Physiological Responses and Tolerance Evaluation of Five Poplar Varieties to Waterlogging

Waterlogging resistance of five poplar varieties, ‘Danhongyang’ (DHY), ‘Juba-261’ (JB-261), ‘Zongqiansanhao’ (ZQ-3), ‘Zhonglin-2025’ (ZL-2025), and ‘Nanlin-895’ (NL-895), was evaluated under the simulated waterlogging conditions. Data on changes in leaf color and morphology as well as in biochemical indices, such as chlorophyll, malonaldehyde, soluble protein, soluble sugar content, superoxide dismutase (SOD), peroxidases (POD), ascorbate peroxidase (APX), glutathione reductase (GR), and glutathione peroxidase (GSH-PX) activities, relevant to submergence stress, were analyzed. The principal component analysis of the data identified the waterlogging resistance coefficient of the indices, which showed that waterflooding brought about different degrees of damage in the five poplar varieties, with DHY having the lowest waterlogging index. The leaf pigment content of the poplar was remarkably decreased by waterlogging, whereas malondialdehyde (MDA) and proline contents were enhanced, but in different extents among the poplar varieties. Nearly all other poplar varieties showed a tendency of decline in JB-261, ZQ-3, ZL-2025, NL-895, except for SOD activity in DHY, which increased under submergence stress. Poplar varieties had varying degree of changes in POD activity, and APX activity tended to increase upon waterlogging. GR also displayed increasing tendency in JB-261, ZL-2025 and NL-895, except for in ZQ-3, which declined under waterlogging stress. GSH-PX except for ZQ-3 displayed no significant change, which showed a tendency of decline in DHY, JB-261, ZL-2025, and NL895. Principal component analysis allowed us to reduce16 indices to four independent indices. The subordinate function analysis identified that the DHY variety had the highest waterlogging tolerance, whereas the NL-895 variety had the lowest waterlogging tolerance among tested varieties

Leptin Increases Expression of 5-HT2B Receptors in Astrocytes Thus Enhancing Action of Fluoxetine on the Depressive Behavior Induced by Sleep Deprivation

The long-lasting loss of sleep is a generally acknowledged risk factor for the occurrence of major depressive disorder (MDD), whereas sleep abnormalities being a key clinic symptom of the MDD. In our previous work, we demonstrated that the sleep deprivation (SD) stimulates activation of nucleotide-binding domain and leucine-rich repeat protein-3 (NLRP3) inflammasomes as well as the release of IL-1β and IL-18 from astrocytes. However, the underlying mechanism connecting SD and MDD still requires further study. Apart of the secretion of the pro-inflammatory cytokines, SD affects production of brain-derived neurotrophic factor (BDNF) while release of BDNF from astrocytes appears a key contributor to mood disorders. If and how the activation of NLRP3 inflammasome following SD affects the level of BDNF remains unknown. Antidepressant fluoxetine acts through astroglial 5-hydroxytryptamine receptor 2B (5-HT2B); these receptors are also related to the sleep-wake cycle. Contribution of leptin to MDD has been discovered recently, although the mechanistic links between leptin and the depressive-like behaviors has not been revealed. In this study, we discovered: (i) that activation of NLRP3 inflammasome was involved in the depressive-like behaviors induced by SD; (ii) decrease in BDNF following SD required the activation of NLRP3 inflammasomes; (iii) leptin augmented the anti-depressive action of fluoxetine through an increase in expression of astrocytic 5-HT2B receptors. We suggest that decrease in BDNF by the activated NLRP3 inflammasomes in astrocytes is the key pathological event of the depressive-like behaviors induced by SD, while the combined treatment with fluoxetine and leptin improves therapeutic outcome for the depression induced by SD

Transcriptomic analysis reveals transcription factors involved in vascular bundle development and tissue maturation in ginger rhizomes (Zingiber officinale Roscoe)

Ginger (Zingiber officinale Roscoe) is an important vegetable with medicinal value. Rhizome development determines ginger yield and quality. However, little information is available about the molecular features underlying rhizome expansion and maturation. In this study, we investigated anatomy characteristics, lignin accumulation and transcriptome profiles during rhizome development. In young rhizomes, the vascular bundle (VB) was generated with only vessels in it, whereas in matured rhizomes, three to five layers of fibre bundle in the xylem were formed, resulting in VB enlargement. It indicates VB development favouring rhizome swelling. With rhizome matured, the lignin content was remarkably elevated, thus facilitating tissue lignification. To explore the regulators for rhizome development, nine libraries including ginger young rhizomes (GYR), growing rhizomes (GGR), and matured rhizomes (GMR) were established for RNA-Seq, a total of 1264 transcription factors (TFs) were identified. Among them, 35, 116, and 14 differentially expressed TFs were obtained between GYR and GGR, GYR and GMR, and GGR and GMR, respectively. These TFs were further divided into three categories. Among them, three ZobHLHs (homologs of Arabidopsis LHW and AtbHLH096) as well as one DIVARICATA homolog in ginger might play crucial roles in controlling VB development. Four ZoWRKYs and two ZoNACs might be potential regulators associated with rhizome maturation. Three ZoAP2/ERFs and one ZoARF might participate in rhizome development via hormone signalling. This result provides a molecular basis for rhizome expansion and maturation in ginger

