Shallow wet irrigation reduces nitrogen leaching loss rate in paddy fields by microbial regulation and lowers rate of downward migration of leaching water: a 15N-tracer study.

China consumes 35% of the world's fertilizer every year; however, most of the nitrogen fertilizers, which are essential for rice cultivation, are not used effectively. In this study, factors affecting the nitrogen leaching loss rate were studied in typical soil and rice varieties in South China. The effects of various irrigation measures on rice growth and nitrogen leaching loss were investigated by conducting experiments with eight groups. These groups included traditional irrigation (TI) and shallow wet irrigation (SWI). The TI is a common irrigation method for farmers in South China, maintaining a water layer of 5-8 cm depth. For SWI, after establishing a shallow water layer usually maintaining at 1-2 cm, paddy is irrigated when the field water level falls to a certain depth, then this process is then repeat as necessary. The nitrogen distribution characteristics were determined using 15N isotope tracing. In addition, the effects of nitrification, denitrification, and microbial composition on soil nitrogen transformation at different depths were studied by microbial functional gene quantification and high-throughput sequencing. The results revealed that in the SWI groups, the total nitrogen leaching loss rate reduced by 0.3-0.8% and the nitrogen use efficiency (NUE) increased by 2.18-4.43% compared with those in the TI groups. After the 15N-labeled nitrogen fertilizer was applied, the main pathways of nitrogen were found to be related to plant absorption and nitrogen residues. Furthermore, paddy soil ammonia-oxidizing archaea were more effective than ammonia-oxidizing bacteria for soil ammonia oxidation by SWI groups. The SWI measures increased the relative abundance of Firmicutes in paddy soil, enhancing the ability of rice to fix nitrogen to produce ammonium nitrogen, thus reducing the dependence of rice on chemical fertilizers. Moreover, SWI enhanced the relative abundance of nirS and nosZ genes within surface soil bacteria, thereby promoting denitrification in the surface soil of paddy fields. SWI also promoted ammonia oxidation and denitrification by increasing the abundance and activity of Proteobacteria, Nitrospirae, and Bacteroidetes. Collectively, SWI effectively reduced the nitrogen leaching loss rate and increase NUE.

Dryopterisjinpingensis, a critically endangered diploid new species of Dryopteridaceae from Yunnan, China.

Dryopterisjinpingensis, a new species of diploid, sexually reproductive ferns of Dryopteridaceae from Yunnan, southwestern China, is described and illustrated. Morphologically, D.jinpingensis is similar to D.gaoligongensis but unique in elongated lanceolate laminae, sessile or subsessile pinna stalks, and overlapping membranous scales adnate to stipe base. Phylogenetic analyses based on both plastome and the nuclear AK1 gene sequences showed that D.jinpingensis is sister to D.gaoligongensis. A detailed taxonomic description with line drawings is provided, and its conservation status is evaluated to be critically endangered.

Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years.

Current biodiversity loss is generally considered to have been caused by anthropogenic disturbance, but it is unclear when anthropogenic activities began to affect biodiversity loss. One hypothesis suggests it began with the Industrial Revolution, whereas others propose that anthropogenic disturbance has been associated with biodiversity decline since the early Holocene. To test these hypotheses, we examined the unique vegetation of evergreen broadleaved forests (EBLFs) in East Asia, where humans have affected landscapes since the early Holocene. We adopted a genomic approach to infer the demographic history of a dominant tree (Litsea elongata) of EBLFs. We used Holocene temperature and anthropogenic disturbance factors to calculate the correlation between these variables and the historical effective population size of L. elongata with Spearman statistics and integrated the maximum-entropy niche model to determine the impact of climate change and anthropogenic disturbance on fluctuation in its effective population size. We identified 9 well-defined geographic clades for the populations of L. elongata. Based on the estimated historical population sizes of these clades, all the populations contracted, indicating persistent population decline over the last 11,000 years. Demographic history of L. elongata and human population change, change in cropland use, and change in irrigated rice area were significantly negatively correlated, whereas climate change in the Holocene was not correlated with demographic history. Our results support the early human impact hypothesis and provide comprehensive evidence that early anthropogenic disturbance may contribute to the current biodiversity crisis in East Asia.

