Publications by authors named "Guangming He"

50 Publications

Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis.

Plant Commun 2022 Jun 26:100351. Epub 2022 Jun 26.

School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address:

When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xplc.2022.100351DOI Listing
June 2022

The B-Type Cyclin CYCB1-1 Regulates Embryonic Development and Seed Size in Maize.

Int J Mol Sci 2022 May 25;23(11). Epub 2022 May 25.

Key Laboratory of Crop Physiology, Ecology and Genetic Breeding Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang 330046, China.

Progress through the cell cycle is a critical process during plant embryo and seed development and its progression is regulated by cyclins. Despite extensive study of cyclins in other systems, their role in embryo and seed development of maize is unclear. In this study, we demonstrate that overexpression significantly accelerated embryo growth and increased seed size. In situ hybridization and toluidine blue staining indicated that was highly expressed in the plumule of embryos, and the cells of the plumule were smaller, denser, and more regularly arranged in overexpression plants. Overexpression of in maize also resulted in an increased ear length and enhanced kernel weight by increasing kernel width. Transcriptome analysis indicated that the overexpression of affected several different metabolic pathways, including photosynthesis in embryos and leaves, and lipid metabolism in leaves. Conversely, knocking out resulted in plants with slow growth. Our results suggest that regulates embryo growth and seed size, making it an ideal target for efforts aimed at maize yield improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms23115907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9180882PMC
May 2022

Fudosteine attenuates acute lung injury in septic mice by inhibiting pyroptosis via the TXNIP/NLRP3/GSDMD pathway.

Eur J Pharmacol 2022 Jul 21;926:175047. Epub 2022 May 21.

Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, and Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China. Electronic address:

There is a dearth of effective pharmacotherapies for sepsis-induced acute lung injury/acute respiratory distress syndrome (ALI/ARDS) to which oxidative stress and excessive inflammation are major contributors. We hypothesized that fudosteine, a cysteine derivative, may protect against sepsis-induced ALI/ARDS given its anti-oxidant capacity. This study aimed to investigate the effects and mechanisms of fudosteine in a mouse model of sepsis-induced ALI. Sepsis was induced by cecal ligation and puncture (CLP). The intragastrical administration of fudosteine (25 mg/kg, 50 mg/kg, and 100 mg/kg) dose-dependently decreased proinflammatory cytokine levels in bronchoalveolar lavage fluid (BALF) and serum and reduced BALF/serum albumin and lung wet/dry weight ratios in septic mice. The lung injury score was significantly lowered by fudosteine [e.g., 0.18 ± 0.03 (100 mg/kg) vs. 0.42 ± 0.03 (CLP), P < 0.0001]. Fudosteine also reduced the biomarkers of lung epithelial injury in BALF and markedly improved oxidative stress indicators in lung tissues [e.g., malondialdehyde: 337.70 ± 23.78 (100 mg/kg) vs. 686.40 ± 28.36 (CLP) nmol/mg protein, P < 0.0001]. Lung tissue transcriptomics analyses revealed suppressed inflammatory responses and oxidative stress with fudosteine and the involvement of the inflammasome and pyroptosis pathways. Western blot analyses indicated that fudosteine inhibited the sepsis-induced activation of gasdermin D (GSDMD) and caspase-1 and the upregulation of thioredoxin-interacting protein (TXNIP), nucleotide-binding domain, leucine-rich repeat-containing receptor, pyrin domain-containing-3 (NLRP3), and apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC). Fudosteine therefore protects against sepsis-induced ALI in mice, and the inhibition of pyroptosis via the TXNIP/NLRP3/GSDMD pathway may be an underlying mechanism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ejphar.2022.175047DOI Listing
July 2022

From hybrid genomes to heterotic trait output: Challenges and opportunities.

Curr Opin Plant Biol 2022 04 23;66:102193. Epub 2022 Feb 23.

School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China. Electronic address:

Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pbi.2022.102193DOI Listing
April 2022

Effect of family enteral nutrition on nutritional status in elderly patients with esophageal carcinoma after minimally invasive radical surgery: a randomized trial.

