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Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

Four phenylethanoid glycosides were isolated from the 75% EtOH extract of Forsythiae Fructus by various column chromatography methods(MCI, silica gel, ODS and semi-preparative HPLC). Their structures were identified as forsythenside M(1), forsythenside K(2), forsythoside I(3) and forsythoside A(4) by physicochemical properties and extensive spectroscopic analysis(UV, 1 D and 2 D NMR, HR-ESI-MS). Among them, compound 1 was one new phenylethanoid glycoside. The in vitro cytotoxic activities of these compounds against MCF-7, A-375, SGC-7901 and B16 F10 were evaluated. The results showed that compounds 1-4 had cytotoxic activities against MCF-7, A-375, SGC-7901 and B16 F10 at 40 μmol·L~(-1).

Heat stress (HS) affects poultry production and welfare, causing enormous damage to poultry. Resveratrol, an antioxidant and anti-inflammatory natural plant polyphenol, is widely used in agriculture for the prevention of oxidative stress-related diseases. This study aimed to explore the effects and potential mechanism of resveratrol on liver oxidative damage in heat-stressed broilers. Sixty SPF chickens were randomly divided into control, heat stress (HS) and HS+ resveratrol (resveratrol) groups. Broilers were exposed to 35 ± 2 ℃ (8 h/d) for 7 consecutive days to induce HS, and the other 16 h/d were kept at 23 ± 2 ℃, similar to the control group. Broilers received 400 mg/kg resveratrol in the basic diet 2 days before exposure to HS and for the following 7 days. The results showed that resveratrol improved growth performance by increasing the average daily gain (ADG) and reducing the feed conversion ratio (FCR), compared with the HS group. Heat stress reduced liver weight and index, increased inflammatory cell infiltration in the liver, enhanced serum AST levels, and decreased TP and ALB II levels, which resulted in liver injury in broilers, and resveratrol effectively alleviated liver injury. Moreover, supplementation with resveratrol enhanced the activities of liver antioxidant enzymes resulting in higher GPX and SOD levels than those in the heat-stressed broilers, and decreased MDA levels. Furthermore, resveratrol alleviated liver oxidative stress by activating the gene and protein levels of Nrf2 and HO-1, enhancing NQO1 and SOD1 gene levels, and decreasing protein levels of HSP70, p62, and Keap1, and thereby alleviated the liver injury of heat-stressed broilers. Compared with the HS group, Nrf2 immunofluorescence was significantly up-regulated in the livers of resveratrol group. These results suggest that resveratrol can enhance the liver antioxidant function by activating the Nrf2-Keap1 signaling pathway to promote growth performance in broilers under HS.

Background Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed. Case presentation We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient’s symptoms were relieved, with improved absorption of the intracranial lesions. Conclusions The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes.

One new cyclopeptide was isolated from the ethyl acetate fraction of the 75% EtOH extract of Selaginella tamariscina by various column chromatography methods(HP-20, polyamide and semi-preparative HPLC). Its structure was identified as selapeptin A(1) by extensive spectroscopic analysis(HR-ESI-MS, 1 D and 2 D NMR). Compound 1 was evaluated for cytotoxic activities by MTT assay. It showed potent cytotoxic activity against B16 F10 with the inhibition rate of 51.57%±4.34% at 40 μmol·L~(-1) while had no impacts on MDA-MB-231 and MDA-MB-468 at 100 μmol·L~(-1).

