Mol Ecol , IF:5.163 , 2020 Dec doi: 10.1111/mec.15773
Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.
State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.; Gladstone Institute, University of California, San Francisco, CA, USA.; Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2 degrees C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.
PMID: 33305411
Plant Physiol Biochem , IF:3.72 , 2021 Jan , V158 : P103-112 doi: 10.1016/j.plaphy.2020.11.052
The regulatory framework of developmentally programmed cell death in floral organs: A review.
Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan. Electronic address: wangyu_kun1@163.com.; Division of Biological Science, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.; Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, PR China.; School of Agricultural Science and Engineering, Shaoguan University, 288 Daxue Road, Shaoguan, 512000, PR China. Electronic address: rf870512@163.com.
Developmentally programmed cell death (dPCD) is a tightly controlled biological process. In recent years, vital roles of dPCD on regulating floral organ growth and development have been reported. It is well known that flower is an essential organ for reproduction and a turning point of plants' life cycle. Hence, uncovering the complex molecular networks which regulates dPCD processes in floral organs is utmost important. So far, our understanding of dPCD on floral organ growth and development is just starting. Herein, we summarize the important factors that involved in the tapetal degeneration, pollen tube rupture, receptive synergid cell death, nucellar degradation, and antipodal cell degradation. Meanwhile, the known factors that involved in transmitting tract formation and self-incompatibility-induced PCD were also introduced. Furthermore, the genes that associated with anther dehiscence and petal senescence and abscission were reviewed as well. The functions of various types of factors involved in floral dPCD processes are highlighted principally. The regulatory panorama described here can provide us some insights about flower-specific dPCD process.
PMID: 33307422
BMC Microbiol , IF:2.989 , 2020 Dec , V20 (1) : P376 doi: 10.1186/s12866-020-02059-0
The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes.
Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.; Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.; Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran. aliahmadigorgani@gmail.com.
BACKGROUND: Streptococcus pneumonia (pneumococcus) is a human bacterial pathogen causing a range of mild to severe infections. The complicated transcriptome patterns of pneumococci during the colonization to infection process in the human body are usually determined by measuring the expression of essential virulence genes and the comparison of pathogenic with non-pathogenic bacteria through microarray analyses. As systems biology studies have demonstrated, critical co-expressing modules and genes may serve as key players in biological processes. Generally, Sample Progression Discovery (SPD) is a computational approach traditionally used to decipher biological progression trends and their corresponding gene modules (clusters) in different clinical samples underlying a microarray dataset. The present study aimed to investigate the bacterial gene expression pattern from colonization to severe infection periods (specimens isolated from the nasopharynx, lung, blood, and brain) to find new genes/gene modules associated with the infection progression. This strategy may lead to finding novel gene candidates for vaccines or drug design. RESULTS: The results included essential genes whose expression patterns varied in different bacterial conditions and have not been investigated in similar studies. CONCLUSIONS: In conclusion, the SPD algorithm, along with differentially expressed genes detection, can offer new ways of discovering new therapeutic or vaccine targeted gene products.
PMID: 33334315