Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.

Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.

Identification of novel circulating miRNAs biomarkers for healthy obese and lean children.

BACKGROUND: The prevalence of childhood obesity and overweight has risen globally, leading to increased rates of metabolic disorders. Various factors, including genetic, epigenetic, and environmental influences such as diet and physical activity, contribute to pediatric obesity. This study aimed to identify specific circulating miRNAs as potential biomarkers for assessing obesity in children. METHODS: Thirty children, including 15 obese and 15 extremely thin individuals, were selected for this study. MiRNA expression in circulating plasma was assessed using miRNA microarrays. The reliability of differential miRNA expression was confirmed using TaqMan qPCR. The correlation between miRNAs and obesity was analyzed through multiple linear regression, receiver operator characteristic (ROC) curve analysis, and odds ratio (OR) calculations. Bioinformatics tools were utilized to identify target genes for the selected miRNAs, and a functional network map was constructed. RESULTS: A total of 36 differentially expressed miRNAs were identified through gene chip analysis, and TaqMan qPCR validation confirmed the upregulation of seven miRNAs: hsa-miR-126-3p, hsa-miR-15b-5p, hsa-miR-199a-3p, hsa-miR-20a-5p, hsa-miR-223-3p, hsa-miR-23a-3p, and hsa-miR-24-3p. Among these, hsa-miR-15b-5p and hsa-miR-223-3p exhibited a statistically significant difference except for hsa-miR-23a-3p. These two miRNAs showed more predicted target genes related to obesity than others. Multiple linear regression analysis revealed an association between obesity and hsa-miR-15b-5p and hsa-miR-223-3p [10.529 (4.974-16.084), -10.225 (-17.852~ -2.657)]. Even after adjusting for age and sex, these two miRNAs remained associated with obesity [8.936 (3.572-14.301), -8.449(-15.634~ -1.303)]. The area under the ROC curve (AUC) reached values of 0.816, 0.711, and 0.929, respectively. Odds ratio analysis demonstrated a significant correlation between obesity and hsa-miR-15b-5p (OR = 143, 95% CI 5.80 to 56,313, p = 0.024) and between obesity and hsa-miR-223-3p (OR = 0.01, 95% CI 0.00 to 0.23, p = 0.037). Importantly, hsa-miR-15b-5p was found to have numerous target genes associated with the FoxO, insulin, Ras, and AMPK signaling pathways. CONCLUSIONS: Differential miRNA expression profiles in the circulation of obese children compared to controls suggest underlying metabolic abnormalities. Hsa-miR-15b-5p and hsa-miR-223-3p may be considered as molecular markers for the screening of obese children and populations at risk of developing metabolic syndrome.

Genome-wide analysis of AP2/ERF superfamily in lotus (Nelumbo nucifera) and the association between NnADAP and rhizome morphology.

BACKGROUND: The AP2/ERF family is widely present in plants and plays a crucial regulatory role in plant growth and development. As an essential aquatic horticultural model plant, lotus has an increasingly prominent economic and research value. RESULTS: We have identified and analysed the AP2/ERF gene family in the lotus. Initially, 121 AP2/ERF family genes were identified. By analysing their gene distribution and protein structure, and their expression patterns during the development of lotus rhizome, combined with previous studies, we obtained an SNP (megascaffold_20:3578539) associated with lotus rhizome phenotype. This SNP was in the NnADAP gene of the AP2 subfamily, and the changes in SNP (C/T) caused amino acid conversion (proline/leucine). We constructed a population of 95 lotus varieties for SNP verification. Through population typing experiments, we found that the group with SNP CC had significantly larger lotus rhizome and higher soluble sugar content among the population. CONCLUSIONS: In conclusion, we speculate that the alteration of the SNP in the NnADAP can affect the size and sugar content of the lotus rhizome.

A CONSTANS-LIKE gene of Nelumbo nucifera could promote potato tuberization.