BackgroundAtrial fibrillation (AF) is a common arrhythmia, and its most severe and dreaded complication is stroke. The CHA2DS2-VASc score is currently recommended for stroke risk assessment in AF. We aimed to explore the relationship between atrial FDG uptake and stroke and whether atrial FDG uptake could provide incremental value above the CHA2DS2-VAS score to predict stroke in AF by 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT).Materials and MethodsFrom September 2017 to December 2020, we retrospectively enrolled 230 patients (115 with AF and 115 without AF as the non-AF group, matched for the date of PET/CT examination and the basic characteristics of the patient) who underwent 18F-FDG PET/CT due to tumor screening or preoperative staging after prolonged fasting and followed up for at least 12 months from the date of PET/CT examination; the endpoint event is the occurrence of stroke. We visually and quantitatively analyzed 18F-FDG uptake in the right and left atria (RA/LA), right and left atrial appendage (RAA/LAA), right and left ventricle (RV/LV), and collected clinical features. In addition, according to the endpoint event (stroke), the enrolled population was divided into the stroke group and non-stroke group, and relevant clinical features and atrial FDG uptake indicators of the two groups were analyzed. Univariate and multivariate Cox regression analyzes were used to analyze the risk factors of stroke events. The Kaplan–Meier survival curve of atrial FDG uptake was drawn, and the log-rank method was used to compare the differences in the survival curves of the two groups. Receiver operating characteristic (ROC) curves were used to examine the discriminatory power of atrial FDG uptake in predicting stroke and determine whether the addition of atrial FDG uptake improves predictive value beyond the CHA2DS2-VASc score for stroke.ResultsIn the AF group, more than half of patients had RA FDG uptake and one-fifth had LA FDG uptake, while one patient had RA FDG uptake and two patients had LA FDG uptake in the non-AF group. In quantitative analysis, the maximum standardized uptake value (SUVmax) of the RA and LA in the AF group was significantly higher than that of the non-AF group (all P < 0.001). We followed up the patients for 28 ± 10 months, and finally, 31 patients had stroke. In the stroke group, atrial fibrillation, RA SUVmax, RAA SUVmax, LAA SUVmax, age ≥ 75 years, and left atrial dilation were significantly higher than those of the non-stroke group (all P < 0.05). Multivariate Cox regression analysis showed that high RA SUVmax (RA SUVmax ≥ 2.62) was an independent risk factor for stroke (HR = 4.264, 95% CI 1.368–13.293, P = 0.012). By using the log-rank test, patients with high RA SUVmax had a significantly higher incidence of stroke compared with patients with low RA SUVmax (P < 0.001). Addition of high RA SUVmax to the CHA2DS2-VASc score could predict stroke more effectively, with a larger AUC 0.790 (P < 0.001).ConclusionThis study found a significant correlation between atrial FDG uptake and AF, especially in RA. Meanwhile, RA FDG uptake is an independent risk factor for stroke, and patients with high RA SUVmax have a significantly higher risk of stroke. Moreover, RA FDG uptake improves prediction of stroke above the CHA2DS2-VASc score in patients with AF.

A new cyclic peptide selapeptin B (

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

Purpose Root exudates play an important role in carbon sequestration in grassland, but the contribution of root exudates to different soil organic carbon (SOC) fractions is poorly understood.Methods In this study, Stipa bungeana was used as the research subject and labeled with 13CO2 in an indoor culture experiment.Results After labeling, the content of SOC and 13C-SOC in rhizosphere soil was larger than that in bulk soil. In rhizosphere, the content of 13C-MBC and 13C-HC increase for 95.77% and 46.44% at the first day after labeling. At the 65 days, the content of 13C-SOC increase for 40.76%, but the 13C-DOC and13C-MBC decrease for 71.79% and 55.56% in rhizosphere.Conclusion The influence of root exudates on SOC was mainly in the early stage, and the influence on SOC gradually decreased. Root exudates had a rapid effect on active organic carbon fractions (MBC and DOC), also affect the humus carbon (HC) in the short term. This study reveals the mechanism of root exudates on SOC pool during plant growth.

Background: Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from a complication of several central nervous system (CNS) infections owing to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose, which makes it easily misdiagnosed. Case presentation: We have reported here a 47-year-old male AIDS patient with visual ghosting and no sweat development on the left head and face. He was accordingly diagnosed with toxoplasma gondii encephalitis (TE) in other hospitals, for which he received regular anti-toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, albeit only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood sample was positive for toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, aspergillus fumigatus was detected in the cerebrospinal fluid with targeted next-generation sequencing (tNGS) and bronchofiberscope alveolar lavage fluid mNGS. The diagnosis was accordingly modified as CNSAG combined with his other clinical manifestations. After administering voriconazole anti-fungal therapy, the patient’s symptoms were relieved, with improved absorption of the intracranial lesions. Conclusions: The present case experience indicated the need for the clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) were helpful for the early diagnosis and treatment, whereby the patients could achieve favorable outcomes.

