Soil Organic Carbon Content and Microbial Functional Diversity Were Lower in Monospecific Chinese Hickory Stands than in Natural Chinese Hickory–Broad-Leaved Mixed Forests

To assess the effects of long-term intensive management on soil carbon cycle and microbial functional diversity, we sampled soil in Chinese hickory (Carya cathayensis Sarg.) stands managed intensively for 5, 10, 15, and 20 years, and in reference Chinese hickory–broad-leaved mixed forest (NMF) stands. We analyzed soil total organic carbon (TOC), microbial biomass carbon (MBC), and water-soluble organic carbon (WSOC) contents, applied 13C-nuclear magnetic resonance analysis for structural analysis, and determined microbial carbon source usage. TOC, MBC, and WSOC contents and the MBC to TOC ratios were lower in the intensively managed stands than in the NMF stands. The organic carbon pool in the stands managed intensively for twenty years was more stable, indicating that the easily degraded compounds had been decomposed. Diversity and evenness in carbon source usage by the microbial communities were lower in the stands managed intensively for 15 and 20 years. Based on carbon source usage, the longer the management time, the less similar the samples from the monospecific Chinese hickory stands were with the NMF samples, indicating that the microbial community compositions became more different with increased management time. The results call for changes in the management of the hickory stands to increase the soil carbon content and restore microbial diversity

Soil Organic Carbon Content and Microbial Functional Diversity Were Lower in Monospecific Chinese Hickory Stands than in Natural Chinese Hickory–Broad-Leaved Mixed Forests

To assess the effects of long-term intensive management on soil carbon cycle and microbial functional diversity, we sampled soil in Chinese hickory (Carya cathayensis Sarg.) stands managed intensively for 5, 10, 15, and 20 years, and in reference Chinese hickory–broad-leaved mixed forest (NMF) stands. We analyzed soil total organic carbon (TOC), microbial biomass carbon (MBC), and water-soluble organic carbon (WSOC) contents, applied 13C-nuclear magnetic resonance analysis for structural analysis, and determined microbial carbon source usage. TOC, MBC, and WSOC contents and the MBC to TOC ratios were lower in the intensively managed stands than in the NMF stands. The organic carbon pool in the stands managed intensively for twenty years was more stable, indicating that the easily degraded compounds had been decomposed. Diversity and evenness in carbon source usage by the microbial communities were lower in the stands managed intensively for 15 and 20 years. Based on carbon source usage, the longer the management time, the less similar the samples from the monospecific Chinese hickory stands were with the NMF samples, indicating that the microbial community compositions became more different with increased management time. The results call for changes in the management of the hickory stands to increase the soil carbon content and restore microbial diversity

Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves

Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining isolation of nuclei tagged in specific cell/tissue types with assay for transposase-accessible chromatin using sequencing and RNA-sequencing. Despite a large overlap, vasculature and epidermis cells responded differently. Long-day predominantly induced accessible chromatin regions (ACRs); in the vasculature, more ACRs were induced and these were located at more distal gene regions, compared with the epidermis. Vascular ACRs induced by long days were highly enriched in binding sites for flowering-related transcription factors. Among the highly ranked genes (based on chromatin and expression signatures in the vasculature), we identified TREHALOSE-PHOSPHATASE/SYNTHASE 9 (TPS9) as a flowering activator, as shown by the late flowering phenotypes of T-DNA insertion mutants and transgenic lines with phloem-specific knockdown of TPS9. Our cell-type-specific analysis sheds light on how the long-day photoperiod stimulus impacts chromatin accessibility in a tissue-specific manner to regulate plant development

2-Methoxyestradiol prevents monocyte adhesion to vascular endothelial cells via downregulation of VCAM-1 expression