MAIN CONCLUSION: CONSTANS-LIKE 5 of Nelumbo nucifera is capable of promoting potato tuberization through CONSTANS-FLOWERING LOCUS T and gibberellin signaling pathways with a probable association with lotus rhizome enlargement. Lotus (Nelumbo nucifera) is an aquatic plant that is affiliated to the Nelumbonaceace family. It is widely used as an ornamental, vegetable, and medicinal herb with its rhizome being a popular vegetable. To explore the molecular mechanism underlying its rhizome enlargement, we conducted a systematic analysis on the CONSTANS-LIKE (COL) gene family, with the results, indicating that this gene plays a role in regulating potato tuber expansion. These analyses included phylogenetic relationships, gene structure, and expressional patterns of lotus COL family genes. Based on these analyses, NnCOL5 was selected for further study on its potential function in lotus rhizome formation. NnCOL5 was shown to be located in the nucleus, and its expression was positively associated with the enlargement of lotus rhizome. Besides, the overexpression of NnCOL5 in potato led to increased tuber weight and starch content under short-day conditions without changing the number of tubers. Further analysis suggested that the observed tuber changes might be mediated by affecting the expression of genes in CO-FT and GA signaling pathways. These results provide valuable insight in understanding the functions of COL gene as well as the enlargement of lotus rhizome.

Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development.

BACKGROUND: Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus. RESULTS: To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis. CONCLUSION: These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.

Integrated Omics Analyses Identify Key Pathways Involved in Petiole Rigidity Formation in Sacred Lotus.

Sacred lotus (Nelumbo nucifera Gaertn.) is a relic aquatic plant with two types of leaves, which have distinct rigidity of petioles. Here we assess the difference from anatomic structure to the expression of genes and proteins in two petioles types, and identify key pathways involved in petiole rigidity formation in sacred lotus. Anatomically, great variation between the petioles of floating and vertical leaves were observed. The number of collenchyma cells and thickness of xylem vessel cell wall was higher in the initial vertical leaves' petiole (IVP) compared to the initial floating leaves' petiole (IFP). Among quantified transcripts and proteins, 1021 and 401 transcripts presented 2-fold expression increment (named DEGs, genes differentially expressed between IFP and IVP) in IFP and IVP, 421 and 483 proteins exhibited 1.5-fold expression increment (named DEPs, proteins differentially expressed between IFP and IVP) in IFP and IVP, respectively. Gene function and pathway enrichment analysis displayed that DEGs and DEPs were significantly enriched in cell wall biosynthesis and lignin biosynthesis. In consistent with genes and proteins expressions in lignin biosynthesis, the contents of lignin monomers precursors were significantly different in IFP and IVP. These results enable us to understand lotus petioles rigidity formation better and provide valuable candidate genes information on further investigation.

Effects of macrophages and CXCR2 on adipogenic differentiation of bone marrow mesenchymal stem cells.

Macrophages and many chemokines are closely associated with the adipogenic differentiation of bone marrow mesenchymal stem cells (MSCs), but their roles in adipogenesis and the underlying mechanisms are not fully understood. Here, we first investigated the influence of macrophages on the differentiation of MSCs in vitro. We found that RAW246.7 macrophages cocultured with MSCs strongly blocked the differentiation progress and inhibited the expression of C-X-C motif chemokine ligand 1 (CXCL1) during adipogenesis. Coculture with MSCs mainly induced macrophages toward M2 polarization. In addition, the expression of CXCL1 and its receptor, C-X-C chemokine receptor type 2, CXCR2 are high during adipogenic differentiation of MSCs and not in mature adipocytes. Although CXCL1 had no effect on adipogenesis, treatment with a specific CXCR2 inhibitor, SB225002, hampered the adipogenic differentiation of MSCs. Blocking CXCR2 decreased p38 and Elk1 phosphorylation but increased the extracellular signal-regulated kinase (ERK) phosphorylation at the initial stage of adipogenesis, which suppressed the phosphorylation of p38/ERK-Elk1 at the late stage. Inhibition of ERK had similar effects on adipogenesis and Elk1 phosphorylation. Our data suggest that MSCs interact with macrophages during adipogenic differentiation. CXCR2 regulates the adipogenic differentiation of MSCs by altering the activation of the p38/ERK-Elk1 signaling pathway.

Proteomic analysis showing the signaling pathways involved in the rhizome enlargement process in Nelumbo nucifera.