We present a simple hot press-based method for processing La(Fe,Si)13-based compounds consisting of La–Fe–Co–Si–C particles and phenolic resin. The magnetic entropy change ΔS per unit mass for the LaFe10.87Co0.63Si1.5C0.2/phenolic resin compounds have nearly the same magnitude with the base materials. With the content of phenolic resin of 5.0 wt%, the compound conductivity is 3.13 W⋅m−1⋅K−1. In order to measure the cooling performance of La(Fe,Si)13-based compounds, the La(Fe11.6–x Co x )Si1.4C0.15 (x = 0.60, 0.65, 0.75, 0.80, 0.85)/phenolic resin compounds were pressed into thin plates and tested in a hybrid refrigerator that combines the active magnetic refrigeration effect with the Stirling cycle refrigeration effect. The test results showed that a maximum cooling power of 41 W was achieved over a temperature span of 30 K.

Addiitional file 2: Supplementary Figure1. GRK3 expression in PDX tumors of GAC and paired primary tumor and PC. A. Diagram demonstrates the several patients’ PC cells (malignant ascites cells) into nude mice to generate PDXs (left). Western blot of GRK3 expression of Primary and ascites from PDX tumor generated from GAC patient (right). B. Representative co-immunofluorescent staining images of GRK3 and SOX9 expression on more PC specimen. Scale bars, 25µm. C. Representative co-immunofluorescent staining images of GRK3 and SOX9 expression on paired human primary tumor and PC samples. Scale bars, 25µm. Supplementary Figure 2. Overexpression of GRK3 in GAC cells increased malignant behaviors of GAC. A. Cell viability assay (MTS) was performed in MKN45-GRK3 and MKN45-GFP control cells. Fold increases of cell growth in day 6 and day 8 in media with the indicated FBS % was plotted on y-axis. **P

This thesis was scanned from the print manuscript for digital preservation and is copyright the author. Researchers can access this thesis by asking their local university, institution or public library to make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.

Additional file 1. Correlationanalysis of expression level of common bands probed by anti-total GR antibody and anti-GRα specific antibody.

Additional file 1: Supplementary Table 1. Designed guide RNA for GRK3 or YAP1knock-down. Supplementary Table 2. Primer sequences used in this study. Supplementary Table 3. Expression of GRK3 with patients’ characteristics. Supplementary Table 4. Univariate and Multivariate analysis of GRK3 in GAC patients. Supplementary Table 5. The correlation between GRK3 and YAP1 expression in GAC.

Gene regulatory networks (GRNs) model the interactions between gene expression regulators and their targets that mediate a myriad of biological functions. Constructing GRNs that integrate multiple data types at increased resolution is improving our understanding of the complex regulatory mechanisms controlling different biological processes in plants. Going beyond transcription factor binding and transcriptome profiles, GRNs that incorporate multiple data types, including chromatin accessibility and long-range chromatin interaction, transcription factor binding site motifs, microRNA, ribosome-associated RNA, and proteomic profiles, were constructed for several cell types and multiple species. The rise of single-cell RNA-seq applications in plants opens up possibilities for studying cell type–specific GRNs in the processes of cell differentiation, development, and responses to the environment. Applications of high-throughput reporter assays and genome editing technologies allow large-scale validation of GRNs. Future advances in refining plant GRNs will most likely involve integration of multi-omics single-cell data and methods for cross-species model translation.

The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics’ perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that, as in most cultivated white grape varieties, the uncolored skin section convened the non-functional alleles of the anthocyanin regulators MYBA1 and MYBA2, explaining the lack of pigments. In contrast, light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the flavonol, terpene and carotenoid pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity-purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of terpene (22) and carotenoid (6) genes, in addition to more than 30 photosynthesis and light-response genes, including the flavonol-regulator HY5 homologue (HYH). We confirmed the activation of TPS35 and HYH promoter:luciferase reporters in the presence of MYB24 and the grape bHLH MYC2, all of which correlate in their higher expression in white skin variegated sections. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonoids (flavonols) and isoprenoids (terpenes, and putatively carotenoids). The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.