Ann Palliat Med 2021 Jun;10(6):6760-6767

Department of Thoracic Surgery, Taixing People's Hospital of Jiangsu Province, Taixing, China.

Background: Postoperative patients with esophageal carcinoma (EC) are prone to malnutrition. Studies have shown that the incidence of malnutrition after EC surgery reaches 60-80%, and deaths due to malnutrition account for about 22%. Patients with EC need at least 3 months to establish a new dietary pattern after surgery, so short-term enteral nutrition is of great significance. The aim of the present study was to investigate the effects of family enteral nutrition (FEN) on nutritional status in elderly patients with EC after minimally invasive radical surgery (MIS).

Methods: A total of 106 elderly patients with EC, who had undergone MIS at the 904th Hospital of the Joint Service Support Center of the Chinese People's Liberation Army and Taixing People's Hospital from January 2017 to July 2019 were selected to participate in the present study and randomly divided into the observation group and control group. There were 53 cases in each group. Patients in the control group were given regular meals after they were discharged from hospital, and the observation group was given FEN support based on the intervention of the control group. Body mass index (BMI), nutritional risk screening, nutritional status, and the incidence of complications were compared between the two groups at discharge and 1 month after discharge.

Results: The BMI of the observation group was higher than that of the control group 1 month after discharge (P<0.05). The nutritional risk ratio of the observation group was lower than that of the control group 1 month after discharge (P<0.05). Hemoglobin, serum albumin, serum total protein, transferrin, and serum prealbumin of the observation group were higher than the control group 1 month after discharge (P<0.05). There was no significant difference in the incidence of total complications between the two groups (P>0.05).

Conclusions: FEN could improve the nutritional status of elderly patients with EC after MIS and reduce the risk of postoperative malnutrition and incidence of complications.

Trial Registration: Chinese Clinical Trial Registry ChiCTR2100046121.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.21037/apm-21-1219DOI Listing
June 2021

A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs.

Nat Commun 2021 04 19;12(1):2317. Epub 2021 Apr 19.

School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

Plant immunity frequently incurs growth penalties, which known as the trade-off between immunity and growth. Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits but rarely for disease resistance. Here, we report that the central circadian oscillator, CCA1, confers heterosis for bacterial defense in hybrids without growth vigor costs, and it even significantly enhances the growth heterosis of hybrids under pathogen infection. The genetic perturbation of CCA1 abrogated heterosis for both defense and growth in hybrids. Upon pathogen attack, the expression of CCA1 in F hybrids is precisely modulated at different time points during the day by its rhythmic histone modifications. Before dawn of the first infection day, epigenetic activation of CCA1 promotes an elevation of salicylic acid accumulation in hybrids, enabling heterosis for defense. During the middle of every infection day, diurnal epigenetic repression of CCA1 leads to rhythmically increased chlorophyll synthesis and starch metabolism in hybrids, effectively eliminating the immunity-growth heterosis trade-offs in hybrids.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-021-22268-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055661PMC
April 2021

Mapping Collaborations and Partnerships in SDG Research.

Front Res Metr Anal 2020 9;5:612442. Epub 2021 Feb 9.

MSU Libraries, Michigan State University, East Lansing, MI, United States.

Collaboration has become an essential paradigm in sustainable development research and in strategies for meeting the United Nations Sustainable Development Goals (SDGs). This study uses bibliometric methods and network analysis to examine research output and collaboration supporting the SDGs and explores means to detect and analyze research collaboration beyond the traditional definition of multiple, one-time co-authorship. We employed two additional lenses of collaboration: repeat collaboration and collaboration time point to quantify and visualize co-authorship data sourced from Microsoft Academic Graph. Our results show an increased collaboration rate over time at the author and institutional levels; however they also indicate that the majority of collaborations in SDG-related research only happened once. We also found out that on average, repeat collaboration happens more frequently, but after a longer duration, at the institutional level than at the author level. For this reason, we further analyzed institutions and identified core institutions that could help influence more consistent collaboration and sustain or grow the SDG-related research network. Our results have implications for understanding sustainable partnerships in research related to SDGs and other global challenges.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/frma.2020.612442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8025970PMC
February 2021

Biological pathway expression complementation contributes to biomass heterosis in .