The successive emergence of ERVL-MaLRs in primates.

Although the ERVL-mammalian-apparent LTR retrotransposons (MaLRs) are the fourth largest family of transposable elements in the human genome, their evolutionary history and relationship have not been thoroughly studied. In this study, through RepeatMasker annotations of some representative species and construction of phylogenetic tree by sequence similarity, all primate-specific MaLR members are found to descend from MLT1A1 retrotransposon. Comparative genomic analysis, transposition-in-transposition inference, and sequence feature comparisons consistently show that each MaLR member evolved from its predecessor successively and had a limited activity period during primate evolution. Accordingly, a novel MaLR member was discovered as successor of MSTB1 in Tarsiiformes. At last, the identification of candidate precursor and intermediate THE1A elements provides further evidence for the previously proposed arms race model between ZNF430/ZNF100 and THE1B/THE1A. Taken together, this study sheds light on the evolutionary history of MaLRs and can serve as a foundation for future research on their interactions with zinc finger genes, gene regulation, and human health implications.

Protective role of perivascular adipose tissue in the cardiovascular system.

This review provides an overview of the key role played by perivascular adipose tissue (PVAT) in the protection of cardiovascular health. PVAT is a specific type of adipose tissue that wraps around blood vessels and has recently emerged as a critical factor for maintenance of vascular health. Through a profound exploration of existing research, this review sheds light on the intricate structural composition and cellular origins of PVAT, with a particular emphasis on combining its regulatory functions for vascular tone, inflammation, oxidative stress, and endothelial function. The review then delves into the intricate mechanisms by which PVAT exerts its protective effects, including the secretion of diverse adipokines and manipulation of the renin-angiotensin complex. The review further examines the alterations in PVAT function and phenotype observed in several cardiovascular diseases, including atherosclerosis, hypertension, and heart failure. Recognizing the complex interactions of PVAT with the cardiovascular system is critical for pursuing breakthrough therapeutic strategies that can target cardiovascular disease. Therefore, this review aims to augment present understanding of the protective role of PVAT in cardiovascular health, with a special emphasis on elucidating potential mechanisms and paving the way for future research directions in this evolving field.

Effect of genetically determined BCAA levels on cardiovascular diseases and their risk factors: A Mendelian randomization study.

BACKGROUND AND AIMS: Observational studies have demonstrated that serum branched-chain amino acids (BCAAs) are associated with the risk of various cardiovascular diseases (CVDs) and their risk factors. However, the causal effect is unclear. The aim of this study was to investigate the effect of genetically determined BCAA levels on CVDs and their risk factors using Mendelian randomization (MR). METHODS AND RESULTS: We performed univariable and multivariable MR analyses using summary-level data from multiple GWASs and the FinnGen consortium to investigate the association between BCAA levels and the risk of CVDs (myocardial infarction, ischemic stroke, and intracerebral hemorrhage) and their risk factors (atrial fibrillation, hypertension, heart failure, and valvular heart disease). We used the random-effects IVW approach as the primary statistical method and incorporated MR estimates from different data sources using the fixed-effects model. We found genetically determined total and individual BCAA levels and a high risk of hypertension. However, there is no evidence of a causal relationship between BCAA levels and 3 cardiovascular diseases and other their risk factors. The odds of hypertension increased per 1-SD increase in BCAA levels (OR = 1.02 95% CI: 1.01, 1.04; P = 0.005), valine (OR = 1.02 95% CI: 1.01, 1.03; P<0.0001), leucine (OR = 1.02 95% CI: 1.01, 1.04; P＜0.01), and isoleucine (OR = 1.02 95% CI: 1.01, 1.03; P < 0.0001). This result was also significant in the multivariable MR. CONCLUSIONS: This MR study suggests that total and individual BCAA levels could be associated with a high risk of hypertension.

A novel subspace outlier detection method by entropy-based clustering algorithm.

Subspace outlier detection has emerged as a practical approach for outlier detection. Classical full space outlier detection methods become ineffective in high dimensional data due to the "curse of dimensionality". Subspace outlier detection methods have great potential to overcome the problem. However, the challenge becomes how to determine which subspaces to be used for outlier detection among a huge number of all subspaces. In this paper, firstly, we propose an intuitive definition of outliers in subspaces. We study the desirable properties of subspaces for outlier detection and investigate the metrics for those properties. Then, a novel subspace outlier detection algorithm with a statistical foundation is proposed. Our method selectively leverages a limited set of the most interesting subspaces for outlier detection. Through experimental validation, we demonstrate that identifying outliers within this reduced set of highly interesting subspaces yields significantly higher accuracy compared to analyzing the entire feature space. We show by experiments that the proposed method outperforms competing subspace outlier detection approaches on real world data sets.

Quantifying the arms race between LINE-1 and KRAB-zinc finger genes through TECookbook.

To defend against the invasion of transposons, hundreds of KRAB-zinc finger genes (ZNFs) evolved to recognize and silence various repeat families specifically. However, most repeat elements reside in the human genome with high copy numbers, making the ChIP-seq reads of ZNFs targeting these repeats predominantly multi-mapping reads. This complicates downstream data analysis and signal quantification. To better visualize and quantify the arms race between transposons and ZNFs, the R package TECookbook has been developed to lift ChIP-seq data into reference repeat coordinates with proper normalization and extract all putative ZNF binding sites from defined loci of reference repeats for downstream analysis. In conjunction with specificity profiles derived from in vitro Spec-seq data, human ZNF10 has been found to bind to a conserved ORF2 locus of selected LINE-1 subfamilies. This provides insight into how LINE-1 evaded capture at least twice and was subsequently recaptured by ZNF10 during evolutionary history. Through similar analyses, ZNF382 and ZNF248 were shown to be broad-spectrum LINE-1 binders. Overall, this work establishes a general analysis workflow to decipher the arms race between ZNFs and transposons through nucleotide substitutions rather than structural variations, particularly in the protein-coding region of transposons.

Design optimization and experiment of corn U-shaped fertilization device.

Aiming at the problems of low utilization rate of corn fertilizer, low precision of fertilization ratio, and time-consuming and laborious topdressing in the later stage, an U-shaped fertilization device with uniform fertilizer mechanism was designed. The device was mainly composed of uniform fertilizer mixing mechanism, fertilizer guide plate and fertilization plate. Compound fertilizer was applied on both sides and slow/controlled release fertilizer was applied at the bottom to form an U-shaped distribution of fertilizer around corn seeds. Through theoretical analysis and calculation, the structural parameters of the fertilization device were determined. Through the simulated soil tank test, the quadratic regression orthogonal rotation combination design was carried out on the main factors affecting the spatial stratification effect of fertilizer. The optimal parameters were obtained as follows: the stirring speed of the stirring structure was 300 r/min, the bending angle of the fertilization tube was 165°, and the operating speed of the fertilization device was 3 km/h. The results of bench verification test showed that under the optimized stirring speed and bending angle, the fertilizer particles were stirred evenly, and the average values of fertilizer flowing out of the fertilization tubes on both sides were 299.5 g and 297.4 g, respectively. The average fertilizer amounts of the three fertilizer outlets were 200.4 g, 203.2 g and 197.7 g, respectively, which met the agronomic requirements of 1:1:1 fertilization, and the variation coefficients of fertilizer amounts on both sides of the fertilizer pipe and each layer were less than 0.1% and 0.4%, respectively. The simulation results of the optimized U-shaped fertilization device can achieve the expected U-shaped fertilization effect around corn seeds. The results of field experiment showed that the U-shaped fertilization device could realize the U-shaped proportional application of fertilizer in soil. The distance between the upper end of fertilization on both sides and the distance between the base fertilizer and the surface were 87.3-95.2 mm and 197.8-206.0 mm, respectively. The transverse distance between the fertilizers on both sides was 84.3-99.4 mm, and the error with the designed theoretical fertilization was within 10 mm. Compared with the traditional side fertilization method, the number of corn roots increased by 5-6, the root length increased by 30-40 mm, and the yield increased by 9.9-14.8%.

Functional Characterization of a New Degradation Peptide BmTX4-P1 from Traditional Chinese Scorpion Medicinal Material.