2-Methoxyestradiol (2-ME) reduces atherosclerotic lesion formation. However, the underlying mechanisms remain largely unknown. In this work, we investigated the effect of 2-ME on monocyte adhesion to vascular endothelial cells. Lipopolysaccharides (LPS) greatly increased the attachment of monocyte onto cultured human umbilical vascular endothelial cells (HUVECs), which was inhibited by 2-ME in a dose- and time-dependent manner, or by the vascular cell adhesion protein-1 (VCAM-1) neutralizing antibody, suggesting that a functional releationship between 2-ME and VCAM-1 may exist. In accordance with this, treatment with 2-ME (10â7â10â5M) for 6â48 h downregulated VCAM-1 protein expression. Meanwhile, the nuclear factor κB (NF-κB) p65 subunit activity and its nuclear translocation was inhibited by 2-ME in HUVECs. The PI3K inhibitor wortmannin or the specific Akt siRNA both inhibited the effects of 2-ME, suggesting that 2-ME inhibited p65 activity via PI3K/Akt signaling. In conclusion, 2-ME inhibits VCAM-1 expression and thus prevents monocyte adhesion to vascular endothelial cells via regulation of PI3K/Akt and NF-κB signaling. These findings will be helpful for better understanding the mechanisms through which 2-ME improves endothelial function

Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data

Although hundreds of colorectal cancer- (CRC-) related genes have been screened, the significant hub genes still need to be further identified. The aim of this study was to identify the hub genes based on protein-protein interaction network and uncover their clinical value. Firstly, 645 CRC patients’ data from the Tumor Cancer Genome Atlas were downloaded and analyzed to screen the differential expression genes (DEGs). And then, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed, and PPI network of the DEGs was constructed by Cytoscape software. Finally, four hub genes (CXCL3, ELF5, TIMP1, and PHLPP2) were obtained from four subnets and further validated in our clinical setting and TCGA dataset. The results showed that mRNA expression of CXCL3, ELF5, and TIMP1 was increased in CRC tissues, whereas PHLPP2 mRNA expression was decreased. More importantly, high expression of CXCL3, ELF5, and TIMP1 was significantly associated with lymphatic invasion, distance metastasis, and advanced tumor stage. In addition, a shorter overall survival was observed in patients with increased CXCL3, TIMP1, and ELF5 expression and decreased PHLPP2 expression. In conclusion, the four hub genes screened by our strategy could serve as novel biomarkers for prognosis prediction of CRC patients

Effects of conversion from a natural evergreen broadleaf forest to a Moso bamboo plantation on the soil nutrient pools, microbial biomass and enzyme activities in a subtropical area

Converting natural forests to plantations would markedly change soil physiochemical and biological properties, as a consequence of changing plant vegetative coverage and management practices. However, the effects of such land-use change on the soil nutrient pools and related enzymes activities still remain unclear. The aim of this study was to explore the effects of conversion from natural evergreen broadleaf forests to Moso bamboo plantations on the pool sizes and forms of soil N, P and K, microbial biomass, and nutrient cycling related enzyme activities. Soil samples from four adjacent evergreen broadleaf forest-Moso bamboo plantation pairs were collected from a subtropical region in Zhejiang Province, China. The soil organic C (SOC), total N (TN), total P (TP) and total K (TK) concentrations and stocks and different N, P and K forms were measured, and the microbial biomass C (MBC), microbial biomass N (MBN), microbial biomass P (MBP) and four soil enzymes (protease, urease, acid phosphatase and catalase) were determined. The results showed that converting broadleaf forests to Moso bamboo plantations decreased the concentration and stock of SOC but increased those of TK in both soil layers (0-20 and 20-40 cm), and such land-use change increased the concentration and stock of TN and TP only in the 0-20 cm soil layer (P <0.05). This land-use conversion increased the concentrations of NH4+-N, NO3- N, resin-Pi, NaHCO3-P-1, NaOH-P-i, HCl-P-i, available K and slowly available K, but decreased the concentrations of water-soluble organic nitrogen (WSON), NaHCO3-P-o and NaOH-P-o (P <0.05). Further, this land-use change decreased the microbial biomass and activities of protease, urease, acid phosphatase and catalase (P <0.05). In addition, the acid phosphatase activity correlated positively with the concentrations of MBP and NaHCO3-P-o, and the activities of urease and protease correlated positively with the concentrations of MBN and WSON (P <0.01). To conclude, converting natural broadleaf forests to Moso bamboo plantations had positive effects on soil inorganic N, P and K pools, and negative effects on soil organic N and P pools, and on N- and P-cycling related enzyme activities. Therefore, management practices that increase organic nutrient pools and microbial activity are needed to be developed to mitigate the depletion of organic nutrient pools after the land-use conversion.Peer reviewe