Proc Natl Acad Sci U S A 2021 04;118(16)

School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China;

The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young seedlings (parental ecotypes [Col-0 and Per-1] and their F hybrid). Weighted gene coexpression network analysis uncovered divergent expression patterns between parents of the network hub genes, in which genes related to the cell cycle were more highly expressed in one parent (Col-0), whereas those involved in photosynthesis were more highly expressed in the other parent (Per-1). Notably, the hybrid exhibited spatiotemporal high-parent-dominant expression complementation of network hub genes in the two pathways during seedling growth. This suggests that the integrated capacities of cell division and photosynthesis contribute to hybrid growth vigor, which could be enhanced by temporal advances in the progression of leaf development in the hybrid relative to its parents. Altogether, this study provides evidence of expression complementation between fundamental biological pathways in hybrids and highlights the contribution of expression dominance in heterosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.2023278118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072403PMC
April 2021

Insertion trauma of a new cochlear implant electrode: evaluated by histology in fresh human temporal bone specimens.

Acta Otolaryngol 2021 May 30;141(5):490-494. Epub 2021 Mar 30.

Shanghai Engineering Research Center of Cochlear Implants, Shanghai, PR China.

Background: Combining acoustic and electrical stimulation has been successfully used in patients with low-frequency residual hearing. Electrode insertion trauma, such as electrode translocation could result in loss of residual hearing.

Objectives: The aim of the study is to evaluate the LCI-20PI electrode array insertion trauma to the intra-cochlear structures in fresh human temporal bone specimens.

Materials And Methods: The LCI-20PI electrode arrays were inserted into scalae tympani through round window membrane in 10 cochleae from ten fresh human cadavers. The intracochlear trauma was evaluated histologically by a scale of 0-4: 0 - no observable trauma, 1 - elevation of basilar membrane, 2 - rupture of basilar membrane or spiral ligament, 3-dislocation into scala vestibuli and 4 - fracture of modiolus or osseous spiral lamina. The insertion depth was measured by radiography.

Results: Histological results revealed no observable trauma in seven specimens; basal membrane elevation and rupture in two specimens; the electrode array misled into scala vestibuli in one specimen. The insertion depth varied from 228° to 288°.

Conclusions And Significance: The insertion of the LCI-20PI electrode arrays caused no trauma in the majority of the fresh temporal bone specimens. No translocation of the electrode arrays from the scala tympani to the scala vestibuli was observed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00016489.2021.1897159DOI Listing
May 2021

CRISPR/Cas9-mediated disruption of TaNP1 genes results in complete male sterility in bread wheat.

J Genet Genomics 2020 05 20;47(5):263-272. Epub 2020 May 20.

Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China. Electronic address:

Male sterile genes and mutants are valuable resources in hybrid seed production for monoclinous crops. High genetic redundancy due to allohexaploidy makes it difficult to obtain the nuclear recessive male sterile mutants through spontaneous mutation or chemical or physical mutagenesis methods in wheat. The emerging effective genome editing tool, CRISPR/Cas9 system, makes it possible to achieve simultaneous mutagenesis in multiple homoeoalleles. To improve the genome modification efficiency of the CRISPR/Cas9 system in wheat, we compared four different RNA polymerase (Pol) III promoters (TaU3p, TaU6p, OsU3p, and OsU6p) and three types of sgRNA scaffold in the protoplast system. We show that the TaU3 promoter-driven optimized sgRNA scaffold was most effective. The optimized CRISPR/Cas9 system was used to edit three TaNP1 homoeoalleles, whose orthologs, OsNP1 in rice and ZmIPE1 in maize, encode a putative glucose-methanol-choline oxidoreductase and are required for male sterility. Triple homozygous mutations in TaNP1 genes result in complete male sterility. We further demonstrated that any one wild-type copy of the three TaNP1 genes is sufficient for maintenance of male fertility. Taken together, this study provides an optimized CRISPR/Cas9 vector for wheat genome editing and a complete male sterile mutant for development of a commercially viable hybrid wheat seed production system.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgg.2020.05.004DOI Listing
May 2020

Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice.

Proc Natl Acad Sci U S A 2020 03 18;117(9):4623-4631. Epub 2020 Feb 18.

School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China;

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, including , , and , therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, including /, , and existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1919086117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060695PMC
March 2020

PTK7 expression is associated with lymph node metastasis, ALK and EGFR mutations in lung adenocarcinomas.

Histol Histopathol 2020 May 8;35(5):489-495. Epub 2019 Nov 8.

Department of Thoracic Surgery, the First Affiliated Hospital of Soochow University, Suzhou, PR China.

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer death worldwide. Lung adenocarcinoma is the main tumor type of NSCLC. Recent advances in the molecular characterization and personalized therapies have improved NSCLC patient prognosis. Previous studies showed that protein tyrosine kinase 7 (PTK7) plays an important role in human cancers. However, the role of PTK7 has not been investigated. PTK7 expression was assessed by immunohistochemistry in 95 patients with lung adenocarcinoma. Correlations of PTK7 expression levels with clinicopathological parameters, EGFR mutation and EML4-ALK fusion were examined. Positive PTK7 expression was detected in 47.4% of lung adenocarcinoma. PTK7 expression was associated with gender (P=0.024), lymph node metastasis (P<0.001), ALK mutation (P=0.050), and EGFR mutations (P=0.014). No significant association was found between PTK7 expression and age (P=0.831), differentiation (P=0.494), adenocarcinoma subtype (P=0.098) and Ki67 (P=0.473). Our data suggest that PTK7 plays an oncogenic role in lung adenocarcinoma and may be a molecular marker for lymph node metastasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.14670/HH-18-183DOI Listing
May 2020

A new regulator of seed size control in Arabidopsis identified by a genome-wide association study.

New Phytol 2019 04 2;222(2):895-906. Epub 2019 Feb 2.

School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.

Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.15642DOI Listing
April 2019

Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis.

Plant J 2019 02 14;97(3):555-570. Epub 2018 Dec 14.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China.

Alternative splicing (AS) plays key roles in plant development and the responses of plants to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from AS) in plant accessions and its contribution to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0 and Ler-1, as well as their F hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing. We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that single nucleotide polymorphisms influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.14142DOI Listing
February 2019

Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings.

BMC Plant Biol 2018 01 9;18(1):10. Epub 2018 Jan 9.

Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan, 571737, China.

Background: Breeding rubber tree seedling with growth heterosis is vital for natural rubber production. It is the prerequisites for effectively utilizing growth heterosis to elucidate its molecular mechanisms, but the molecular mechanisms remain poorly understood in rubber tree. To elucidate seedling growth heterosis, we conducted comparative transcriptomic analyses between the two hybrids and their parents.

Results: By identifying and comparing differently expressed genes (DEGs), we found that the hybrids (BT 3410 and WC 11) show significantly differential expression profiles from their parents (PR 107 and RRIM 600). In BT 3410-parent triad, 1092 (49.95%) and 1094 (50.05%) DEGs indicated clear underdominance or overdominance, respectively. Whereas in WC 11-parent triad, most DEGs (78.2%, 721) showed low- or high-parent dominance; 160 (17.35%) exhibited expression patterns that are not statistically distinguishable from additivity, and 8 (0.87%) and 33 (3.58%) DEGs exhibited underdominance and overdominance, respectively. Furthermore, some biological processes are differentially regulated between two hybrids. Interestingly, the pathway in response to stimulus is significantly downregulated and metabolic pathways are more highly regulated in BT 3410.