Thermally processed Buthus martensii Karsch scorpion is an important traditional Chinese medical material that has been widely used to treat various diseases in China for over one thousand years. Our recent work showed that thermally processed Buthus martensii Karsch scorpions contain many degraded peptides; however, the pharmacological activities of these peptides remain to be studied. Here, a new degraded peptide, BmTX4-P1, was identified from processed Buthus martensii Karsch scorpions. Compared with the venom-derived wild-type toxin peptide BmTX4, BmTX4-P1 missed some amino acids at the N-terminal and C-terminal regions, while containing six conserved cysteine residues, which could be used to form disulfide bond-stabilized α-helical and ß-sheet motifs. Two methods (chemical synthesis and recombinant expression) were used to obtain the BmTX4-P1 peptide, named sBmTX4-P1 and rBmTX4-P1. Electrophysiological experimental results showed that sBmTX4-P1 and rBmTX4-P1 exhibited similar activities to inhibit the currents of hKv1.2 and hKv1.3 channels. In addition, the experimental electrophysiological results of recombinant mutant peptides of BmTX4-P1 indicated that the two residues of BmTX4-P1 (Lys22 and Tyr31) were the key residues for its potassium channel inhibitory activity. In addition to identifying a new degraded peptide, BmTX4-P1, from traditional Chinese scorpion medicinal material with high inhibitory activities against the hKv1.2 and hKv1.3 channels, this study also provided a useful method to obtain the detailed degraded peptides from processed Buthus martensii Karsch scorpions. Thus, the study laid a solid foundation for further research on the medicinal function of these degraded peptides.

Primulinajiulianshanensis, a new species of Gesneriaceae from Jiangxi Province, China.

Primulinajiulianshanensis F.Wen & G.L.Xu, a new species of Gesneriaceae from Jiulianshan National Nature Reserve of Jiangxi Province, China, is described and illustrated here. Molecular evidence showed it was sister to P.wenii Jian Li & L.J.Yan, while the morphological observation found clear differences between them, petiole, both sides of leaf blades, adaxial surface of the calyx lobes, corolla inside toward the bottom, bract margins covered glandular-pubescent hairs in P.jiulianshanensis (vs. no glandular-pubescent hairs in P.wenii); lateral bracts 4-9 × ca. 2 mm, the central one 2-5 × 1-1.5 mm, adaxially glabrous but sparsely pubescent at apex (vs. lateral bracts 14-16 × 2.5-3.0 mm, the central one 10-12 × 1.3-1.6 mm, all adaxially pubescent); calyx lobes 8-11 × ca. 2 mm, each side with several brown serrate teeth at apex (vs. 14-15 × ca. 2.5 mm, margin entire); filaments and staminodes sparsely yellow glandular-puberulent (vs. white, glabrous).

THE1B may have no role in human pregnancy due to ZNF430-mediated silencing.

THE1-family retrovirus invaded the primate genome more than 40 million years ago. Dunn-Fletcher et al. reported one THE1B element upstream of CRH gene alters gestation length by upregulating corticotropin-releasing hormone expression in transgenic mice and concluded it has the same role in human as well. However, no promoter or enhancer mark has been detected around this CRH-proximal element in any human tissue or cell, so probably some anti-viral factor exists in primates to prevents it from wreaking havoc. Here I report two paralogous zinc finger genes, ZNF430 and ZNF100, that emerged during the simian lineage to specifically silence THE1B and THE1A, respectively. Contact residue changes in one finger confers each ZNF the unique ability to preferentially repress one THE1 sub-family over the other. The reported THE1B element contains an intact ZNF430 binding site, thus under the repression of ZNF430 in most tissues including placenta, it is questionable whether or not this retrovirus has any role in human pregnancy. Overall, this analysis highlights the need to study human retroviruses' functions in suitable model system.

On the dependent recognition of some long zinc finger proteins.