Spatial Variation of Biomass Carbon Density in a Subtropical Region of Southeastern China

Spatial pattern information of forest biomass carbon (FBC) density in forest ecosystems plays an important role in evaluating carbon sequestration potentials and forest management. The spatial variation of FBC density in a subtropical region of southeastern China was studied using geostatistics combined with Moran’s I and geographical information systems (GIS). Forest biomass carbon density values were variable, ranging from 0.12 Mg ha−1 to 182.12 Mg ha−1, with an average of 27.33 Mg ha−1. The FBC density had the strongest positive correlation with forest age, followed by forest litter and elevation. The FBC density had significant positive spatial autocorrelation revealed by global Moran’s I. Clear spatial patterns were observed based on local Moran’s I. High FBC density values were mainly distributed in the northwestern and southwestern parts of Zhejiang province, which were related to adopting long-term policy of forest conservation in these areas, while low FBC density values located in the middle part and southeastern coastal area of the study area due to low forest coverage and intensive management of economic forests. The Moran’s I combined with geostatistical interpolation proved to be a useful tool for studying spatial variation of FBC density

Profiles of alternative splicing in colorectal cancer and their clinical significance: A study based on large-scale sequencing dataResearch in Context

Background: Alternative splicing (AS), as a potent and pervasive mechanism of transcriptional regulatory, expands the genome's coding capacity and involves in the initiation and progression of cancer. Systematic analysis of alternative splicing in colorectal cancer (CRC) is lacking and greatly needed. Methods: RNA-Seq data and corresponding clinical information of CRC cohort were downloaded from the TCGA data portal. Then, a java application, known as SpliceSeq, was used to evaluate the RNA splicing patterns and calculate the Percent Spliced In (PSI) value. Differently expressed AS events (DEAS) were identified based on PSI value between paired CRC and adjacent tissues. DEAS and its splicing networks were further analyzed by bioinformatics methods. Kaplan-Meier, Cox proportional regression and unsupervised clustering analysis were used to evaluate the association between DEAS and patients' clinical features. Results: After strict filtering, a total of 34,334 AS events were identified, among which 421 AS events were found expressed differently. Parent genes of these DEAS play a important role in regulating CRC-related processes such as protein kinase activity (FDR<0.0001), PI3K-Akt signaling pathway (FDR = 0.0024) and p53 signaling pathway (FDR = 0.0143). 37 DEAS events were found to be associated with OS, and 68 DEAS events were found to be associated with DFS. Stratifying patients according to the PSI value of AT in CXCL12 and RI in CSTF3 formed significant Kaplan-Meier curves in both OS and DFS survival analysis. Unsupervised clustering analysis using DEAS revealed four clusters with distinct survival patterns, and associated with consensus molecular subtypes. Conclusions: Large differences of AS events in CRC appear to exist, and these differences are likely to be important determinants of both prognosis and biological regulation. Our identified CRC-related AS events and uncovered splicing networks are valuable in deciphering the underlying mechanisms of AS in CRC, and provide clues of therapeutic targets to further validations. Keywords: CRC, Alternative splicing, RNA-Seq, Prognosi

<i>Novel Seed Size</i>: A Novel Seed-Developing Gene in <i>Glycine max</i>

Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans