Brief Bioinform , IF:8.99 , 2019 May , V20 (3) : P1021-1031 doi: 10.1093/bib/bbx152
Construction of a hierarchical gene regulatory network centered around a transcription factor.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.; School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
We have modified a multitude of transcription factors (TFs) in numerous plant species and some animal species, and obtained transgenic lines that exhibit phenotypic alterations. Whenever we observe phenotypic changes in a TF's transgenic lines, we are always eager to identify its target genes, collaborative regulators and even upstream high hierarchical regulators. This issue can be addressed by establishing a multilayered hierarchical gene regulatory network (ML-hGRN) centered around a given TF. In this article, a practical approach for constructing an ML-hGRN centered on a TF using a combined approach of top-down and bottom-up network construction methods is described. Strategies for constructing ML-hGRNs are vitally important, as these networks provide key information to advance our understanding of how biological processes are regulated.
PMID: 29186304
Bioresour Technol , IF:7.539 , 2019 May , V280 : P229-238 doi: 10.1016/j.biortech.2019.02.015
Succession of organics metabolic function of bacterial community in response to addition of earthworm casts and zeolite in maize straw composting.
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China.; Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; Office of Mountain-River-Lake Development Committee of Jiangxi Province, Nanchang 330046, China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China. Electronic address: jbzhang@issas.ac.cn.
Succession and metabolism functions of bacterial communities were determined in maize straw composting with earthworm casts and zeolite addition by using high-throughput sequencing, Biolog and PICRUSt. Results showed that earthworm casts and zeolite addition increased the temperature, decreased NH4(+) contents and affected bacterial community structure. The relative abundances of Firmicutes and Betaproteobacteria increased with earthworm casts and zeolite addition in the late stage. The abundances of genes related to carbohydrate metabolism, amino acid metabolism, and energy metabolism were increased by these two additives in the early stage, but decreased in the late stage. Network analysis demonstrated that members of Bacillaceae were identified as the keystone taxa. Temperature showed negative relationship with Georgenia, while NH4(+) exhibited positive associations with Georgenia, Devosia, Ruania and Mycobacterium. These results indicated that earthworm casts and zeolite addition benefitted the keystone species and enhanced the metabolism capacity of bacterial community, thereby improved the quality of compost.
PMID: 30772635
J Exp Bot , IF:5.908 , 2019 May , V70 (10) : P2615-2622 doi: 10.1093/jxb/erz106
Reconstructing the ancestral flower of extant angiosperms: the 'war of the whorls' is heating up.
Friedrich Schiller University Jena, Matthias Schleiden Institute - Genetics, Philosophenweg, Jena, Germany.
The origin of the angiosperm flower is a long-standing problem of botany and evolutionary biology. One widely accepted milestone towards solving it is the reconstruction of the ancestral flower of extant angiosperms, here termed 'AFEA'. A recent approach employing novel methods gave results that were not anticipated. Most notably the reconstructed phyllotaxis of AFEA soon was criticized and sparked a heated debate in the literature. To better explain, clarify, and perhaps cool the debate, we first summarize the results of previous attempts to reconstruct AFEA and contrast them with the more recent, controversial prediction of its structure. We then outline the major arguments made by contrasting parties in the recent debate. Finally, we discuss two key topics, the molecular mechanism of phyllotaxis and the role of gene regulatory networks during flower development and evolution, that may help to clarify the issue in the intermediate future.
PMID: 30870567
Int J Mol Sci , IF:4.556 , 2019 May , V20 (9) doi: 10.3390/ijms20092202
Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. ysn785620774@126.com.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. 2016201034@njau.edu.cn.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. hjbreg@163.com.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. zkadrian@163.com.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. yanli1@njau.edu.cn.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China. sri@njau.edu.cn.
Soybean is one of the most important oil crops in the world. Revealing the molecular basis and exploring key candidate genes for seed oil synthesis has great significance for soybean improvement. In this study, we found that oil accumulation rates and gene expression levels changed dynamically during soybean seed development. The expression levels of genes in metabolic pathways such as carbon fixation, photosynthesis, glycolysis, and fatty acid biosynthesis were significantly up-regulated during the rapid accumulation of oil in developing soybean seeds. Through weighted correlation network analysis, we identified six co-expression modules associated with soybean seed oil content and the pink module was the most positively correlated (r = 0.83, p = 7 x 10(-4)) network. Through the integration of differential expression and co-expression analysis, we predicted 124 candidate genes potentially affecting soybean seed oil content, including seven genes in lipid metabolism pathway, two genes involved in glycolysis, one gene in sucrose metabolism, and 12 genes belonged to transcription factors as well as other categories. Among these, three genes (GmABI3b, GmNFYA and GmFAD2-1B) have been shown to control oil and fatty acid content in soybean seeds, and other newly identified candidate genes would broaden our knowledge to understand the molecular basis for oil accumulation in soybean seeds.
PMID: 31060266
FEMS Microbiol Ecol , IF:3.675 , 2019 May , V95 (5) doi: 10.1093/femsec/fiz056
Co-occurrence analysis reveal that biotic and abiotic factors influence soil fungistasis against Fusarium graminearum.
Universite de Brest, EA 3882, Laboratoire Universitaire de Biodiversite et Ecologie Microbienne, IBSAM, ESIAB, Technopole Brest-Iroise, 29280 Plouzane, France.; Lallemand SAS, 4 route de Beaupuy, 31180 Castelmaurou, France.; Ottawa Research & Development Centre, Science & Technology Branch, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, ON, K1A 0C6, Canada.
The current study determined the levels of soil fungistasis against a soil-borne pathogen inoculum, Fusarium graminearum (Fg, a major causal agent of Fusarium Head Blight (FHB)), in 31 wheat fields by quantifying Fg growth after a 15-day incubation period using qPCR in autoclaved versus non-autoclaved soils. The results were used to define the six most Fg-resistant and the six most Fg-conducive soils. By using a metabarcoding approach, the diversity of the bacterial communities was significantly higher in Fg-resistant soils than in Fg-conducive soils. Microbial taxa potentially contributing to Fg-fungistasis of soil were selected if they were significantly more prevalent and/or abundant in Fg-resistant soils than in Fg-conducive soils. Some of these candidate indicators, e.g. Pseudomonas spp. and Bacillus spp., have been reported previously as effective biocontrol agents against plant pathogens. Correlation-based network analysis further showed that the members of the bacterial communities in Fg-resistant soils were more connected than in Fg-conducive soils. Moreover, network modules was found significantly correlated with certain edaphic abiotics factors (such as the soil manganese and nitrogen content) and Fg-fungistasis. Such observations may suggest and emphasize, although conceptual, the importance of synergistic rather than individual effects of network members, and the nutrient use efficiency in contributing to Fg-resistance of soils in wheat fields in France.
PMID: 30998232
Fungal Genet Biol , IF:3.071 , 2019 May , V126 : P25-36 doi: 10.1016/j.fgb.2019.01.009
Comparative transcriptome analysis reveals regulatory networks and key genes of microsclerotia formation in the cotton vascular wilt pathogen.
Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China; The School of Life Science, Chongqing University, Chongqing 401331, China.; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China.; The School of Life Science, Southwest University, Chongqing 400715, China.; Chongqing Engineering Research Center of Specialty Crop Resources and The College of Life Science, Chongqing Normal University, Chongqing 401331, China. Electronic address: yangxy94@swu.edu.cn.
