Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat.

The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.

Visit-to-visit HbA1c variability is associated with poor prognosis in peritoneal dialysis patients with type 2 diabetes mellitus.

BACKGROUND: The prognosis of diabetic peritoneal dialysis patients is poor. HbA1c serves as a crucial indicator for monitoring blood glucose control in patients with diabetes. Nevertheless, the relationship between visit-to-visit HbA1c variability and prognosis in peritoneal dialysis with diabetes remains unclear. METHODS: All participants were categorized into 3 groups based on the HbA1c variability score (HVS), which is the frequency of 0.5% (5.5 mmol/mol) alter in visit-to-visit HbA1c values. Then, the hazard ratio to HVS with all-cause mortality was analyzed using the Cox hazard model, followed by the Fine-Gray competing risk model for major adverse cardiovascular events. Subgroup and sensitivity analysis were conducted to ascertain the robustness of the findings. RESULTS: Eight hundred twenty patients with type 2 diabetes were finally enrolled in this study from 2,855 participants with a mean age of 56.9 ± 14.6 years and a median follow-up time of 44 months [IQR: 27-70], death occurred in 496 (60.2%) individuals. Compared with the lowest category (HVS < 1/3) after being adjusted by potential confounding factors, the hazard ratio for all-cause mortality was 4.59 (3.74-5.64) and the sub-distribution hazard ratio for major adverse cardiovascular events was 1.91 (1.46-2.51) of the highest category (HVS ≥ 2/3). Subgroup interaction and sensitivity analysis, including the adjustment for variables such as time-weighted average HbA1c, HbA1c measurement times and expansion, confirmed the reliability of the results. CONCLUSION: The HVS is related to the risk of poor prognosis in peritoneal dialysis with type 2 diabetes mellitus, independently of clinical multiple variables, and is a novel indicator with clinical guidance.

Efficient and Selective Removal of Organic Cationic Dyes by Peel of Brassica juncea Coss. var. gemmifera Lee et Lin-Based Biochar.

The design and preparation of cheaper, greener and more efficient adsorbents is essential for the removal of pollutants by adsorption. In this study, biochar was prepared from peel of Brassica juncea var. gemmifera Lee et Lin (PoBJ) using a facile, low-temperature and vacuum pyrolysis, and the adsorption mechanism toward organic dyes in aqueous solution was elucidated. The adsorbent was characterized by XPS, FT-IR and SEM, and zeta potential techniques. The adsorption ability of PoBJ biochar for cationic dyes (methylene blue, brilliant green, calcein-safranine, azure I, rhodamine B), anionic dyes (alizarin yellow R), and neutral dyes (neutral red) revealed that the biochar exhibited adsorption selectivity toward cationic dyes. The effects of different factors on the adsorption performance of PoBJ biochar, as well as the adsorption kinetics and thermodynamics, were further investigated by using methylene blue as the model adsorbate. These factors included temperature, pH, contact time and dye concentration. The experimental results showed that BJ280 and BJ160 (prepared at 280 °C and 160 °C, respectively) possessed relatively higher adsorption capacity of 192.8 and 167.40 mg g-1 for methylene blue (MB), respectively, demonstrating the possibility of utilization of PoBJ biochar as a superior bio-adsorbent. The experimental data of BJ160 toward MB were correlated with various kinetic and isothermal models. The results indicated that the adsorption process was consistent with the Langmuir isotherm model and nonlinear pseudo-second-order kinetic model. Thermodynamic parameters indicated that the adsorption of MB onto BJ160 was exothermic. Thus, the low-temperature prepared PoBJ biochar was an environmentally friendly, economic and efficient cationic dye adsorbent.

Metabolomics analysis and metabolite-agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines.

Plants produce numerous metabolites that are important for their development and growth. However, the genetic architecture of the wheat metabolome has not been well studied. Here, utilizing a high-density genetic map, we conducted a comprehensive metabolome study via widely targeted LC-MS/MS to analyze the wheat kernel metabolism. We further combined agronomic traits and dissected the genetic relationship between metabolites and agronomic traits. In total, 1260 metabolic features were detected. Using linkage analysis, 1005 metabolic quantitative trait loci (mQTLs) were found distributed unevenly across the genome. Twenty-four candidate genes were found to modulate the levels of different metabolites, of which two were functionally annotated by in vitro analysis to be involved in the synthesis and modification of flavonoids. Combining the correlation analysis of metabolite-agronomic traits with the co-localization of methylation quantitative trait locus (mQTL) and phenotypic QTL (pQTL), genetic relationships between the metabolites and agronomic traits were uncovered. For example, a candidate was identified using correlation and co-localization analysis that may manage auxin accumulation, thereby affecting number of grains per spike (NGPS). Furthermore, metabolomics data were used to predict the performance of wheat agronomic traits, with metabolites being found that provide strong predictive power for NGPS and plant height. This study used metabolomics and association analysis to better understand the genetic basis of the wheat metabolism which will ultimately assist in wheat breeding.

