Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents.

Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes that modulates gene expression by generating transcript variants. The development of young panicles in rice is a critical stage that determines grain number and weight. However, the regulatory mechanisms and inheritance patterns of APA during this process remain poorly understood.

Integrating transcriptomics and proteomics to analyze new regulatory genes related to rice grain development.

The regulation of seed size in rice represents a significant concern within the domain of developmental biology. Nevertheless, our understanding of the mechanisms by which plants determine seed size remains limited, despite its critical importance. The transcriptome and proteome sequencing of rice kernels, derived from the recombinant inbred line (RIL) population between the large-grain line AD3 and the small-grain line AD148, were conducted at the third stage of spikelet development (stage Sp 3: formation of lemma primordium), the sixth stage of spikelet development (stage Sp 6: formation of stamen primordia), as well as nine days post anthesis (9DPA).

Identification of the gene family in rice () and its response to rice blast.

To better understand RNA-binding proteins in rice, a comprehensive investigation was conducted on the gene family of rice. It encompassed genome-wide identification and exploration of its role in rice blast resistance. The physicochemical properties of the rice gene family were analyzed.

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.

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.

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.

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).

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.

Effects of cadmium on the synthesis of active ingredients in .

Cadmium (Cd) could pose threats to human health by affecting (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 Cd stress.

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.

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

, a medicinal and edible plant, has been extensively applied to treat cardiovascular diseases and chronic hepatitis. Cadmium (Cd) affects the quality of , posing serious threats to human health. To reveal the metabolic mechanisms of 's resistance to Cd stress, metabolite changes in roots treated with 0 (CK), 25 (T1), 50 (T2) and 100 (T3) mg kg Cd by liquid chromatography coupled to mass spectrometry (LC-MS/MS) were investigated.

Fine Mapping of a Novel Major Quantitative Trait Locus, , 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 Changhui121 as the recurrent parent and Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, , and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

[Effects of Microbial Activities on Mercury Methylation in Farmland near Mercury Mining Area].

In order to study the main effect of microbial activities on mercury(Hg) methylation in farmland, mercury contaminated upland soils and paddy soils near Hg mining area were sampled as experimental soils. Four treatments were designed including only sterilization as the control, accelerating the activities of sulfate reducing bacteria(SRB), inhibiting the SRB's activities, and accelerating the activities of iron-reducing bacteria(FeRB), to know the effects of microbial and non-microbial factors on mercury methylation in soils. The results were as follows:the highest concentration of methylmercury(MeHg) was observed in soils with SRB accelerated treatment, and the increments of MeHg concentrations in upland soils and paddy soils ranged from 0.

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.

Position-specific intron retention is mediated by the histone methyltransferase SDG725.

Background: Intron retention (IR), the most prevalent alternative splicing form in plants, plays a critical role in gene expression during plant development and stress response. However, the molecular mechanisms underlying IR regulation remain largely unknown.

Results: Knockdown of SDG725, a histone H3 lysine 36 (H3K36)-specific methyltransferase in rice, leads to alterations of IR in more than 4700 genes.