BACKGROUND: Rhizome is the storage underground stem of lotus (Nelumbo nucifera), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable with abundant starch, proteins, and vitamins. Enlargement of lotus rhizome is not only significance for itself to survive from the cold winter, but also important for its economic value. RESULTS: To explore the mechanism underlying its enlargement, integrative analyses of morphology, physiology and proteomics were conducted on the rhizome at stolon, middle, and enlarged stages. Morphological observation and physiological analyses showed that rhizomes were gradually enlarged during this process, in which the starch accumulation was also initiated. Quantitative proteomic analysis on the rhizomes at these three stages identified 302 stage-specific proteins (SSPs) and 172 differently expressed proteins (DEPs), based on which GO and KEGG enrichment analyses were conducted. The results indicated that light and auxin signal might be transduced through secondary messenger Ca2+, and play important roles in lotus rhizome enlargement. CONCLUSION: These results will provide new insights into understanding the mechanism of lotus rhizome enlargement. Meanwhile, some candidate genes might be useful for further studies on this process, as well as breeding of rhizome lotus.

A time-resolved proteomic analysis of transcription factors regulating adipogenesis of human adipose derived stem cells.

Adipogenesis is one of the key processes during obesity development. Better understanding of this process could advance our knowledge on obesity and its treatment. Transcription factors (TFs) are master regulators during adipogenesis, however, a system-wide analysis of TFs dynamic proteome during adipogenesis is lacking. Here, we profiled 472 TFs and systematically elucidated their roles during the first 7 days of adipogenesis of human adipose-derived stem cells (hADSCs) on proteome scale. We identified two main and four sub-phases during adipogenesis. The commitment phase (0 h-8 h) mainly mediated stem cell proliferation, differentiation and chromatin remodeling, in which proteins of SWI/SNF family are the key centroid nodes. The determination phase (1D-7D) predominately regulated fat cell differentiation and response to lipid and oxygen, which could be associated with terminal differentiation of adipocyte and responsible for maturation. PPARγ, CREB1 and MYC are the centroid nodes of this phase. Remarkably, we identified and verified three TFs (BATF3, MAFF and MXD4) as novel regulators of adipogenesis, whose over-expression could inhibit adipogenesis of hADSCs in vitro. Overall, our study provided a valuable TFs resource to understand the complex process of adipogenesis.

miR-140-5p could suppress tumor proliferation and progression by targeting TGFBRI/SMAD2/3 and IGF-1R/AKT signaling pathways in Wilms' tumor.

BACKGROUND: Wilms' tumor is also called nephroblastoma and is the most common pediatric renal cancer. Several genetic and epigenetic factors have been found to account for the development of Wilms' tumor. MiRNAs play important roles in this tumorigenic process. In the present study, we aimed to investigate the role of miR-140-5p in nephroblastoma by identifying its targets, as well as its underlying molecular mechanism of action. METHODS: The miRNA expression profile of nephroblastoma samples was investigated and the targets of miR-140-5p were predicted and validated using the miRNA luciferase reporter method. Moreover, the roles of miR-140-5p in regulating nephroblastoma cell proliferation, migration and cell cycle were analyzed by the CCK8, migration and flow cytometry assays, respectively. The downstream protein of the direct target of miR-140-5p was also identified. RESULTS: miR-140-5p was downregulated in Wilms' tumor tissues, whereas in the nephroblastoma cell lines G401 and WT-CLS1 that exhibited high levels of miRNA-140-5p, inhibition of cellular proliferation and metastasis were noted as well as cell cycle arrest at the G1/S phase. TGFBRI and IGF1R were identified as direct target genes for miRNA-140-5p. In addition, SMAD2/3 and p-AKT were regulated by TGFBRI and IGF1R separately and participated in the miRNA-140-5p regulatory network. Ectopic expression of TGFBR1 and IGF-1R could abrogate the inhibitory effect of miR-140-5p. CONCLUSION: We demonstrated that miRNA-140-5p participates in the progression of Wilms' tumor by targeting the TGFBRI/SMAD2/3 and the IGF-1R/AKT signaling pathways.

The Latest Studies on Lotus (Nelumbo nucifera)-an Emerging Horticultural Model Plant.

Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and has been widely used, especially in Southeast Asia. Recently, the lotus obtained a lot of attention from the scientific community. An increasing number of research papers focusing on it have been published, which have shed light on the mysteries of this species. Here, we comprehensively reviewed the latest advancement of studies on the lotus, including phylogeny, genomics and the molecular mechanisms underlying its unique properties, its economic important traits, and so on. Meanwhile, current limitations in the research of the lotus were addressed, and the potential prospective were proposed as well. We believe that the lotus will be an important model plant in horticulture with the generation of germplasm suitable for laboratory operation and the establishment of a regeneration and transformation system.