Metabolite-based genome-wide association study enables dissection of the flavonoid decoration pathway of wheat kernels.

The marriage of metabolomic approaches with genetic design has proven a powerful tool in dissecting diversity in the metabolome and has additionally enhanced our understanding of complex traits. That said, such studies have rarely been carried out in wheat. In this study, we detected 805 metabolites from wheat kernels and profiled their relative contents among 182 wheat accessions, conducting a metabolite-based genome-wide association study (mGWAS) utilizing 14 646 previously described polymorphic SNP markers. A total of 1098 mGWAS associations were detected with large effects, within which 26 candidate genes were tentatively designated for 42 loci. Enzymatic assay of two candidates indicated they could catalyse glucosylation and subsequent malonylation of various flavonoids and thereby the major flavonoid decoration pathway of wheat kernel was dissected. Moreover, numerous high-confidence genes associated with metabolite contents have been provided, as well as more subdivided metabolite networks which are yet to be explored within our data. These combined efforts presented the first step towards realizing metabolomics-associated breeding of wheat.

Morphology-Reserved Synthesis of Discrete Nanosheets of CuO@SAPO-34 and Pore Mouth Catalysis for One-Pot Oxidation of Cyclohexane.

Discrete nanosheets of silicon-doped AlPO4 molecular sieves (SAPO-34) with a thickness of ≈7 nm have been prepared through morphology-reserved synthesis with a lamellar aluminum phosphate as precursor. Cages of the nanosheets are in situ incorporated with copper oxide clusters. The CuO@SAPO-34 nanosheets exhibit a large external surface area with a high number of (010) channel pores on the surface. Due to the thin morphology, copper oxide clusters occupy the outmost cages with a probability >50 %. The distinctive configuration facilitates a new concept of pore mouth catalysis, i.e., reactant molecules larger than the pores cannot enter the interior of the molecular sieves but can interact with the CuO clusters at "the mouth" of the pore. In heterogeneous catalysis, CuO@SAPO-34 nanosheets have shown top performance in one-pot oxidation of cyclohexane to adipic acid by O2 , a key compound for the manufacture of nylon-66, which is so far produced using non-green nitric acid oxidation.

Arginine methylation of HSP70 regulates retinoid acid-mediated RARß2 gene activation.

Although "histone" methyltransferases and demethylases are well established to regulate transcriptional programs and to use nonhistone proteins as substrates, their possible roles in regulation of heat-shock proteins in the nucleus have not been investigated. Here, we report that a highly conserved arginine residue, R469, in HSP70 (heat-shock protein of 70 kDa) proteins, an evolutionarily conserved protein family of ATP-dependent molecular chaperone, was monomethylated (me1), at least partially, by coactivator-associated arginine methyltransferase 1/protein arginine methyltransferase 4 (CARM1/PRMT4) and demethylated by jumonji-domain-containing 6 (JMJD6), both in vitro and in cultured cells. Functional studies revealed that HSP70 could directly regulate retinoid acid (RA)-induced retinoid acid receptor ß2 (RARß2) gene transcription through its binding to chromatin, with R469me1 being essential in this process. HSP70's function in gene transcriptional regulation appears to be distinct from its protein chaperon activity. R469me1 was shown to mediate the interaction between HSP70 and TFIIH, which involves in RNA polymerase II phosphorylation and thus transcriptional initiation. Our findings expand the repertoire of nonhistone substrates targeted by PRMT4 and JMJD6, and reveal a new function of HSP70 proteins in gene transcription at the chromatin level aside from its classic role in protein folding and quality control.

The hemoglobin, albumin, lymphocyte, and platelet (HALP) is a potent indicator for the prognosis in hemodialysis patients.