Verticillium dahliae is a soil-borne, hemibiotrophic phytopathogenic fungus that causes Verticillium wilt in a broad range of economic crops. The microsclerotia (MS), which act as the main host inoculum, can survive long-term in soil resulting in uncontrollable disease. In order to clarify the mechanism of MS formation, we sequenced the whole genome-wide expression profile of V. dahliae strain V991. Compared with M1 (no MS formation), during the process of MS formation and maturation, 1354, 1571, and 1521 unique tags were significantly regulated in M2, M3, and M4 library, respectively. During MS formation, melanin synthesis-related genes were preferentially upregulated. The process is more likely to regulated by transcription factors (TFs) including C2H2, Zn2Cys6, bZIP, and fungal-specific TF domain-containing proteins; additionally, G-protein coupled receptors, Ca(2+), small GTPases, and cAMP were involved in signalling transduction. Protein kinase-encoding (VDAG_06474) and synthase-encoding (VDAG_05314) genes were demonstrated to negatively and positively influence MS production, respectively. The gene expression dynamics revealed during MS formation provide comprehensive theoretical knowledge to further understanding of the metabolism and regulation of MS development in V. dahliae, potentially providing targets to control Verticillium wilt through interfering MS formation.
PMID: 30710746
Environ Sci Pollut Res Int , IF:3.056 , 2019 May , V26 (14) : P13948-13962 doi: 10.1007/s11356-019-04768-0
Way forward for straw burning pollution research: a bibliometric analysis during 1972-2016.
College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, People's Republic of China.; College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, People's Republic of China. huangkai@bjfu.edu.cn.; College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, People's Republic of China. liminbjfu@126.com.
Straw burning has become a hot topic in recent years as it poses a great risk not only to the lung health of residents in exposed areas but also to large-scale haze events. In order to have a more comprehensive understanding of straw burning research, based on the bibliometric analysis of Science Citation Index Expanded from Web of Science, the research progress of straw burning pollution from 1972 to 2016 and the future research trends were carried out in this paper. The research focuses on the document type, language, publication year, times cited and its output characteristics, subject category, journal, national and institutional distribution, author, etc. The results show that the study of straw burning pollution has shown a significant increase over the past 45 years. A total of 813 publications were found, and English was the most commonly used language. Articles were the most frequently appeared document types, and the researches were strongly embracing with the top 3 popular subject categories of "environmental sciences and ecology," "agriculture," and "meteorology and atmospheric sciences." We identified that the major journals publishing straw burning pollution research were Atmospheric Environment, followed by Atmospheric Chemistry and Physics. China as a leader in paper quantity played an important role in the research field of straw burning pollution, while the USA and India were located in the second and third positions. The most productive institution was Chinese Academy of Sciences, followed by Peking University and University Arkansas. Based on our analysis and the consideration of current environmental problems, more studies should focus on the following three aspects in the future: driving mechanism of emission characteristics, construction of high-resolution emission inventories, and the influencing mechanism of straw burning pollutants on climate change and human health. Our analysis and prospects can be served as a useful reference for future studies.
PMID: 30888617
Multivariate Behav Res , IF:2.75 , 2019 May : P1-19 doi: 10.1080/00273171.2019.1616526
Quantifying the Reliability and Replicability of Psychopathology Network Characteristics.
a Department of Psychology, Centre for Emotional Health , Macquarie University , Sydney , NSW , Australia.; b Department of Psychology , University of Pittsburgh , Pittsburgh , PA , USA.; c Department of Psychological and Brain Sciences , University of Iowa , Iowa City , IA , USA.; d Department of Psychology , University of Minnesota , Minneapolis , MN , USA.
Pairwise Markov random field networks-including Gaussian graphical models (GGMs) and Ising models-have become the "state-of-the-art" method for psychopathology network analyses. Recent research has focused on the reliability and replicability of these networks. In the present study, we compared the existing suite of methods for maximizing and quantifying the stability and consistency of PMRF networks (i.e., lasso regularization, plus the bootnet and NetworkComparisonTest packages in R) with a set of metrics for directly comparing the detailed network characteristics interpreted in the literature (e.g., the presence, absence, sign, and strength of each individual edge). We compared GGMs of depression and anxiety symptoms in two waves of data from an observational study (n = 403) and reanalyzed four posttraumatic stress disorder GGMs from a recent study of network replicability. Taken on face value, the existing suite of methods indicated that overall the network edges were stable, interpretable, and consistent between networks, but the direct metrics of replication indicated that this was not the case (e.g., 39-49% of the edges in each network were unreplicated across the pairwise comparisons). We discuss reasons for these apparently contradictory results (e.g., relying on global summary statistics versus examining the detailed characteristics interpreted in the literature) and conclude that the limited reliability of the detailed characteristics of networks observed here is likely to be common in practice, but overlooked by current methods. Poor replicability underpins our concern surrounding the use of these methods, given that generalizable conclusions are fundamental to the utility of their results.
PMID: 31140875
J Plant Res , IF:2.185 , 2019 May , V132 (3) : P301-309 doi: 10.1007/s10265-019-01100-2
A gene regulatory network for root hair development.
RIKEN Center for Sustainable Resource Science, 230-0045, Yokohama, Japan. michitaro.shibata@riken.jp.; RIKEN Center for Sustainable Resource Science, 230-0045, Yokohama, Japan.
Root hairs play important roles for the acquisition of nutrients, microbe interaction and plant anchorage. In addition, root hairs provide an excellent model system to study cell patterning, differentiation and growth. Arabidopsis root hairs have been thoroughly studied to understand how plants regulate cell fate and growth in response to environmental signals. Accumulating evidence suggests that a multi-layered gene regulatory network is the molecular secret to enable the flexible and adequate response to multiple signals. In this review, we describe the key transcriptional regulators controlling cell fate and/or cell growth of root hairs. We also discuss how plants integrate phytohormonal and environmental signals, such as auxin, ethylene and phosphate availability, and modulate the level of these transcriptional regulators to tune root hair development.
PMID: 30903397
Heliyon , 2019 May , V5 (5) : Pe01676 doi: 10.1016/j.heliyon.2019.e01676
New perspectives for weeds control using autochthonous fungi with selective bioherbicide potential.
Center for Agricultural Sciences, Federal University of Santa Catarina, Admar Gonzaga Highway, Itacorubi, Florianopolis, Brazil.; Graduate Program in Plant Science, Federal University of Rio Grande do Sul, Bento Goncalves Avenue, Porto Alegre, Brazil.; Graduate Program in Agronomy, Federal University of Santa Maria, Roraima Avenue, Camobi, Santa Maria, Brazil.; Laboratory of Agroecology, Federal University of Fronteira Sul, Erechim campus, RS-135, Rural Area, Erechim, Brazil.; Department of Chemical Engineering, Federal University of Santa Catarina, Joao Pio Duarte Silva street, Corrego Grande, Florianopolis, Brazil.; Department of Chemical Engineering, Federal University of Santa Maria, Roraima Avenue, Camobi, Santa Maria, Brazil.; Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim campus, RS-135, Rural Area, Erechim, Brazil.; Laboratory of Sustainable Management of Agricultural Systems, Department of Environmental Science and Technology, Federal University of Fronteira Sul, Erechim, Brazil.
The prospection of bioherbicides has been an alternative to weed control, aiming at mitigating chemical risks to human, animal and environmental health due to extreme use of synthetic herbicides. In the present study, various fungi were isolated from plants with symptoms of fungal diseases for bioherbicide purposes against weeds (Urochloa plantaginea, Euphorbia heterophylla and Bidens pilosa). Fungi isolated were identified by molecular methods and enzymatic products obtained by fungi fermentation (cellulase, lipase, peroxidase, and amylase) were quantified. Bioherbicide selectivity study was performed on crops (soybean and corn), as well as on resistant weeds. Among the isolated fungi, Fusarium oxysporum, Fusarium ploriferatum, and Trichoderma koningiopsis presented bioherbicide potential. T. koningiopsis, in particular, presented the highest effect on Euphorbia heterophylla (popular name - Mexican fire plant), causing up to 60% of foliar damage, without presenting phytotoxicity against corn crop. New perspectives for weeds control and their use in corn crops were prospected, considering the bioherbicide selectivity described in this study.
PMID: 31193093