[Effect of LINE1-ORF1p overexpression on the proliferation of nephroblastoma WT_CLS1 cells].

OBJECTIVE: To prepare the LINE1-ORF1p polyclonal antibody, and to study the effect of LINE1-ORF1p on the proliferation of nephroblastoma WT_CLS1 cells. METHODS: A genetic engineering method was used to achieve prokaryotic expression of LINE1-ORF1p, and rabbits were immunized with LINE1-ORF1p to prepare polyclonal antibody. Indirect ELISA was used to evaluate antibody titer, and Western blot and immunohistochemistry were used to evaluate the specific ability of antibody to recognize LINE1-ORF1p. The eukaryotic expression vector pEGFP-N1-LINE1-ORF1 was constructed and used to transfect WT_CLS1 cells. Western blot and qRT-PCR were used to measure the protein and mRNA expression of LINE1-ORF1, respectively, and cell proliferation assay and colony-forming assay were used to evaluate the effect of LINE1-ORF1p on the proliferation of WT_CLS1 cells and the formation of tumor cell clone. RESULTS: The LINE1-ORF1p antibody prepared had a titer of >1:16 000 and could specifically recognize LINE1-ORF1p in cells and tumor tissue. WT_CLS1 cells transfected with pEGFP-N1-LINE1-ORF1 had significant increases in the mRNA and protein expression of LINE1-ORF1 and significantly enhanced cell proliferation ability and colony formation ability (P<0.05). CONCLUSIONS: LINE1-ORF1p can promote the growth of nephroblastoma cells and the formation of tumor cell clone, and may be involved in the pathogenesis of nephroblastoma.

Long Non-Coding RNA Expression Profiling in Obesity Mice with Folic Acid Supplement.

BACKGROUND/AIMS: Obesity is a major contributor to the growing prevalence of metabolic and cardiovascular diseases. This study was designed to investigate the effect of folic acid (FA) on obese mice by detecting the genome-wide expression profile of lncRNAs and mRNAs in the heart. METHODS: Heart samples were collected from mice fed with standard diet (SD), high-fat diet (HFD) and high-fat diet with FA intake (HFDF). LncRNAs and mRNAs between HFD and HFDF group were analyzed by lncRNA microarray. Nine lncRNAs and mRNAs were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Bioinformatics prediction was used to investigate the potential function of these differentially expressed lncRNAs. Co-expresson analysis was used to determine the transcriptional regulatory relationship of differentially expressed lncRNAs and mRNAs between two groups. RESULTS: The expression of 58,952 lncRNAs and 20,145 mRNAs in HFD and HFDF groups was profiled by using microarrays. Gene Ontology and pathway analyses indicated that the biological functions of differentially expressed mRNAs were related to inflammation, energy metabolism, and cell differentiation. Co-expression networks composed of lncRNAs and mRNAs were also constructed to investigate the potential regulatory roles of differentially expressed lncRNAs on mRNAs. LncRNAs, namely, NONMMUT033847, NONMMUT070811, and NONMMUT015327, were validated through qRT-PCR, and these lncRNAs may be important factors regulating inflammation, energy metabolism, and cell differentiation. The expression levels of Dnajb1, Egr2, Hba-a1, Il1ß, Cxcl2, and Tnfsf9 were significantly different between HFD and HFDF. CONCLUSIONS: Results suggested that FA may improve the cardiovascular function of obesity and contribute to those lncRNAs associated with inflammation and cell differentiation. In a nutshell, the present study identified a panel of lncRNAs and mRNAs that may be potential biomarkers or drug targets relevant to the high-fat diet related obesity.

Association of the ADIPOQ T45G polymorphism with insulin resistance and blood glucose: a meta-analysis.

