and decreased expression during senescence, led to senescence-associated phenotypes and global IR changes. Intriguingly, U2AF1-KD-induced IR changes also negatively correlated with gene expression. Furthermore, we demonstrated that U2AF1-mediated IR of specific gene (CPNE1 as an example) contributed to cellular senescence. Decreased expression of U2AF1, higher IR of CPNE1, and reduced expression of CPNE1 were also discovered in dermal fibroblasts with age. We discovered prevalent IR could fine-tune gene expression and contribute to senescence-associated phenotypes, largely extending the biological significance of IR.

A bioenergetic shift is required for spermatogonial differentiation.

A bioenergetic balance between glycolysis and mitochondrial respiration is particularly important for stem cell fate specification. It however remains to be determined whether undifferentiated spermatogonia switch their preference for bioenergy production during differentiation. In this study, we found that ATP generation in spermatogonia was gradually increased upon retinoic acid (RA)-induced differentiation. To accommodate this elevated energy demand, RA signaling concomitantly switched ATP production in spermatogonia from glycolysis to mitochondrial respiration, accompanied by increased levels of reactive oxygen species. Disrupting mitochondrial respiration significantly blocked spermatogonial differentiation. Inhibition of glucose conversion to glucose-6-phosphate or pentose phosphate pathway also repressed the formation of c-Kit+ differentiating germ cells, suggesting that metabolites produced from glycolysis are required for spermatogonial differentiation. We further demonstrated that the expression levels of several metabolic regulators and enzymes were significantly altered upon RA-induced differentiation, with both RNA-seq and quantitative proteomic analyses. Taken together, our data unveil a critically regulated bioenergetic balance between glycolysis and mitochondrial respiration that is required for spermatogonial proliferation and differentiation.

Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice.

Abrupt drought-flood alternation is a frequent meteorological disaster during the summer in Southern China. The study of physiological and translation mechanisms of rice yield recovery after abrupt drought-flood alternation has great potential benefits in field production. Our results showed that yield recovery upon nitrogen (N) application after abrupt drought-flood alternation was due to the increase in effective panicle numbers per plant. The N application resulted in the regulation of physiological and biochemical as well as growth development processes, which led to a rapid growth recovery effect after abrupt drought-flood alternation stress in rice. Using ribosome profiling combined with RNA sequencing (RNA-seq) technology, the interactions between transcription and translation for N application after abrupt drought-flood alternation were analyzed. It was found that a small proportion of response genes were shared at the transcriptional and translational levels, that is, 14% of the expressed genes were upregulated and 6.6% downregulated. Further analysis revealed that the translation efficiency (TE) of the genes was influenced by their sequence characteristics, including their GC content, coding sequence length and normalized minimal free energy. Compared with the number of untranslated upstream open reading frames (uORFs), the increased number of translated uORFs promoted the improvement of TE. The TE of the uORFs for N application was lower than the control without N application after abrupt drought-flood alternation. This study characterizes the translational regulatory pattern in response to N application after abrupt drought-flood alternation stress.

Tempo-spatial alternative polyadenylation analysis reveals that 3' UTR lengthening of Mdm2 regulates p53 expression and cellular senescence in aged rat testis.

Although tissue aging is accompanied with cellular senescence, it is much complicated than senescence given both types and number of cells change with age. Alternative polyadenylation (APA) had shown tissue specificity and APA-mediated 3' untranslated region (3' UTR) lengthening could regulate senescence-associated phenotypes. However, whether tissue aging shows similar trends remains unknown. Here, we performed a comprehensive analysis on RNA-seq datasets derived from multiple cells and rat tissues of young and old age. Although APA-mediated 3' UTR lengthening in various senescent cells reinforced the previous discovery, tissue aging showed much more complexity in APA. Interestingly, testis was the only tissue displaying dramatic 3' UTR lengthening and decreased expression trend of corresponding genes in aged rat. Genes with longer 3' UTR in aged testis were enriched in senescence-associated pathways, among which, Mdm2, encoding an E3 ligase of p53, favored distal poly(A) site resulting in lengthened 3' UTR and decreased expression. Longer 3' UTR of Mdm2 generated less protein, and decreased Mdm2 expression led to senescence-associated phenotypes along with increased p53 and p21 protein abundance, which could all be reversed by Mdm2 overexpression. Our work revealed complicated APA changes during tissue aging and discovered APA-mediated 3' UTR lengthening of Mdm2 is a hidden layer in regulating the well-known senescence-related p53-p21 signal axis during testis aging, and also has potential implications regarding declined male fertility along aging.

Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana.

The post-transcriptional regulation involved in the responses of diatoms to silicon is poorly understood. Using a poly(A)-tag sequencing (PAT-seq) technique that interrogates only the junctions of 3'-untranslated region (UTR) and the poly(A) tails at the transcriptome level, a comprehensive comparison of alternative polyadenylation (APA) was performed to understand the role of post-transcriptional regulation in various silicon-related cellular responses for the marine diatom Thalassiosira pseudonana. In total, 23 701 poly(A) clusters and 6894 APA genes, treated with silicon starvation and replenishment, were identified at nine time points. Significant APA was found in numerous genes (e.g. five cingulin genes) closely associated with the silicon-starvation response, girdle bands and valve synthesis, suggesting that many genes participated in the responses to silicon availability and biosilica formation through changes in transcript isoforms. The poly(A) site usage profiles were distinct during various stages of silicon biomineralization responses. Moreover, a correlation between APA and expression levels of APA switching genes was also discovered. This is an interesting study that presents a genome-wide profile of transcript ends in diatoms, which is distinct from that of higher plants, animals and other microalgae. This work provides an important resource to understand a different aspect of cell-wall synthesis.

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica.

Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.

Mercury in soil, vegetable and human hair in a typical mining area in China: Implication for human exposure.

Concentrations of total mercury (T-Hg) and methylmercury (MeHg) in soil, vegetables, and human hair were measured in a mercury mining area in central China. T-Hg and MeHg concentrations in soil ranged from 1.53 to 1054.97mg/kg and 0.88 to 46.52µg/kg, respectively. T-Hg concentrations was correlated with total organic carbon (TOC) content (R2=0.50, p<0.01) and pH values (R2=0.21, p<0.05). A significant linear relationship was observed between MeHg concentrations and the abundance of sulfate-reducing bacteria (SRB) (R2=0.39, p<0.05) in soil. Soil incubation experiments amended with specific microbial stimulants and inhibitors showed that Hg methylation was derived from SRB activity. T-Hg and MeHg concentrations in vegetables were 24.79-781.02µg/kg and 0.01-0.18µg/kg, respectively; levels in the edible parts were significantly higher than in the roots (T-Hg: p<0.05; MeHg: p<0.01). Hg species concentrations in rhizosphere soil were positively correlated to those in vegetables (p<0.01), indicating that soil was an important source of Hg in vegetables. Risk assessment indicated that the consumption of vegetables could result in higher probable daily intake (PDI) of T-Hg than the provisional tolerable daily intake (PTDI) for both adults and children. In contrast, the PDI of MeHg was lower than the reference dose. T-Hg and MeHg concentrations in hair samples ranged from 1.57 to 12.61mg/kg and 0.04 to 0.94mg/kg, respectively, and MeHg concentration in hair positively related to PDI of MeHg via vegetable consumption (R2=0.39, p<0.05), suggesting that vegetable may pose health risk to local residents.