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Frequency and intensity of wildfires are expected to increase due to climate change, especially in areas with a long summer drought. Forests are a major sink for the global pollutant mercury (Hg), and fluvial transport of Hg from recently burned watersheds has not been widely investigated. Here, we examined two years of fluvial transport of Hg and its speciation (total Hg, methyl-Hg, particulate, and dissolved forms) under storm events and baseflow in two recently burned watersheds with different burned proportions and one nonburned reference watershed in the Coastal Ranges of northern California. We examined postfire storm-event transport of Hg and its methylated form (methyl-Hg), addressed the importance of the initial runoff pulse to postfire Hg fluvial transport and its predominant association with suspended solids, and elucidated potential sources of Hg exports from the burned landscapes using geochemical indicators, which suggested that ash materials were likely the significant sources of particulates in the first high-flow season postfire but not subsequently. The maximum total suspended solid and total Hg levels in the first pulse at the severely burned watershed were 442 and 46 times higher, respectively, than those at the reference watershed. Stream suspended solid and Hg levels declined substantially in the burned watersheds after just a few months of rainfall likely due to the rapid regrowth of vegetation commonly observed in postfire landscapes, implying that the wildfire effects on immediate Hg inputs from the burned landscape are at most transient in nature.

Tea is one of the worlds most popular and widely consumed beverages. It is a common pastime to enjoy a cup of tea in the sunshine. However, little attention has been given to understanding the possible photochemical reactions occurring beneath the calm surface of brewed tea. Epigallocatechin gallate (EGCG), which is widely used in food and beverages, is the most significant active ingredient found in tea. In this study, we investigated the presence of free radicals in both an aqueous EGCG solution and brewed tea under simulated sunlight conditions. To our surprise, we unexpectedly observed the production of hydroxyl radicals (•OH) in brewed tea. It was found that sunlight irradiation played a critical role in the formation of •OH, independent of the presence of metal ions. Furthermore, we demonstrated that the •OH generated from the EGCG aqueous solution induced cell cytotoxicity and DNA damage in vitro. Considering the crucial role of •OH in various fields, including human health and the environment, it is important to further explore the practical implications of •OH production in brewed tea under sunlight. In summary, our study unveils the unexpected formation of •OH in brewed tea and emphasizes the significance of sunlight-induced reactions. The observed cytotoxic and DNA-damaging effects of •OH emphasize the importance of understanding the potential health consequences associated with tea consumption. Further research in this area will contribute to a better understanding of the broader implications of •OH production in brewed tea under sunlight.

BackgroundThe polygenic nature of Alzheimer's disease (AD) suggests that multiple variants jointly contribute to disease susceptibility. As an individual's genetic variants are constant throughout life, evaluating the combined effects of multiple disease-associated genetic risks enables reliable AD risk prediction. Because of the complexity of genomic data, current statistical analyses cannot comprehensively capture the polygenic risk of AD, resulting in unsatisfactory disease risk prediction. However, deep learning methods, which capture nonlinearity within high-dimensional genomic data, may enable more accurate disease risk prediction and improve our understanding of AD etiology. Accordingly, we developed deep learning neural network models for modeling AD polygenic risk.MethodsWe constructed neural network models to model AD polygenic risk and compared them with the widely used weighted polygenic risk score and lasso models. We conducted robust linear regression analysis to investigate the relationship between the AD polygenic risk derived from deep learning methods and AD endophenotypes (i.e., plasma biomarkers and individual cognitive performance). We stratified individuals by applying unsupervised clustering to the outputs from the hidden layers of the neural network model.ResultsThe deep learning models outperform other statistical models for modeling AD risk. Moreover, the polygenic risk derived from the deep learning models enables the identification of disease-associated biological pathways and the stratification of individuals according to distinct pathological mechanisms.ConclusionOur results suggest that deep learning methods are effective for modeling the genetic risks of AD and other diseases, classifying disease risks, and uncovering disease mechanisms.

Soil carbohydrates, such as glucose and fructose, are essential components of soil organic matter (SOM). They serve as the primary carbon and energy sources for soil microorganisms and play a crucial role in regulating SOM stability, both directly and indirectly. Despite their ecological importance, the transformation processes and forms of soil carbohydrates are still not well-understood, despite centuries of extensive study. The use of stable carbon isotopes as natural tracers offers distinct advantages over radioisotope techniques, including safety, cleanliness, and ease of control. As a result, stable carbon isotope analysis has been widely employed in soil carbon cycling research. The examination of carbon isotopic variation in carbohydrates using stable carbon isotope tracers contributes to our understanding of carbohydrate transformation and accumulation processes within the plant-soil-microorganism system. It also enhances our comprehension of soil carbon metabolism. This paper provides an introduction to the types, sources, and pretreatment methods of soil carbohydrates. Furthermore, it reviews the theory and methods of stable carbon isotope analysis as applied to carbohydrates and their relevance to the study of soil carbon cycling. Lastly, it offers a comprehensive summary of current research challenges and prospects for future advancements in soil carbon cycling research.

Recent findings regarding nicotinamide adenine dinucleotide (NAD+)-capped RNAs (NAD-RNAs) indicate that prokaryotes and eukaryotes employ noncanonical RNA capping to regulate gene expression. Two methods for transcriptome-wide analysis of NAD-RNAs, NAD captureSeq and NAD tagSeq, are based on copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry to label NAD-RNAs. However, copper ions can fragment/degrade RNA, interfering with the analyses. Here we report development of NAD tagSeq II, which uses copper-free, strain-promoted azide-alkyne cycloaddition (SPAAC) for labeling NAD-RNAs, followed by identification of tagged RNA by single-molecule direct RNA sequencing. We used this method to compare NAD-RNA and total transcript profiles of Escherichia coli cells in the exponential and stationary phases. We identified hundreds of NAD-RNA species in E. coli and revealed genome-wide alterations of NAD-RNA profiles in the different growth phases. Although no or few NAD-RNAs were detected from some of the most highly expressed genes, the transcripts of some genes were found to be primarily NAD-RNAs. Our study suggests that NAD-RNAs play roles in linking nutrient cues with gene regulation in E. coli.

Nicotinamide adenine diphosphate (NAD+) is a novel messenger RNA 5' cap in Escherichia coli, yeast, mammals, and Arabidopsis Transcriptome-wide identification of NAD+-capped RNAs (NAD-RNAs) was accomplished through NAD captureSeq, which combines chemoenzymatic RNA enrichment with high-throughput sequencing. NAD-RNAs are enzymatically converted to alkyne-RNAs that are then biotinylated using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Originally applied to E. coli RNA, which lacks the m7G cap, NAD captureSeq was then applied to eukaryotes without extensive verification of its specificity for NAD-RNAs vs. m7G-capped RNAs (m7G-RNAs). In addition, the Cu2+ ion in the CuAAC reaction causes RNA fragmentation, leading to greatly reduced yield and loss of full-length sequence information. We developed an NAD-RNA capture scheme utilizing the copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC). We examined the specificity of CuAAC and SPAAC reactions toward NAD-RNAs and m7G-RNAs and found that both prefer the former, but also act on the latter. We demonstrated that SPAAC-NAD sequencing (SPAAC-NAD-seq), when combined with immunodepletion of m7G-RNAs, enables NAD-RNA identification with accuracy and sensitivity, leading to the discovery of new NAD-RNA profiles in Arabidopsis Furthermore, SPAAC-NAD-seq retained full-length sequence information. Therefore, SPAAC-NAD-seq would enable specific and efficient discovery of NAD-RNAs in prokaryotes and, when combined with m7G-RNA depletion, in eukaryotes.

RNA capping and decapping tightly coordinate with transcription, translation, and RNA decay to regulate gene expression. Proteins in the DXO/Rai1 family have been implicated in mRNA decapping and decay, and mammalian DXO was recently found to also function as a decapping enzyme for NAD+ -capped RNAs (NAD-RNA). The Arabidopsis genome contains a single gene encoding a DXO/Rai1 protein, AtDXO1. Here we show that AtDXO1 possesses both NAD-RNA decapping activity and 5'-3' exonuclease activity but does not hydrolyze the m7 G cap. The atdxo1 mutation increased the stability of NAD-RNAs and led to pleiotropic phenotypes, including severe growth retardation, pale color, and multiple developmental defects. Transcriptome profiling analysis showed that the atdxo1 mutation resulted in upregulation of defense-related genes but downregulation of photosynthesis-related genes. The autoimmunity phenotype of the mutant could be suppressed by either eds1 or npr1 mutation. However, the various phenotypes associated with the atdxo1 mutant could be complemented by an enzymatically inactive AtDXO1. The atdxo1 mutation apparently enhances post-transcriptional gene silencing by elevating levels of siRNAs. Our study indicates that AtDXO1 regulates gene expression in various biological and physiological processes through its pleiotropic molecular functions in mediating RNA processing and decay.

The 5' end of a eukaryotic mRNA transcript generally has a 7-methylguanosine (m7G) cap that protects mRNA from degradation and mediates almost all other aspects of gene expression. Some RNAs in Escherichia coli, yeast, and mammals were recently found to contain an NAD+ cap. Here, we report the development of the method NAD tagSeq for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs). The method uses an enzymatic reaction and then a click chemistry reaction to label NAD-RNAs with a synthetic RNA tag. The tagged RNA molecules can be enriched and directly sequenced using the Oxford Nanopore sequencing technology. NAD tagSeq can allow more accurate identification and quantification of NAD-RNAs, as well as reveal the sequences of whole NAD-RNA transcripts using single-molecule RNA sequencing. Using NAD tagSeq, we found that NAD-RNAs in Arabidopsis were produced by at least several thousand genes, most of which are protein-coding genes, with the majority of these transcripts coming from

Simple Summary: The domestication of carnivorous largemouth bass by formula diet has been well developed in the aquaculture industry in China. Three distinct POMCa genotypes were identified in largemouth bass; significant shifts in genotype frequency were observed between the non-selection population fed on forage fish and the selection population domesticated by formula diet. The random inheritance of allele frequency might be affected by decades of selection on feeding traits of largemouth bass. The increased frequency of POMC-A I in the selection population, along with its association with superior growth and physiological responses, provides novel insights into the genetic adaptation of largemouth bass to artificial diets in aquaculture. Diverse feeding habits in teleosts involve a wide range of appetite-regulating factors. As an appetite-suppressing gene, the polymorphisms of POMCa in largemouth bass (Micropterus salmoides) were validated via sequencing and high-resolution melting (HRM). The frequency distribution of different POMCa genotypes were analyzed in two populations, and physiological responses of different POMCa genotypes to feed domestication were investigated. The indel of an 18 bp AU-rich element (ARE) in the 3′ UTR and four interlocked SNP loci in the ORF of 1828 bp of POMCa cDNA sequence were identified in largemouth bass and constituted three genotypes of POMC-A I, II, and III, respectively. POMC-A I and Allele I had increased frequencies in the selection population than in the non-selection population (p < 0.01), 63.55% vs. 43.33% and 0.7850 vs. 0.6778, respectively. POMC-A I possessed the lowest value of POMCa mRNA during fasting (p < 0.05) and exhibited growth and physiological advantages under food deprivation and refeeding according to the levels of body mass and four physiological indicators, i.e., cortisol (Cor), growth hormone (GH), insulin-like growth factor-1 (IGF-1), and glucose (Glu). The identification of three POMCa genotypes, alongside their varying physiological responses during feed domestication, suggests a selective advantage that could be leveraged in molecular marker-assisted breeding of largemouth bass that are adapted to feeding on formula diet. [ABSTRACT FROM AUTHOR]

Background: The 2020 edition of the Pharmacopoeia of the People’s Republic of China (Chinese Pharmacopoeia 2020 edition) has 255 Chinese prescriptions with different dosage forms, accounting for 21.09% of the total prescriptions (1,209) in Chinese Pharmacopoeia 2020 edition. However, the scientific rationality of the phenomenon of “Different Dosage Forms of the Same Prescription” of Chinese proprietary medicine has been less explored. Based on the dosage form theory of “components in pills release slowly and take effect in slow-acting manner, while in powders release quickly and take effect in fast-acting way,” we provided the in vitro dissolution experiment and in vivo pharmacokinetics of Chuanxiong Chatiao powders and pills in order to rationalize the phenomenon of “Different Dosage Forms of the Same Prescription” of Chuanxiong Chatiao prescription.Materials and Methods: Chuanxiong Chatiao powders and pills were prepared in the laboratory referring to the preparation methods in the Chinese Pharmacopoeia 2020 edition, and the contents of tetramethylpyrazine, ferulic acid, nodakenin, and isoimperatorin were determined by the external standard method. We measured the in vitro dissolution of four analytes of Chuanxiong Chatiao powders and pills according to the second method for dissolution determination (paddle method) in the Chinese Pharmacopoeia 2020 edition, and their corresponding contents in each sampling point were determined by LC-MS/MS. We also provided a pharmacokinetic study of Chuanxiong Chatiao powders and pills. Six female domestic rabbits were divided into two groups (powder and pill groups) and given Chuanxiong Chatiao powders and pills (9.85 g/kg) by surgical administration separately. Blood samples were collected at 5, 15, 30, 45, 60, 90, 120, 150, 180, 240, 360, 480, 720, and 1,440 min after drug administration to measure the plasma concentration of the four analytes by LC-MS/MS.Results: The results of in vitro dissolution experiment showed that the dissolution rate of four analytes in the powder group was greater than that of the pill group. However, the solubilities of tetramethylpyrazine and isoimperatorin were very low in the powder and pill, which may be related to their low solubility properties. The results of the in vivo pharmacokinetic study of Chuanxiong Chatiao powders and pills showed that Tmax (h) of ferulic acid and nodakenin in the powder group was 0.420 and 0.053 times that of the pill group and t1/2 (h) of ferulic acid, nodakenin, and isoimperatorin of the powder group was 0.910, 0.262, and 0.661 times that of the pill group, respectively.Conclusion: The in vitro dissolution rate and in vivo pharmacokinetic parameters of four analytes in CXCTF could partly explain the scientific rationality of the classic theory of “丸者缓也, 散者散也” as in Chinese, which is helpful for providing a basis for the comparison of subsequent dosage forms. The results of our studies also suggest the complexity of the design of dosage forms of Chinese proprietary medicines and imply that we should pay more attention to the scientific rationality of the phenomenon of “Different Dosage Forms of the Same Prescription.”