Results of published studies on the association of the ADIPOQ T45G polymorphism with insulin resistance (IR) and blood glucose are conflicting. In this study, we performed a meta-analysis to further investigate such an association. Articles that evaluate the effect of the T45G polymorphism on IR and blood glucose were identified from the PubMed and Embase databases. Five indices, including fasting blood glucose (FBG), fasting insulin (F-insulin), 2-h blood glucose (2-h BG), 2-h insulin, and homeostasis model assessment insulin resistance index (HOMA-IR), were used to assess the effects of the T45G polymorphism on IR and blood glucose under a dominant model. 24 articles involving 7630 subjects were included. Twenty-two studies on FBG, 17 on F-insulin, 20 on HOMA-IR, and 3 on 2-h BG were included. No study on 2-h insulin was found. This meta-analysis revealed no significant association between the ADIPOQ T45G polymorphism and IR and blood glucose in the overall population and subgroup subjects under a dominant model, regardless of whether FBG, F-insulin, 2-h BG, or HOMA-IR was used. The present meta-analysis indicated that the mutation allele may have no function in IR development. The ADIPOQ T45G polymorphism is not associated with IR and blood glucose.

Enhancing chemical synthesis research with NLP: Word embeddings for chemical reagent identification-A case study on nano-FeCu.

Nanoparticle synthesis is complex, influenced by multiple variables including reagent selection. This study introduces a specialized corpus focused on "Fe, Cu, synthesis" to train a domain-specific word embedding model using natural language processing (NLP) in an unsupervised environment. Evaluation metrics included average cosine similarity, visual analysis via t-distributed stochastic neighbor embedding (t-SNE), synonym analysis, and analogy reasoning analysis. Results indicate a strong correlation between learning rate and cosine similarity, with enhanced chemical specificity in the tailored model compared to general models. The framework facilitates rapid identification of potential reagents for nano-FeCu synthesis, enhancing precision in nanomaterial research. This innovative approach offers a data-driven pathway for chemical material synthesis, demonstrating significant interdisciplinary applications.

Exploring the potentials of Sesuvium portulacastrum L. for edibility and bioremediation of saline soils.

Sesuvium portulacastrum L. is a flowering succulent halophyte in the ice plant family Aizoaceae. There are various ecotypes distributed in sandy coastlines and salty marshlands in tropical and subtropical regions with the common name of sea purslane. These plants are tolerant to salt, drought, and flooding stresses and have been used for the stabilization of sand dunes and the restoration of coastal areas. With the increased salinization of agricultural soils and the widespread pollution of toxic metals in the environment, as well as excessive nutrients in waterbodies, S. portulacastrum has been explored for the desalination of saline soils and the phytoremediation of metals from contaminated soils and nitrogen and phosphorus from eutrophic water. In addition, sea purslane has nutraceutical and pharmaceutical value. Tissue analysis indicates that many ecotypes are rich in carbohydrates, proteins, vitamins, and mineral nutrients. Native Americans in Florida eat it raw, pickled, or cooked. In the Philippines, it is known as atchara after being pickled. S. portulacastrum contains high levels of ecdysteroids, which possess antidiabetic, anticancer, and anti-inflammatory activities in mammals. In this review article, we present the botanical information, the physiological and molecular mechanisms underlying the tolerance of sea purslane to different stresses, its nutritional and pharmaceutical value, and the methods for its propagation and production in saline soils and waterbodies. Its adaptability to a wide range of stressful environments and its role in the production of valuable bioactive compounds suggest that S. portulacastrum can be produced in saline soils as a leafy vegetable and is a valuable genetic resource that can be used for the bioremediation of soil salinity and eutrophic water.

Transcriptomic and metabolomic analyses reveal mechanisms underpinning resistance of Chinese wild grape to Colletotrichum viniferum.

Grape ripe rot is one of the most important diseases caused by Colletotrichum spp. Chinese wild grape (Vitis davidii) is highly resistant to Colletotrichum viniferum infection. But mechanisms underlying the resistance remain largely unclear. In this study, transcriptomic and metabolomic responses of V. davidii to C. viniferum were studied before and after 1, 2, 4, and 6 days of inoculation. C. viniferum infection induced the expression of a large number of defense-related genes. KEGG analysis indicated that the differentially expressed genes (DEGs) were largely those involved in alpha-linolenic acid metabolism, flavonoid biosynthesis, phenylpropanoid biosynthesis, stilbenoid biosynthesis, and other defense-related metabolic pathways. Based on transcriptome data and experimental analysis, we found that jasmonic acid (JA) biosynthesis was closely related to V. davidii resistance to C. viniferum. In addition, many genes related to the synthesis of lignin and phytoalexin resveratrol are upregulated by pathogen infection, and metabolomic analysis showed that there was an increasing accumulation of resveratrol on day 6 of C. viniferum inoculation. Further analysis indicated that transcription factors, such as VdWRKY75 regulated the biosynthesis of lignin and stilbenes. A working model for V. davidii against C. viniferum infection was proposed. The infection of C. viniferum induced JA production, JA along with transcription factors regulated the biosynthesis of secondary metabolites, such as lignin and resveratrol that enhanced plant resistance to C. viniferum. This study elucidated molecular mechanisms underlying the resistance of Chinese wild V. davidii to C. viniferum which can provide a theoretical basis for grape disease resistance breeding.

A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth.

Introduction: Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect. Methods: Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses. Results: Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes. Discussion: Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.

Proteomic and metabolomic analyses uncover integrative mechanisms in Sesuvium portulacastrum tolerance to salt stress.

Introduction: Salt stress is a major constraint affecting crop productivity worldwide. Investigation of halophytes could provide valuable information for improving economically important crops to tolerate salt stress and for more effectively using halophytes to remediate saline environments. Sesuvium portulacastrum L. is a halophyte species widely distributed in tropical and subtropical coastal regions and can absorb a large amount of sodium (Na). This study was to analyze S. portulacastrum responses to salt stress at morphological, physiological, proteomic, and metabolomic levels and pursue a better understanding of mechanisms behind its salt tolerance. Methods: The initial experiment evaluated morphological responses of S. portulacastrum to different concentrations of NaCl in a hydroponic system, and subsequent experiments compared physiological, proteomic, and metabolomic changes in S. portulacastrum after being exposed to 0.4 M NaCl for 24 h as immediate salt stress (IS) to 14 days as adaptive salt stress (AS). Through these analyses, a working model to illustrate the integrative responses of S. portulacastrum to salt stress was proposed. Results: Plants grown in 0.4 M NaCl were morphologically comparable to those grown in the control treatment. Physiological changes varied in control, IS, and AS plants based on the measured parameters. Proteomic analysis identified a total of 47 and 248 differentially expressed proteins (DEPs) in leaves and roots, respectively. KEGG analysis showed that DEPs, especially those occurring in roots, were largely related to metabolic pathways. Root metabolomic analysis showed that 292 differentially expressed metabolites (DEMs) occurred in IS plants and 371 in AS plants. Among them, 20.63% of upregulated DEMs were related to phenolic acid metabolism. Discussion: Based on the integrative analysis of proteomics and metabolomics, signal transduction and phenolic acid metabolism appeared to be crucial for S. portulacastrum to tolerate salt stress. Specifically, Ca2+, ABA, and JA signalings coordinately regulated salt tolerance in S. portulacastrum. The stress initially activated phenylpropanoid biosynthesis pathway through Ca2+ signal transduction and increased the content of metabolites, such as coniferin. Meanwhile, the stress inhibited MAPK signaling pathway through ABA and JA signal transduction, which promoted Na sequestration into the vacuole to maintain ROS homeostasis and enhanced S. portulacastrum tolerance to salt stress.

Chronic exercise remodels the lysine acetylome in the mouse hippocampus.

Physical exercise benefits hippocampal function through various molecular mechanisms. Protein acetylation, a conserved and widespread post-translational modification, is involved in the synaptic plasticity and memory. However, whether exercise can change global acetylation and the role of acetylated proteins in the hippocampus have remained largely unknown. Herein, using healthy adult mice running for 6 weeks as exercise model and sedentary mice as control, we analyzed the hippocampal lysine acetylome and proteome by Liquid chromatography-tandem mass spectrometry. As a result, we profiled the lysine acetylation landscape for the hippocampus and identified 3,876 acetyl sites and 1,764 acetylated proteins. A total of 272 acetyl sites on 252 proteins were differentially regulated by chronic exercise, among which 18.58% acetylated proteins were annotated in mitochondria. These proteins were dominantly deacetylated and mainly associated with carbon-related metabolism, the Hippo signaling pathway, ribosomes, and protein processing. Meanwhile, 21 proteins were significantly expressed and enriched in the pathway of complement and coagulation cascades. Our findings provide a new avenue for understanding the molecular mechanisms underlying the benefits of exercise for hippocampal function and can contribute to the promotion of public health.