This study aimed to investigate the protective effect and potential mechanism of Yinhuang oral liquid (YOL) against acetaminophen (APAP) induced liver injury in mice. C57BL/6 mice were randomly divided into control group, model group (300 mg/kg APAP), NAC group and YOL group. Mice were treated intragastrical with YOL (8 g/kg) and N-Acetylcysteine (NAC, 300 mg/kg) 6 h before and 6 h after the APAP (300 mg/kg) intraperitoneal injection. 12 h after APAP exposure, blood and liver samples were collected for subsequent testing. The results showed that APAP decreased liver index, induced liver pathological injury with hepatocytes swelling, necrosis and apoptosis and inflammatory cell infiltration. APAP exposure significantly increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels to 35 and 6 multiples than their original levels. YOL alleviated liver pathological damage, decreased the serum levels of ALT and AST in APAP exposure mice, and it worked better than NAC. Moreover, APAP promoted oxidative stress by increasing lipid peroxidation (MDA) and decreasing anti-oxidant enzyme activities of SOD and GSH, inhibited the mRNA levels of Nrf2, HO-1, Gclc and Gclm, and decreased the protein levels of Nrf2, HO-1 and Keap1, compared to control group. Furthermore, APAP exposure significantly down-regulated the mRNA and protein levels of autophagy related genes (Beclin-1, LC3-II, LC3-I, Atg4B, Atg5, Atg16L1 and Atg7). However, the gene levels of mTOR and p-mTOR increased, and p-ULK1 protein level decreased in liver of APAP treated mice. Additionally, YOL alleviated the oxidative injury by up-regulating Nrf2 pathway. The gene and protein levels of autophagy-related genes Beclin-1, LC3-II, LC3-I, Atg4B, Atg5, Atg16L1 and Atg7 reached the basal levels after YOL treatment. In conclusion, YOL had a protective and therapeutic role in APAP-induced liver injury in mice by activating Nrf2 signaling pathway and autophagy.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.

In the metabolic glycosylation grid of steviol glycosides, UGT76G1 was shown to catalyze at least eight different glucosylation steps, including the formation of rebaudioside B (Reb B) and rebaudioside A (Reb A) (Olsson et al., 2016). In this study, the accumulation of steviolbioside, Reb B, stevioside (ST) and Reb A in more than 140 samples of stevia leaves collected from different regions in China were analyzed by high-performance liquid chromatography (HPLC), and five genotypes, ‘N01-N05’, with significantly different levels of the abovementioned glycosides were discovered. Mutations in the UGT76G1 gene cloned from cDNAs from these five genotypes were identified, and the functions of the recombinant UGT76G1 variants were ascertained by adding steviolbioside and ST substrates. In addition, homology modeling and molecular docking were used to elucidate the functional differences between variants and UGT76G1. Comparing the sequences of the five variants ‘N01-N05’ with UGT76G1 (AY345974.1) revealed that base substitutions were not observed in ‘N01’. By contrast, ‘N02’ exhibited 9 single nucleotide polymorphisms (SNPs) and 9 associated amino acid substitutions or insertions with notable variations in the protein structure; however, an enzyme assay showed similar functionalities between the variant and UGT76G1. In ‘N03’, 49 SNPs and 29 associated amino acid substitutions or insertions were identified and shown to induce significant variations in the protein structure, especially in the binding pocket, resulting in the lack of functionality of this variant in the enzyme assay. These results were in agreement with the docking profiles. Moreover, a nonsense mutation of p.1090T > G in ‘N04’ and an insertion of a 68 base fragment in ‘N05’ were found, and both produced a premature protein without any catalytic activity. Therefore, UGT76G1, which is vital to the content of main steviol glycosides, should be a key gene marker for the molecular breeding of Stevia rebaudiana. Our investigations also revealed the location and orientation of active groups of the receptors and donors in the UGT76G1 enzyme, which play key roles in determining whether the enzyme has any enzymatic activity.