Conclusions: Taken together, the genotypes, transcriptomes and biological pathways (especially, carbohydrate metabolism) are highly divergent between two hybrids, which may be associated with growth heterosis and weakness. Analyzing gene action models in hybrid-parent triads, we propose that overdominance may play important roles on growth heterosis, whereas dominance on hybrid weakness in rubber tree seedlings. These findings bring new insights into our understanding of growth heterosis of rubber tree seedling.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12870-017-1203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759766PMC
January 2018

[Progresses of immunomodulatory therapy in sever acute pancreatitis].

Zhonghua Wei Zhong Bing Ji Jiu Yi Xue 2017 Oct;29(10):954-957

Department of Critical Care Medicine, Sichuan Cancer Hospital, Chengdu 610041, Sichuan, China (He GM, Xiong GZ, Lu S, Xu SL); Institute of Digestive Surgery, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China (Chen KL). Corresponding author: Chen Keling, Email:

Severe acute pancreatitis (SAP) is accompanied with complex pathogenic course and high mortality. The imbalance of immune response is an important cause which leads the SAP patients to the severe situation and even death. The immunomodulatory therapy can regulate the imbalance of inflammation, alleviate SAP-associated organ injury, and improve the prognosis of patients. Previous immunomodulatory therapy had some problems, such as single-object and simple-method. In recent years, some new methods of immunomodulatory therapy, such as regulating the apoptosis and mature of immune cells, applying of mesenchymal stem cells (MSCs) and multi-regulation methods, provide some new ideas and hopes for SAP therapy. This paper reviewed the history and recent research progresses of SAP immunomodulatory therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3760/cma.j.issn.2095-4352.2017.10.020DOI Listing
October 2017

Genomic architecture of biomass heterosis in .

Proc Natl Acad Sci U S A 2017 07 10;114(30):8101-8106. Epub 2017 Jul 10.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China

Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome-wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include , , and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in , in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus-responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1705423114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544317PMC
July 2017

Involvement of Ca-activated K channel 3.1 in hypoxia-induced pulmonary arterial hypertension and therapeutic effects of TRAM-34 in rats.

Biosci Rep 2017 08 27;37(4). Epub 2017 Jul 27.

Laboratory of Pulmonary Diseases and Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China

Pulmonary artery hypertension (PAH) is an incurable disease associated with the proliferation of pulmonary artery smooth muscle cells (PASMCs) and vascular remodeling. The present study examined whether TRAM-34, a highly selective blocker of calcium-activated potassium channel 3.1 (Kca3.1), can help prevent such hypertension by reducing proliferation in PASMCs. Rats were exposed to hypoxia (10% O) for 3 weeks and treated daily with TRAM-34 intraperitoneally from the first day of hypoxia. Animals were killed and examined for vascular hypertrophy, Kca3.1 expression, and downstream signaling pathways. In addition, primary cultures of rat PASMCs were exposed to hypoxia (3% O) or normoxia (21% O) for 24 h in the presence of TRAM-34 or siRNA against Kca3.1. Activation of cell signaling pathways was examined using Western blot analysis. In animal experiments, hypoxia triggered significant medial hypertrophy of pulmonary arterioles and right ventricular hypertrophy, and it significantly increased pulmonary artery pressure, mRNA levels and ERK/p38 MAP kinase signaling. These effects were attenuated in the presence of TRAM-34. In cell culture experiments, blocking Kca3.1 using TRAM-34 or siRNA inhibited hypoxia-induced ERK/p38 signaling. Kca3.1 may play a role in the development of PAH by activating ERK/p38 MAP kinase signaling, which may then contribute to hypoxia-induced pulmonary vascular remodeling. TRAM-34 may protect against hypoxia-induced PAH.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1042/BSR20170763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529208PMC
August 2017

Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis).

Sci Rep 2016 Mar 23;6:23540. Epub 2016 Mar 23.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China.

Tapping panel dryness (TPD) is a serious threat to natural rubber yields from rubber trees, but the molecular mechanisms underlying TPD remain poorly understood. To identify TPD-related genes and reveal these molecular mechanisms, we sequenced and compared the transcriptomes of bark between healthy and TPD trees. In total, 57,760 assembled genes were obtained and analyzed in details. In contrast to healthy rubber trees, 5652 and 2485 genes were up- or downregulated, respectively, in TPD trees. The TPD-related genes were significantly enriched in eight GO terms and five KEGG pathways and were closely associated with ROS metabolism, programmed cell death and rubber biosynthesis. Our results suggest that rubber tree TPD is a complex process involving many genes. The observed lower rubber yield from TPD trees might result from lower isopentenyl diphosphate (IPP) available for rubber biosynthesis and from downregulation of the genes in post-IPP steps of rubber biosynthesis pathway. Our results not only extend our understanding of the complex molecular events involved in TPD but also will be useful for developing effective measures to control TPD of rubber trees.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep23540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804210PMC
March 2016

Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid.

J Integr Plant Biol 2016 May 24;58(5):466-74. Epub 2015 Dec 24.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.

Histone modifications affect gene expression, but the mechanism and biological consequence of natural variation in histone modifications remain unclear. Here, we generated genome-wide integrated maps of H3K27me3 modification and transcriptome for Col, C24 and their F1 hybrid. A total of 1,828 genomic regions showing variation in H3K27me3 modification between Col and C24 were identified, most of which were associated with genic regions. Natural variation of H3K27me3 modification between parents could result in allelic bias of H3K27me3 in hybrids. Furthermore, we found that H3K27me3 variation between Col and C24 was negatively correlated with gene expression differences between two accessions, especially with those arising from the cis-effect. Importantly, mutation of CLF, an Arabidopsis methyltransferase for H3K27, altered gene expression patterns between the parents. Together, these data provide insights into natural variation of histone modifications and their association with gene expression differences between Arabidopsis ecotypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jipb.12443DOI Listing
May 2016

Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids.

Nat Commun 2015 Jun 12;6:7309. Epub 2015 Jun 12.

1] Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China [2] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.

Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits in Arabidopsis thaliana, but its effect on defence remains largely unexplored. Here, we show that hybrids between some A. thaliana accessions show increased resistance to the biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. Comparisons of transcriptomes between these hybrids and their parents after inoculation reveal that several key salicylic acid (SA) biosynthesis genes are significantly upregulated in hybrids. Moreover, SA levels are higher in hybrids than in either parent. Increased resistance to Pst DC3000 is significantly compromised in hybrids of pad4 mutants in which the SA biosynthesis pathway is blocked. Finally, increased histone H3 acetylation of key SA biosynthesis genes correlates with their upregulation in infected hybrids. Our data demonstrate that enhanced activation of SA biosynthesis in A. thaliana hybrids may contribute to their increased resistance to a biotrophic bacterial pathogen.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms8309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4490401PMC
June 2015

Downregulation of VGLL4 in the progression of esophageal squamous cell carcinoma.

Tumour Biol 2015 Feb 30;36(2):1289-97. Epub 2014 Oct 30.

Department of Thoracic Surgery, Taixing People's Hospital of Jiangsu Province, 1 of Changzheng Rd, Taixing City, Jiangsu Province, 225400, China.

VGLL4, a member of the Vestigial-like (VGLL) proteins, has been reported to be dysregulated in several cancer types. However, its function in esophageal squamous cell carcinoma (ESCC) remains poorly understood. Here, it was found that the expression level of VGLL4 was decreased in ESCC tissues. Moreover, forced expression of VGLL4 in ESCC cells inhibited cell growth and migration, while knockdown of VGLL4 expression promoted the tumorigenecity of ESCC cells. Mechanistically, VGLL4 regulated the growth and motility of ESCC cells through downregulating the expression of connective tissue growth factor (CTGF), a known oncogene in the progression of ESCC. Taken together, our study suggested that downregulation of VGLL4 was very important in the progression of ESCC, and restoring the function of VGLL4 might be a promising therapeutic strategy for ESCC.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13277-014-2701-7DOI Listing
February 2015

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.

Proc Natl Acad Sci U S A 2014 Jul 30;111(28):10359-64. Epub 2014 Jun 30.

State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China;Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520

Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikingly, phylogenetic analysis reveals that many land plants have conserved homologs of HID1 and that its rice homolog can rescue the mutant phenotype when expressed in Arabidopsis hid1 mutants. We thus concluded that HID1 is a previously uncharacterized noncoding RNA whose function represents another layer of regulation in the precise control of seedling photomorphogenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1409457111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104870PMC
July 2014

Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis.

Mol Plant 2014 Mar 7;7(3):514-27. Epub 2014 Jan 7.

College of Life Sciences, Beijing Normal University, Beijing 100875, China.

Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50~300 nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5'-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/mp/sst177DOI Listing
March 2014

Nonlinear effects of group size on collective action and resource outcomes.

Proc Natl Acad Sci U S A 2013 Jul 17;110(27):10916-21. Epub 2013 Jun 17.

Center for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, USA.

For decades, scholars have been trying to determine whether small or large groups are more likely to cooperate for collective action and successfully manage common-pool resources. Using data gathered from the Wolong Nature Reserve since 1995, we examined the effects of group size (i.e., number of households monitoring a single forest parcel) on both collective action (forest monitoring) and resource outcomes (changes in forest cover) while controlling for potential confounding factors. Our results demonstrate that group size has nonlinear effects on both collective action and resource outcomes, with intermediate group size contributing the most monitoring effort and leading to the biggest forest cover gain. We also show how opposing effects of group size directly and indirectly affect collective action and resource outcomes, leading to the overall nonlinear relationship. Our findings suggest why previous studies have observed differing and even contradictory group-size effects, and thus help guide further research and governance of the commons. The findings also suggest that it should be possible to improve collective action and resource outcomes by altering factors that lead to the nonlinear group-size effect, including punishing free riding, enhancing overall and within-group enforcement, improving social capital across groups and among group members, and allowing self-selection during the group formation process so members with good social relationships can form groups autonomously.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1301733110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704000PMC
July 2013

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids.

Genome Biol 2013 Jun 12;14(6):R57. Epub 2013 Jun 12.

Background: Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.

Results: Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.

Conclusions: These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2013-14-6-r57DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707063PMC
June 2013

Epigenetic variations in plant hybrids and their potential roles in heterosis.

J Genet Genomics 2013 May 5;40(5):205-10. Epub 2013 Apr 5.

Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgg.2013.03.011DOI Listing
May 2013

Performance and prospects of payments for ecosystem services programs: evidence from China.

J Environ Manage 2013 Sep 15;127:86-95. Epub 2013 May 15.

Center for Systems Integration and Sustainability, Michigan State University, East Lansing, MI 48823-5243, USA.

Systematic evaluation of the environmental and socioeconomic effects of Payments for Ecosystem Services (PES) programs is crucial for guiding policy design and implementation. We evaluated the performance of the Natural Forest Conservation Program (NFCP), a national PES program of China, in the Wolong Nature Reserve for giant pandas. The environmental effects of the NFCP were evaluated through a historical trend (1965-2001) analysis of forest cover to estimate a counter-factual (i.e., without-PES) forest cover baseline for 2007. The socioeconomic effects of the NFCP were evaluated using data collected through household interviews carried out before and after NFCP implementation in 2001. Our results suggest that the NFCP was not only significantly associated with increases in forest cover, but also had both positive (e.g., labor reduction for fuelwood collection) and negative (e.g., economic losses due to crop raiding by wildlife) effects on local households. Results from this study emphasize the importance of integrating local conditions and understanding underlying mechanisms to enhance the performance of PES programs. Our findings are useful for the design and implementation of successful conservation policies not only in our study area but also in similar places around the world.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jenvman.2013.04.019DOI Listing
September 2013

A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa.

Mol Plant 2013 May 17;6(3):830-46. Epub 2012 Sep 17.

Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.

Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5' and 3' termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/mp/sss087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716300PMC
May 2013
-->