The hemoglobin, albumin, lymphocyte, and platelet (HALP) values were marked as a original index of general nutritional and inflammatory conditions. The purpose of this investigation was to evaluate the potential relationship between HALP and prognosis in hemodialysis (HD) patients. Patients with maintenance HD from multiple dialysis centers in China were retrospectively analyzed. The primary poor outcome were cardiovascular disease (CVD) and all-cause death. The computational equation of HALP values as the follows: hemoglobin (g/L) × albumin (g/L) × lymphocytes (/L)/ platelets (/L). All participants were divided into Tertile 1, Tertile 2, and Tertile 3 according to the tertiles of baseline HALP values. The Kaplan-Meier curve and the Cox regression was done to figure out the relationship about HALP and adverse outcomes. The restricted cubic splines further identified the possible associations. The time-dependent receiver operating characteristic curve and C-index were implemented for evaluate the predictive values of the HALP composite model. There were 4796 patients incorporate into ultimate study. Compared with patients in Tertile 1, patients in Tertile 3 had an lower risk of all-cause mortality [hazard ratios = 0.66, 95% confidence intervals: 0.49-0.86, P = .007] and CVD mortality [sub-distribution hazard ratio = 0.51, 95% confidence intervals: 0.34-0.80, P = .005]. The composite model with the supplement of HALP outperformed the traditional factor model in the time-dependent receiver operating characteristic curve. High HALP values at baseline are related to a diminished risk of CVD death and all-cause death in HD patients. HALP is a novel and potent index for the prognosis of HD patients.

A Minimally-Invasive Method for Serial Cerebrospinal Fluid Collection and Injection in Rodents with High Survival Rates.

Cerebrospinal fluid (CSF) is an important sample source for diagnosing diseases in the central nervous system (CNS), but collecting and injecting CSF in small animals is technically challenging and often results in high mortality rates. Here, we present a cost-effective and efficient method for accessing the CSF in live rodents for fluid collection and infusion purposes. The key element of this protocol is a metal needle tool bent at a unique angle and length, allowing the successful access of the CSF through the foramen magnum. With this method, we can collect 5-10 µL of the CSF from mice and 70-100 µL from rats for downstream analyses, including mass spectrometry. Moreover, our minimally-invasive procedure enables iterative CSF collection from the same animal every few days, representing a significant improvement over prior protocols. Additionally, our method can be used to inject solutions into mice cisterna magna with high success rates and high postoperative recovery rates. In summary, we provide an efficient and minimally-invasive protocol for collecting and infusing reagents into the CSF in live rodents. We envision this protocol will facilitate biomarker discovery and drug development for diseases in the central nervous system.

MAVI1, an endoplasmic reticulum-localized microprotein, suppresses antiviral innate immune response by targeting MAVS on mitochondrion.

Pattern recognition receptor-mediated innate immunity is critical for host defense against viruses. A growing number of coding and noncoding genes are found to encode microproteins. However, the landscape and functions of microproteins in responsive to virus infection remain uncharacterized. Here, we systematically identified microproteins that are responsive to vesicular stomatitis virus infection. A conserved and endoplasmic reticulum-localized membrane microprotein, MAVI1 (microprotein in antiviral immunity 1), was found to interact with mitochondrion-localized MAVS protein and inhibit MAVS aggregation and type I interferon signaling activation. The importance of MAVI1 was highlighted that viral infection was attenuated and survival rate was increased in Mavi1-knockout mice. A peptide inhibitor targeting the interaction between MAVI1 and MAVS activated the type I interferon signaling to defend viral infection. Our findings uncovered that microproteins play critical roles in regulating antiviral innate immune responses, and targeting microproteins might represent a therapeutic avenue for treating viral infection.

Rationalization of Nonlinear Adsorption Energy-Strain Relations and Brønsted-Evans-Polanyi and Transition State Scaling Relationships under Strain.

Scaling relations play a vital role in high-throughput screening of catalytic materials, and more and more attention is being paid to strain-based regulation of catalytic performance. Here we investigated the variation of several energetics, including adsorption energies in the initial state, transition state, and final state, reaction energies, and energy barriers with strain, by studying CO, BH, NH, CH, and NO adsorption and dissociation on M(111) (M = Cu, Ag, Ni, Pd, or Pt) surfaces. We show that energy barriers, reaction energies, and adsorption energies can vary either linearly or nonlinearly (quadratically) with strain. Systems with stronger adsorbate-substrate interaction and weaker atom-atom interaction in substrates are more likely to exhibit nonlinear relations. The well-known Brønsted-Evans-Polanyi relationships and transition state scaling relationships under strain were also examined, and both of them can be nonlinear under strain, in principle. The observed nonlinear relationships were satisfactorily rationalized with the equations derived from Mechanics of Solids.

Chronic colitis induces meninges traffic of gut-derived T cells, unbalances M1 and M2 microglia/macrophage and increases ischemic brain injury in mice.