To investigate the immunopathology and immunomodulatory roles of interleukin-12 (IL-12) in periodontal disease.Ninety-eight patients with chronic periodontitis from January 2016 to January 2019 were enrolled and divided into mild group (30 cases), moderate group (35 cases) and severe group (33 cases) according to the severity of periodontitis; meanwhile, 30 healthy subjects who underwent periodontal examination in our hospital were selected as the control group. Clinical periodontal indicators including probing depth(PD), attachment loss(AL), plaque index(PLI), bleeding index(BI), Th cell expression (Th1, Th2, Th17) in peripheral blood, IL-12 levels in gingival crevicular fluid (GCF) and serum were measured. SPSS 20.0 software package was performed to analyze the correlation between IL-12 levels in GCF and serum and Th1, Th2, Th17, PD, AL, PLI, and BI.The differences of PD, PLI and BI among the groups were statistically significant(P0.05). The levels of PD, PLI and BI in the mild, moderate and severe group were significantly higher than those in the control group (P0.05). The difference of AL index among mild, moderate and severe group was statistically significant(P0.05). The PD, AL, PLI, and BI in the moderate and severe group was significantly higher than those in the mild group(P0.05), and the severe group was significantly higher than the mild group(P0.05). Th1, Th2 and Th17 were significantly higher in the mild, moderate and severe group than in the control group(P0.05); the moderate, severe group was significantly higher than the mild group in terms of Th1, Th2 and Th17 (P0.05), and the severe group was significantly higher than the moderate group (P0.05). The IL-12 levels in GCF and serum of the mild, moderate, and severe groups were significantly higher than those of the control group (P0.05); IL-12 levels in the the moderate and severe groups were significantly higher than those in the mild group (P0.05), and the IL-12 were significantly higher in the severe group than in the moderate group (P0.05); IL-12 was positively correlated with PD, AL, PLI, BI, Th1, Th2 and Th17(P0.05). H-E staining showed there were fewer lymphocytes in the mild group, more lymphocytes in the moderate group, and dense lymphocytes in the severe group with significant hemorrhage in intercellular mesenchyme. The IL-12 protein positive staining results were expressed in gingival tissue lymphocyte pulp with significant brown observed. The positive staining of IL-12 protein in the gingival tissues in the mild, moderate and severe group was significantly higher than in the control group, and the staining was aggravated with mild, moderate and severe inflammatory changes.IL-12 is involved in the immunoregulatory mechanism of periodontal disease and may be a key pro-inflammatory cytokine in the development of periodontitis.

The stilbenoid pathway is responsible for the production of resveratrol and its derivatives in grapevine. A few transcription factors (TFs) have been previously identified as regulators of this pathway but the extent of this control is yet to be fully understood. Here we demonstrate how DNA affinity purification sequencing (DAP-Seq) allows for genome-wide TF binding site interrogation in a non-model species. We obtained 5,190 and 4,443 binding events assigned to 4,041 and 3,626 genes for MYB14 and MYB15, respectively (around 40% of peaks being located within -10kb of transcription start sites). DAP-Seq of MYB14 and MYB15 was combined with aggregate gene centred co-expression networks built from more than 1,400 transcriptomic datasets from leaves, fruits and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15 and MYB13, a third uncharacterised member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS ) targets, these three regulators bind to 30 out of 47 STS family genes. Moreover all three MYBs bind to several PAL, C4H and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and novel resveratrol-modifying gene candidates amongst which ROMT2 -3 were validated enzymatically. A high proportion of DAP-Seq bound genes was induced in the activated transcriptomes of transient MYB15 -overexpressing stilbenoid-producing grapevine leaves, validating our methodological approach for identifying gene regulatory networks of specialised metabolism. Overall, MYB genes from Subgroup 2 appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production.

Note: for full list of Plant Cell Atlas Consortium, see publication (p17). With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them., National Science Foundation 1916797 David W Ehrhardt, Kenneth D Birnbaum, Seung Yon Rhee; National Science Foundation 2052590 Seung Yon Rhee

As the main participants of ecosystem functions, the response of microorganisms to variations in soil moisture caused by the changes in precipitation amounts should be quantified to evaluate the impact of climate change on semi-arid ecosystems. For this purpose, a two-year simulation of the changes in the rainfall patterns was conducted on the Loess Plateau, and five precipitation treatments (80% and 40% decrease in precipitation, D80, D40; natural precipitation, NP; 40% and 80% increase in precipitation, I40, I80) were set up. The results showed that: ① Compared with NP, the carbon-to-nitrogen ratio (C/N) was lower in DP80 or IP80, while it reached the maximum value in I40. The mean C/N value of the 0-20 cm soil layer was 10.76. The microbial biomass carbon to microbial biomass nitrogen ratio (MBC/MBN) varied significantly with the soil layer in the treatments of D80 and I80, and the maximum value was 14.15 in D80. ② In the grassland soil naturally growing on the Loess Plateau, at the phylum level, the dominant phyla were Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. At the class level, Actinobacteria, Acidobacteria