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

INTRODUCTION Although much effort has been devoted to studying yeast in the past few decades, our understanding of this model organism is still limited. Rapidly developing DNA synthesis techniques have made a “build-to-understand” approach feasible to reengineer on the genome scale. Here, we report on the completion of a 770-kilobase synthetic yeast chromosome II (synII). SynII was characterized using extensive Trans-Omics tests. Despite considerable sequence alterations, synII is virtually indistinguishable from wild type. However, an up-regulation of translational machinery was observed and can be reversed by restoring the transfer RNA (tRNA) gene copy number. RATIONALE Following the “design-build-test-debug” working loop, synII was successfully designed and constructed in vivo. Extensive Trans-Omics tests were conducted, including phenomics, transcriptomics, proteomics, metabolomics, chromosome segregation, and replication analyses. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium. RESULTS To efficiently construct megabase-long chromosomes, we developed an I- Sce I–mediated strategy, which enables parallel integration of synthetic chromosome arms and reduced the overall integration time by 50% for synII. An I- Sce I site is introduced for generating a double-strand break to promote targeted homologous recombination during mitotic growth. Despite hundreds of modifications introduced, there are still regions sharing substantial sequence similarity that might lead to undesirable meiotic recombinations when intercrossing the two semisynthetic chromosome arm strains. Induction of the I- Sce I–mediated double-strand break is otherwise lethal and thus introduced a strong selective pressure for targeted homologous recombination. Since our strategy is designed to generate a markerless synII and leave the URA3 marker on the wild-type chromosome, we observed a tenfold increase in URA3 -deficient colonies upon I- Sce I induction, meaning that our strategy can greatly bias the crossover events toward the designated regions. By incorporating comprehensive phenotyping approaches at multiple levels, we demonstrated that synII was capable of powering the growth of yeast indistinguishably from wild-type cells (see the figure), showing highly consistent biological processes comparable to the native strain. Meanwhile, we also noticed modest but potentially significant up-regulation of the translational machinery. The main alteration underlying this change in expression is the deletion of 13 tRNA genes. A growth defect was observed in one very specific condition—high temperature (37°C) in medium with glycerol as a carbon source—where colony size was reduced significantly. We targeted and debugged this defect by two distinct approaches. The first approach involved phenotype screening of all intermediate strains followed by a complementation assay with wild-type sequences in the synthetic strain. By doing so, we identified a modification resulting from PCRTag recoding in TSC10 , which is involved in regulation of the yeast high-osmolarity glycerol (HOG) response pathway. After replacement with wild-type TSC10 , the defect was greatly mitigated. The other approach, debugging by SCRaMbLE, showed rearrangements in regions containing HOG regulation genes. Both approaches indicated that the defect is related to HOG response dysregulation. Thus, the phenotypic defect can be pinpointed and debugged through multiple alternative routes in the complex cellular interactome network. CONCLUSION We have demonstrated that synII segregates, replicates, and functions in a highly similar fashion compared with its wild-type counterpart. Furthermore, we believe that the iterative “design-build-test-debug” cycle methodology, established here, will facilitate progression of the Sc2.0 project in the face of the increasing synthetic genome complexity. SynII characterization. ( A ) Cell cycle comparison between synII and BY4741 revealed by the percentage of cells with separated CEN2-GFP dots, metaphase spindles, and anaphase spindles. ( B ) Replication profiling of synII (red) and BY4741 (black) expressed as relative copy number by deep sequencing. ( C ) RNA sequencing analysis revealed that the significant up-regulation of translational machinery in synII is induced by the deletion of tRNA genes in synII. </jats:sec

Transcriptome Analysis Reveals Molecular Signatures of Luteoloside Accumulation in Senescing Leaves of Lonicera macranthoides

Lonicera macranthoides is an important medicinal plant widely used in traditional Chinese medicine. Luteoloside is a critical bioactive compound in L. macranthoides. To date, the molecular mechanisms underlying luteoloside biosynthesis are still largely unknown. In this work, high performance liquid chromatography (HPLC) was employed to determine the luteoloside contents in leaves, stems, and flowers at different developmental stages. Results showed that senescing leaves can accumulate large amounts of luteoloside, extremely higher than that in young and semi-lignified leaves and other tissues. RNA-Seq analysis identified that twenty-four differentially expressed unigenes (DEGs) associated with luteoloside biosynthesis were significantly up-regulated in senescing leaves, which are positively correlated with luteoloside accumulation. These DEGs include phenylalanine ammonia lyase 2, cinnamate 4-hydroxylase 2, thirteen 4-coumarate-CoA ligases, chalcone synthase 2, six flavonoid 3′-monooxygenase (F3′H) and two flavone 7-O-β-glucosyltransferase (UFGT) genes. Further analysis demonstrated that two F3′Hs (CL11828.Contig1 and CL11828.Contig2) and two UFGTs (Unigene2918 and Unigene97915) might play vital roles in luteoloside generation. Furthermore, several transcription factors (TFs) related to flavonoid biosynthesis including MYB, bHLH and WD40, were differentially expressed during leaf senescence. Among these TFs, MYB12, MYB75, bHLH113 and TTG1 were considered to be key factors involved in the regulation of luteoloside biosynthesis. These findings provide insights for elucidating the molecular signatures of luteoloside accumulation in L. macranthoides

Constructing the Logical Regression Model to Predict the Target of Jianpi Jiedu Decoction in the Treatment of Hepatocellular Carcinoma

Objectives. The purpose of this study was to identify the molecular mechanism and prognosis-related genes of Jianpi Jiedu decoction in the treatment of hepatocellular carcinoma. Methods. The gene expression data of hepatocellular carcinoma samples and normal tissue samples were downloaded from TCGA database, and the potential targets of drug composition of Jianpi Jiedu decoction were obtained from TCMSP database. The genes were screened out in order to obtain the expression of these target genes in patients with hepatocellular carcinoma. The differential expression of target genes was analyzed by R software, and the genes related to prognosis were screened by univariate Cox regression analysis. Then, the LASSO model was constructed for risk assessment and survival analysis between different risk groups. At the same time, independent prognostic analysis, GSEA analysis, and prognostic analysis of single gene in patients with hepatocellular carcinoma were performed. Results. 174 compounds of traditional Chinese medicine were screened by TCMSP database, corresponding to 122 potential targets. 39 upregulated genes and 9 downregulated genes were screened out. A total of 20 candidate prognostic related genes were screened out by univariate Cox analysis, of which 12 prognostic genes were involved in the construction of the LASSO regression model. There was a significant difference in survival time between the high-risk group and low-risk group (p<0.05). Among the genes related to prognosis, the expression levels of CCNB1, NQO1, NUF2, and CHEK1 were high in tumor tissues (p<0.05). Survival analysis showed that the high expression levels of these four genes were significantly correlated with poor prognosis of HCC (p<0.05). GSEA analysis showed that the main KEGG enrichment pathways were lysine degradation, folate carbon pool, citrate cycle, and transcription factors. Conclusions. In the study, we found that therapy target genes of Jianpi Jiedu decoction were mainly involved in metabolism and apoptosis in hepatocellular carcinoma, and there was a close relationship between the prognosis of hepatocellular carcinoma and the genes of CCNB1, NQO1, NUF2, and CHEK1

Fabrication, Structure, Performance, and Application of Graphene-Based Composite Aerogel

Graphene-based composite aerogel (GCA) refers to a solid porous substance formed by graphene or its derivatives, graphene oxide (GO) and reduced graphene oxide (rGO), with inorganic materials and polymers. Because GCA has super-high adsorption, separation, electrical properties, and sensitivity, it has great potential for application in super-strong adsorption and separation materials, long-life fast-charging batteries, and flexible sensing materials. GCA has become a research hotspot, and many research papers and achievements have emerged in recent years. Therefore, the fabrication, structure, performance, and application prospects of GCA are summarized and discussed in this review. Meanwhile, the existing problems and development trends of GCA are also introduced so that more will know about it and be interested in researching it

Sleep Deprivation Selectively Down-Regulates Astrocytic 5-HT_2B Receptors and Triggers Depressive-Like Behaviors via Stimulating P2X₇ Receptors in Mice

Chronic loss of sleep damages health and disturbs the quality of life. Long-lasting sleep deprivation (SD) as well as sleep abnormalities are substantial risk factors for major depressive disorder, although the underlying mechanisms are not clear. Here, we showed that chronic SD in mice promotes a gradual elevation of extracellular ATP, which activates astroglial P2X7 receptors (P2X7Rs). Activated P2X7Rs, in turn, selectively down-regulated the expression of 5-HT2B receptors (5-HT2BRs) in astrocytes. Stimulation of P2X7Rs induced by SD selectively suppressed the phosphorylation of AKT and FoxO3a in astrocytes, but not in neurons. The over-expression of FoxO3a in astrocytes inhibited the expression of 5-HT2BRs. Down-regulation of 5-HT2BsRs instigated by SD suppressed the activation of STAT3 and relieved the inhibition of Ca2+-dependent phospholipase A2. This latter cascade promoted the release of arachidonic acid and prostaglandin E2. The depression-like behaviors induced by SD were alleviated in P2X7R-KO mice. Our study reveals the mechanism underlying chronic SD-induced depression-like behaviors and suggests 5-HT2BRs as a key target for exploring therapeutic strategies aimed at the depression evoked by sleep disorders.</p