Ischemic stroke is one of the most common diseases leading to death and is the primary cause of physical handicap. Recent studies have reported that chronic colitis increases the risk of ischemic stroke, but it is unknown whether chronic colitis participates in ischemic brain injury directly. A combined mouse model of chronic colitis induced by dextran sodium sulfate (DSS) and ischemic stroke induced by photochemical infarction was used in this study. We demonstrated that chronic colitis significantly increased the infarction volume, activated microglia/macrophage numbers, proliferation of M1 microglia/macrophage, non-gut-derived CD4+ T lymphocyte penetration and decreased neuron numbers in the peri-infarction at 7 d after stroke. Furthermore, gut-derived CD4+ T cell accumulation on the meninges was observed at 7 d after stroke. In addition, selective depletion of meningeal macrophages resulted in a reduction of infarction volume and the non-gut-derived CD4+ T lymphocyte penetration. We concluded that chronic colitis exacerbated ischemic stroke by promoting CD4+ T cell migration from the gut to the meninges and disequilibrium of M1 and M2 microglia/macrophages. We speculated that the gut-derived CD4+ T cells may interact with meningeal macrophages and result in non-gut-derived CD4+ T lymphocyte infiltration that aggravated brain injury in ischemic stroke.

Vagus Nerve Stimulation Attenuates Cerebral Microinfarct and Colitis-induced Cerebral Microinfarct Aggravation in Mice.

Cerebral cortical microinfarct (CMI) is common in patients with dementia and cognitive decline. Emerging studies reported that intestinal dysfunction influenced the outcome of ischemic stroke and that vagus nerve stimulation (VNS) protected against ischemic stroke. However, the effects of intestinal dysfunction and VNS on CMI are not clear. Therefore, we examined the influence of colitis and VNS on CMI and the mechanisms of VNS attenuating CMI in mice with colitis. CMI was induced using a two-photon laser. Colitis was induced using oral dextran sodium sulfate (DSS). The cervical vagus nerve was stimulated using a constant current. In vivo blood-brain barrier (BBB) permeability was evaluated using two-photon imaging. Infarct volume, microglial and astrocyte activation, oxidative stress and proinflammatory cytokine levels were assessed using immunofluorescent and immunohistochemical staining. The BBB permeability, infarct volume, activation of microglia and astrocytes and oxidative stress increased significantly in mice with colitis and CMI compared to those in mice with CMI. However, these processes were reduced in CMI mice when VNS was performed. Brain lesions in mice with colitis and CMI were significantly ameliorated when VNS was performed during the acute phase of colitis. Our study demonstrated that VNS alleviated CMI and this neuroprotection was associated with the suppression of BBB permeability, neuroinflammation and oxidative stress. Also, our results indicated that VNS reduced colitis-induced microstroke aggravation.

Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat.

Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.

Methylation of transcription factor YY2 regulates its transcriptional activity and cell proliferation.

Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context-specific manner compared with YY1. Despite its functional importance, how YY2's DNA-binding activity and function are regulated, particularly by PTMs, remains completely unknown. Here we report the first PTM with functional characterization on YY2, namely lysine 247 monomethylation (K247me1), which was found to be dynamically regulated by SET7/9 and LSD1 both in vitro and in cultured cells. Functional study revealed that SET7/9-mediated YY2 methylation regulated its DNA-binding activity in vitro and in association with chromatin examined by chromatin immunoprecipitation coupled with sequencing (ChIP-seq) in cultured cells. Knockout of YY2, SET7/9 or LSD1 by CRISPR (clustered, regularly interspaced, short palindromic repeats)/Cas9-mediated gene editing followed by RNA sequencing (RNA-seq) revealed that a subset of genes was positively regulated by YY2 and SET7/9, but negatively regulated by LSD1, which were enriched with genes involved in cell proliferation regulation. Importantly, YY2-regulated gene transcription, cell proliferation and tumor growth were dependent, at least partially, on YY2 K247 methylation. Finally, somatic mutations on YY2 found in cancer, which are in close proximity to K247, altered its methylation, DNA-binding activity and gene transcription it controls. Our findings revealed the first PTM with functional implications imposed on YY2 protein, and linked YY2 methylation with its biological functions.

Regulation of Transcription Factor Yin Yang 1 by SET7/9-mediated Lysine Methylation.

Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it is regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remains completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. Functional studies revealed that SET7/9-mediated YY1 methylation regulated YY1 DNA-binding activity both in vitro and at specific genomic loci in cultured cells. Consistently, SET7/9-mediated YY1 methylation was shown to involve in YY1-regulated gene transcription and cell proliferation. Our findings revealed a novel regulatory strategy, methylation by lysine methyltransferase, imposed on YY1 protein, and linked YY1 methylation with its biological functions.