Significance The endocannabinoid system has a modulatory role in brain reward and cognitive processes. It has been hypothesized that repeated interference with endocannabinoid signaling (e.g., through abuse of cannabis or synthetic cannabinoids) can remodel the adolescent brain and make it respond differently to more addictive substances, such as cocaine. In the present study, we demonstrate that a history of synthetic cannabinoid exposure in adolescent animals results in distinct molecular and epigenetic changes following initial exposure to cocaine. These changes were pronounced in the prefrontal cortex and associated with an enhanced response to cocaine’s stimulatory effects. The prefrontal cortex is a brain region that still undergoes maturation in adolescence and its dysfunction contributes to the development of addictions., The initial response to an addictive substance can facilitate repeated use: That is, individuals experiencing more positive effects are more likely to use that drug again. Increasing evidence suggests that psychoactive cannabinoid use in adolescence enhances the behavioral effects of cocaine. However, despite the behavioral data, there is no neurobiological evidence demonstrating that cannabinoids can also alter the brain’s initial molecular and epigenetic response to cocaine. Here, we utilized a multiomics approach (epigenomics, transcriptomics, proteomics, and phosphoproteomics) to characterize how the rat brain responds to its first encounter with cocaine, with or without preexposure to the synthetic cannabinoid WIN 55,212-2 (WIN). We find that in adolescent (but not in adult) rats, preexposure to WIN results in cross-sensitization to cocaine, which correlates with histone hyperacetylation and decreased levels of HDAC6 in the prefrontal cortex (PFC). In the PFC, we also find that WIN preexposure blunts the typical mRNA response to cocaine and instead results in alternative splicing and chromatin accessibility events, involving genes such as Npas2. Moreover, preexposure to WIN enhances the effects of cocaine on protein phosphorylation, including ERK/MAPK-targets like gephyrin, and modulates the synaptic AMPAR/GluR composition both in the PFC and the nucleus accumbens (NAcc). PFC–NAcc gene network topological analyses, following cocaine exposure, reveal distinct top nodes in the WIN preexposed group, which include PACAP/ADCYAP1. These preclinical data demonstrate that adolescent cannabinoid exposure reprograms the initial behavioral, molecular, and epigenetic response to cocaine.

Single-cell genomics and particularly single-cell transcriptome profiling by RNA sequencing (scRNA-seq) have transformed the possibilities to relate genes to functions, structures, and eventually phenotypes. We can now observe changes in each cell’s transcriptome and among its neighborhoods, interrogate the sequence of transcriptional events, and assess their influence on subsequent events. This paradigm shift in biology enables us to infer causal relationships in these events with high accuracy. Here we review the latest single-cell studies in plants that uncover how cellular phenotypes emerge as a result of the transcriptome process such as waves of expression, trajectories of development and responses to the environment, and spatial information. With an eye on the advances made in animal and human studies, we further highlight some of the needed areas for future research and development, including computational methods.

To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro-expressed TF, and TF-DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be derived. A researcher with molecular biology experience should be able to follow this protocol, processing up to 400 samples per week.

Decades of ecological restoration on the Loess Plateau has achieved significant on-site benefits to reduce soil erosion and improve soil quality, with remarkable off-site effects of reducing sediment delivery to Yellow River. However, regional forest community succession is still far from being adequately developed. The Ziwuling forest region and its highly developed forest community, as an advanced eco-zone, can lend practical experience to other regions on the Loess Plateau and help to identify the most suitable tree species for a better regional restoration in the future. With the aim to systematically understand the potential effects of typical local tree species to soil properties, three typical and well-established artificial forests in the Ziwuling region, Robinia pseudoacacia, Pinus tabuliformis and Platycladus orientalis were investigated in this study, with the climax community Quercus wutaishanica as a reference. All the four forest type had comparable stand age (25 years). Soil samples from 0-20 cm layers were collected from those four plantations. The soil microbial biomass (carbon and nitrogen), soil enzyme (invertase, urease and alkaline phosphatase) activities and their correlations were measured and analyzed. The results showed that: 1) soil invertase activity ranged from 16.94 to 64.49 mg·g数十年来,黄土高原的生态恢复取得了显著的效益,不仅遏制了当地的土壤流失,改善了土壤质量,同时也减少了向黄河的输沙量.但是,区域森林物种和群落演替还远未得到充分发展.子午岭林区及其高度发达的森林群落,作为先进的生态区,可以将实践经验和知识借鉴到中国黄土高原的其他地区,有助于确定最有效的人工林树种,以便今后更好地进行生态恢复.为了系统地了解典型的当地树种对土壤性质的潜在影响,本研究以黄土高原子午岭天然次生林区生长状况较好的人工林(刺槐、油松和侧柏)为研究对象,并以子午岭林区顶极群落辽东栎天然林为对照,这4种林型具有较一致的树龄(25年)、立地条件等.采用传统方法测定4种乔木林0～20 cm土壤理化性质、土壤酶活性(蔗糖酶、脲酶和碱性磷酸酶)和土壤微生物生物量碳、氮.结果表明: 1)土壤蔗糖酶活性为16.94～64.49 mg·g

Carbon (C), nitrogen (N) and phosphorus (P) stoichiometry from the aboveground parts of plants, roots, plant litter and soils, as well as their relationships were studied in grassland under four distinct types of vegetation recovery including natural grassland, grassland with shrubs, grassland after grazing exclusion, and abandoned cropland in Yunwu Mountain, China. The results showed that there was significant correlation among the ecological stoichiometric characteristics of soils with the aboveground parts and roots. The relation between the aboveground parts and roots was closer in P concentration than in N concentration. The linkage of plants and soils was closer in N concentration than in P concentration. The ecological stoichiometric relationships between soils and litter as well as between roots and litter were weak. There was no significant difference between the aboveground parts and roots in total C and N storages among four distinct recovery methods. How-ever, the P storage differed greatly among the four recovery types with the maximum of 0.49 g·m研究云雾山天然草地、灌草地、禁牧地、撂荒地4种恢复方式下草地各植物组分(植物地上部分、枯落物、根系)与土壤C、N、P化学计量特征及其相互关系.结果表明: 土壤与植物地上部分和根系的化学计量学特征显著相关,并且植物地上部分与根系之间P的联系比N紧密,土壤与植物地上部分和根系之间N的联系比P紧密,而土壤与枯落物、根系与枯落物的化学计量学特征相关性不显著.不同恢复方式间植物地上部分和根系总体的C、N储量无显著差异,P储量差异显著且以撂荒地最大(0.49 g·m

This study was conducted in the forest, forest-steppe and steppe vegetation zones along the Yanhe River Basin, where the leaf and litter samples from four dominant herbaceous plants including Lespedeza davurica, Stipa bungeana, Artemisia sacrorum, Artemisia giraldii were taken. By measuring the concentrations of carbon (C), nitrogen (N), phosphorus (P) and potassium (K), we measured the concentrations and their ratios to explore the limit and resorption of nutrient in the herbaceous plants. The results showed that the leaf N/P of four herbaceous plants was all lower than 14, suggesting their growth was mainly limited by N content. Except for L. davurica, the mean nutrient resorption efficiency of K, N and P in the other three plants was 79.9%, 48.7% and 32.5%, respectively. The higher nutrient resorption efficiency and K concentration in the leaf were beneficial for soil water competition of A. sacrorum and A. giraldii. The litter C/N in A. sacrorum was significantly lower than that in S. bungeana and A. giraldii, which was easy to decompose to benefit the nutrient recycling. This resulted in the wide distribution of A. sacrorum in the three vegetation areas.以黄土高原延河流域森林、森林草原和草原3个植被区的4种典型草本植物达乌里胡枝子、长芒草、铁杆蒿、茭蒿的叶片和枯落物为对象,测定叶片和枯落物中碳(C)、氮(N)、磷(P)、钾(K)含量及其比值,分析草本植物在该区域的养分限制及再吸收规律.结果表明: 4种植物叶片N/P均小于14,生长主要受氮元素含量限制;除达乌里胡枝子外,其他3种植物N、P、K的养分再吸收效率平均值分别为48.7%、32.5%、79.9%.茭蒿和铁杆蒿较高的N、P、K养分再吸收效率和叶片K含量有助于其在水分竞争中占据优势.铁杆蒿枯落物的C/N显著低于长芒草和茭蒿的枯落物,因而更易分解和进行养分循环.这可能是铁杆蒿在3个植被区分布广泛的原因之一.