The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP recognition model asserts longer finger arrays should recognize longer DNA-binding sites. However, recent experimental efforts to identify in vivo ZFP binding sites contradict this assumption, with many exhibiting short motifs. Here we use ZFY, CTCF, ZIM3, and ZNF343 as examples to address three closely related questions: What are the reasons that impede current motif discovery methods? What are the functions of those seemingly unused fingers and how can we improve the motif discovery algorithms based on long ZFPs' biophysical properties? Using ZFY, we employed a variety of methods and find evidence for 'dependent recognition' where downstream fingers can recognize some previously undiscovered motifs only in the presence of an intact core site. For CTCF, high-throughput measurements revealed its upstream specificity profile depends on the strength of its core. Moreover, the binding strength of the upstream site modulates CTCF's sensitivity to different epigenetic modifications within the core, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates the epigenetic control by CTCF. Our results establish that, because of irregular motif structures, variable spacing and dependent recognition between sub-motifs, the specificities of long ZFPs are significantly underestimated, so we developed an algorithm, ModeMap, to infer the motifs and recognition models of ZIM3 and ZNF343, which facilitates high-confidence identification of specific binding sites, including repeats-derived elements. With revised concept, technique, and algorithm, we can discover the overlooked specificities and functions of those 'extra' fingers, and therefore decipher their broader roles in human biology and diseases.

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change.

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.

Salvia miltiorrhiza extract may exert an anti-obesity effect in rats with high-fat diet-induced obesity by modulating gut microbiome and lipid metabolism.

BACKGROUND: Studies have shown that a high-fat diet (HFD) can alter gut microbiota (GM) homeostasis and participate in lipid metabolism disorders associated with obesity. Therefore, regulating the construction of GM with the balance of lipid metabolism has become essential for treating obesity. Salvia miltiorrhiza extract (Sal), a common traditional Chinese medicine, has been proven effective against atherosclerosis, hyperlipidemia, obesity, and other dyslipidemia-related diseases. AIM: To investigate the anti-obesity effects of Sal in rats with HFD-induced obesity, and explore the underlying mechanism by focusing on GM and lipid metabolism. METHODS: Obesity was induced in rats with an HFD for 7 wk, and Sal (0.675 g/1.35 g/2.70 g/kg/d) was administered to treat obese rats for 8 wk. The therapeutic effect was evaluated by body weight, body fat index, waistline, and serum lipid level. Lipid factors (cAMP, PKA, and HSL) in liver and fat homogenates were analyzed by ELISA. The effect of Sal on GM and lipid metabolism was assessed by 16S rRNA-based microbiota analysis and untargeted lipidomic analysis (LC-MS/MS), respectively. RESULTS: Sal treatment markedly reduced weight, body fat index, serum triglycerides (TG), total cholesterol (TC), low-density lipoprotein, glucose, free fatty acid, hepatic lipid accumulation, and adipocyte vacuolation, and increased serum high-density lipoprotein (HDL-C) in rats with HFD-induced obesity. These effects were associated with increased concentrations of lipid factors such as cAMP, PKA, and HSL in the liver and adipose tissues, enhanced gut integrity, and improved lipid metabolism. GM analysis revealed that Sal could reverse HFD-induced dysbacteriosis by promoting the abundance of Actinobacteriota and Proteobacteria, and decreasing the growth of Firmicutes and Desulfobacterita. Furthermore, LC-MS/MS analysis indicated that Sal decreased TGs (TG18:2/18:2/20:4, TG16:0/18:2/22:6), DGs (DG14:0/22:6, DG22:6/22:6), CL (18:2/ 18:1/18:1/20:0), and increased ceramides (Cers; Cer d16:0/21:0, Cer d16:1/24:1), (O-acyl)-ω-hydroxy fatty acids (OAHFAs; OAHFA18:0/14:0) in the feces of rats. Spearman's correlation analysis further indicated that TGs, DGs, and CL were negatively related to the abundance of Facklamia and Dubosiella, and positively correlated with Blautia and Quinella, while OAHFAs and Cers were the opposite. CONCLUSION: Sal has an anti-obesity effect by regulating the GM and lipid metabolism.

Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae.

BACKGROUND: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference. RESULTS: The phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene. CONCLUSION: This study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives.

Assessment of Morphological Features and Imaging Characteristics of Patients with Intracranial Artery Dissection: A High-Resolution MRI Study.

BACKGROUND: Intracranial artery dissection (IAD) is a pathological dissection of the arterial wall. .However, the morphological features and imaging characteristics of patients with intracranial artery dissection (IAD) remain poorly understood. METHODS: The study reports on 70 IAD patients (30 culprit and 40 non-culprit). All participants underwent high-resolution magnetic resonance imaging (HR-MRI) scans. The morphological features and imaging characteristics of artery dissection were carefully investigated. Demographics and clinical characteristics of culprit and non-culprit patients were also collected. Apparent differences between the two groups, which could be used as biomarkers for ischemic event caused by the culprit dissection, were identified by receiver operating characteristic (ROC) curve analysis. RESULTS: The IAD patients studied could be classified into five different types on the basis of morphological features: classical dissection (n = 31), fusiform aneurysm (n = 2), long dissected aneurysm (n = 9), dolichoectatic dissecting aneurysm (n = 6), and saccular aneurysm (n = 22). The direct sites of artery dissection (double lumen and intimal flap) can be seen in most IAD patients on HR-MRI. Additionally, the presence of hypertension, double lumen and intimal flap were associated with culprit lesions and might be considered biomarkers for the ischemic event caused by the culprit dissection. CONCLUSIONS: Analysis showed that HR-MRI allowed easy visualization of abnormal morphology of artery dissection lesions. This was of great significance for the diagnosis of IAD and gave a better understanding of its pathophysiological mechanism.

Sishen Pill Ameliorates Dextran Sulfate Sodium (DSS)-Induced Colitis with Spleen-Kidney Yang Deficiency Syndromes: Role of Gut Microbiota, Fecal Metabolites, Inflammatory Dendritic Cells, and TLR4/NF-κB Pathway.

Sishen pill (SSP) is an old Chinese medicine used to treat colitis with spleen-kidney-yang deficiency (SKYD) syndromes. However, its exact mechanism of action has not yet been fully elucidated. The aim of this study was to evaluate the effects and potential mechanisms of SSP on colitis with SKYD syndromes in mice. Colitis with SKYD syndromes was induced by rhubarb, hydrocortisone, and dextran sulfate sodium (DSS), and treatment was provided with SSP. Flow cytometry was performed to examine the inflammatory dendritic cell (infDC) regulations of SSP. The changes in the gut microbiota (GM) and fecal metabolites post-SSP treatment were investigated using the combination of 16S rRNA sequencing and untargeted metabolomics. Additionally, we also examined whether SSPs could regulate the infDCs by modifying TLR4/NF-κB signaling pathways. Compared with the DSS group, the disease activity index, colonic weight, index of colonic weight, and colonic injury scores, as well as the levels of tumor necrosis factor (TNF)-α, interleukin (IL)-1ß, IL-6, and IL-12p70 decreased significantly in the DSS + SSP group, while free triiodothyronine (FT3), free tetraiodothyronine (FT4), testosterone (TESTO), body weight change, colonic length, and the levels of IL-10 increased. Also, SSP decreased the amounts of CD103+CD11c+iNOS+, CD103+CD11c+TNF-α +, CD11c+CD103+CD324+, CD103+CD11c+MHC-II+, and CD103+CD11c+CD115+. Interestingly, 16S rRNA sequencing and untargeted metabolomics showed that SSP treatment restored the dysbiosis of GM and improved the dysfunction in fecal metabolism in colitis mice with SKYD syndromes. Correlation analysis indicated that the modulatory effects of SSP on FT3, FT4, IL-10, colonic weight index, CD103+CD11c+TNF-α +, CD103+CD11c+MHC-II+, and 13 common differential metabolites were related to alterations in the abundance of Parvibacter, Aerococcus, norank_f_Lachnospiraceae, Lachnospiraceae_UCG-006, Akkermansia, and Rhodococcus in the GM. In addition, SSP markedly inhibited the activation of the TLR4, MyD88, TRAF6, TAB2, and NF-κBp65 proteins and activated IκB. These results indicate that SSP can effectively alleviate colitis mice with SKYD syndrome by regulating infDCs, GM, fecal metabolites, and TLR4/NF-κB signaling pathways.

Correction to "Optimized Design and Experiment of a Spatially Stratified Proportional Fertilizer Application Device for Summer Corn".

[This corrects the article DOI: 10.1021/acsomega.2c01273.].

Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the "reversed" gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.