With the method of litter bags, the characteristics of soil enzyme activities, soil microbial diversity at later stage of decomposition, and the relationships between soil enzyme activity and initial soil property were investigated in the process of stem and leaf decomposition of three typical herbs, i.e., Stipa bungeana, Artemisia sacrorum and Thymus mongolicus in the south Ningxia loess hilly region, Northwest China. The results showed that soil enzyme activity increased under different treatments after 480 d during stem and leaf decomposition. Soil sucrose activity (32.40 mg·g采用凋落物分解袋法,以宁南山区典型草本植物长芒草、铁杆蒿、百里香为研究对象,分析了3种植物茎叶分解过程中土壤酶活性变化特征和分解后期微生物多样性特征,以及土壤酶活性与初始土壤化学性质的关系.结果表明: 植物茎叶分解480 d后,各处理土壤酶活性均有不同程度的增加,且长芒草处理土壤蔗糖酶活性和碱性磷酸酶活性最高,分别为32.40和1.99 mg·g

In order to research into the influence of Grain to Green Project in Ziwuling forest region, this paper took three typical plantations which were Robinia pseudoacacia plantation, Pinus tabuliformis plantation, and Platycladus orientalis plantation in the Ziwuling forest region of Shaanxi Province as research objects and analyzed the carbon, nitrogen and phosphorus contents of leaf, litter and soil among the three plantations. The results showed that the contents of C, N and P in the three plantations were in order of leaflittersoil, the contents of N and P in leaf of R. pseu-doacacia plantation were significantly higher than that of P. tabuliformis plantation and P. orientalis. Leaf N:P was 12.21, 5.36 and 6.09 in R. pseudoacacia plantation, P. tabuliformis plantation and P. orientalis plantation, respectively. It was indicated that the three species were all subject to N deficiency. C:N and C:P showed the trend of litterleafsoil, and N:P demonstrated the trend of leaflittersoil. There were highly significant positive relationships in C:N between leaf and litter in P. tabuliformis plantation. N and P in the leaf development process of R. pseu-doacacia plantation were proportionally absorbed, and proportionally remained in the litter after N and P resorption. R. pseudoacacia was the better plantation species than P. tabuliformis and P. orientalis in the south fo-rest zone on the Loess Plateau.为探究“退耕还林(牧)”工程对陕西省子午岭林区的影响,分析3种典型的人工林(刺槐林、油松林和侧柏林)叶片-凋落叶-土壤的C、N、P含量及其生态化学计量特征.结果表明: 3种人工林不同组分中C、N、P含量大小均为叶片凋落叶土壤,刺槐林叶片N、P含量显著高于油松林和侧柏林.刺槐林、油松林和侧柏林叶片N∶P分别为12.2、5.4和6.1,油松和侧柏较刺槐林存在N亏损,C∶N和C∶P大小均为凋落叶叶片土壤,N∶P为叶片凋落叶土壤.油松林叶片C∶N与凋落叶C∶N间存在显著正相关关系.刺槐叶片在生长周期内吸收利用的N和P存在比例关系,且其凋落叶在元素再吸收后N和P的残留量也存在比例关系.与油松和侧柏相比,刺槐是黄土高原南部森林带最适宜的造林树种.

Plants have evolved various mechanisms that protect against the harmful effects of UV-B radiation (280–315 nm) on growth and development. Cyclobutane pyrimidine dimer (CPD) photolyase, the repair enzyme for UV-B-induced CPDs, is essential for protecting cells from UV-B radiation. Expression of the CPD photolyase gene (PHR) is controlled by light with various wavelengths including UV-B, but the mechanisms of this regulation remain poorly understood. In this study, we investigated the regulation of PHR expression by light with various wavelengths, in particular low-fluence UV-B radiation (280 nm, 0.2 µmol m–2 s –1), in Arabidopsis thaliana seedlings grown under light–dark cycles for 7 d and then adapted to the dark for 3 d. Low-fluence UV-B radiation induced CPDs but not reactive oxygen species. AtPHR expression was effectively induced by UV-B, UV-A (375 nm) and blue light. Expression induced by UV-A and blue light was predominantly regulated by the cryptochrome-dependent pathway, whereas phytochromes A and B played a minor but noticeable role. Expression induced by UV-B was predominantly regulated by the UVR8-dependent pathway. AtPHR expression was also mediated by a UVR8-independent pathway, which is correlated with CPD accumulation induced by UV-B radiation. These results indicate that Arabidopsis has evolved diverse mechanisms to regulate CPD photolyase expression by multiple photoreceptor signaling pathways, including UVR8-dependent and -independent pathways, as protection against harmful effects of UV-B radiation.

5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology.