Trends Plant Sci , IF:18.313 , 2022 Jul doi: 10.1016/j.tplants.2022.06.002
Towards a hierarchical gene regulatory network underlying somatic embryogenesis.
National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China. Electronic address: jwwang@sippe.ac.cn.
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
PMID: 35810071
Trends Microbiol , IF:17.079 , 2022 Jul doi: 10.1016/j.tim.2022.06.006
Synthetic plant microbiota challenges in nonmodel species.
Department of Biology, University of Florence, Florence, Italy.; Department of Biology, University of Florence, Florence, Italy. Electronic address: alessio.mengoni@unifi.it.
Plant-associated microbiota are becoming central in the development of ways to improve plant productivity and health. However, most research has focussed mainly on a few model plant species. It is essential to translate discoveries to the many nonmodel crops, allowing the design and application of effective synthetic microbiota.
PMID: 35843854
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Aug , V119 (35) : Pe2204400119 doi: 10.1073/pnas.2204400119
The generality of cryptic dietary niche differences in diverse large-herbivore assemblages.
Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, 08544.; Institut de Sciences de l'Evolution de Montpellier, University of Montpellier, CNRS, Institut de Recherche pour le Developpement, Montpellier, 34095, France.; Department of Biology, Wake Forest University, Winston-Salem, NC, 27109.; Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, 3584 CB, The Netherlands.; Centre for African Conservation Ecology, Nelson Mandela University, Port Elizabeth, 6031, South Africa.; Niassa Carnivore Project, Niassa National Reserve, Mozambique.; Laboratoire d'Ecologie Alpine, Universite Grenoble Alpes, Centre National de la Recherche Scientifique, Grenoble, F-38000, France.; Argaly, Batiment Cleanspace, F-73800 Sainte Helene du Lac, France.; School of Natural Resources, Department of Zoology & Aquatic Sciences, Copperbelt University, Kitwe, Zambia.; Centre d'Ecologie Fonctionnelle et Evolutive, University of Montpellier, Centre National de la Recherche Scientifique, Ecole Pratique des Hautes Etudes, IRD, Montpellier, 34293, France.; Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria, Hatfield 0028, South Africa.; Department of Wildlife, Fish & Environmental Studies, Swedish University of Agricultural Sciences, Umea, SE-901 83, Sweden.; Odum School of Ecology, University of Georgia, Athens, GA, 30602.; Department of National Parks and Wildlife, Lilongwe, 3, Malawi.; Mpala Research Centre, Nanyuki, 10400, Kenya.; Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, 83844.; Serengeti Wildlife Research Institute, Seronera, Tanzania.; School of Environmental Sciences, University of Liverpool, Liverpool, L3 5DA, United Kingdom.; Department of Zoology and Entomology, University of Pretoria, Pretoria, Hatfield 0028, South Africa.; School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits, Braamfontein 2000, Johannesburg, South Africa.; Tromso Museum, UiT The Arctic University of Norway, Tromso, Langnes N-9037, Norway.; Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912.; Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912.
Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing approximately 4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families-grasses and legumes-accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.
PMID: 35994662
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Aug , V119 (35) : Pe2208795119 doi: 10.1073/pnas.2208795119
Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells.
Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan.; Department of Plant Biology, Michigan State University, East Lansing, MI 48824.; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI 48824.; Department of Bioagricultural Science, National Chiayi University, Chiayi 600, Taiwan.; School of Biological Sciences, Washington State University, Pullman, WA 99164.; Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan.; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637.
The superior photosynthetic efficiency of C4 leaves over C3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.
PMID: 36001691
New Phytol , IF:10.151 , 2022 Aug , V235 (4) : P1426-1441 doi: 10.1111/nph.18255
Trihelix transcription factors GTL1 and DF1 prevent aberrant root hair formation in an excess nutrient condition.
RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.; Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan.; KU Leuven Plant Institute (LPI), KU Leuven, Kasteelpark Arenberg 31, Leuven, B-3001, Belgium.; Department of Biological Sciences, University of Tokyo, Tokyo, 119-0033, Japan.
Root hair growth is tuned in response to the environment surrounding plants. While most previous studies focused on the enhancement of root hair growth during nutrient starvation, few studies investigated the root hair response in the presence of excess nutrients. We report that the post-embryonic growth of wild-type Arabidopsis plants is strongly suppressed with increasing nutrient availability, particularly in the case of root hair growth. We further used gene expression profiling to analyze how excess nutrient availability affects root hair growth, and found that RHD6 subfamily genes, which are positive regulators of root hair growth, are downregulated in this condition. However, defects in GTL1 and DF1, which are negative regulators of root hair growth, cause frail and swollen root hairs to form when excess nutrients are supplied. Additionally, we observed that the RHD6 subfamily genes are mis-expressed in gtl1-1 df1-1. Furthermore, overexpression of RSL4, an RHD6 subfamily gene, induces swollen root hairs in the face of a nutrient overload, while mutation of RSL4 in gtl1-1 df1-1 restore root hair swelling phenotype. In conclusion, our data suggest that GTL1 and DF1 prevent unnecessary root hair formation by repressing RSL4 under excess nutrient conditions.
PMID: 35713645
Plant Biotechnol J , IF:9.803 , 2022 Aug , V20 (8) : P1561-1577 doi: 10.1111/pbi.13833
Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.; College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
Adventitious rooting is an essential biological process in the vegetative propagation of economically important horticultural and forest tree species. It enables utilization of the elite genotypes in breeding programmes and production. Promotion of adventitious root (AR) formation has been associated with starvation of inorganic phosphate and some factors involved in low phosphorus (LP) signalling. However, the regulatory mechanism underlying LP-mediated AR formation remains largely elusive. We established an efficient experimental system that guaranteed AR formation through short-term LP treatment in Populus ussuriensis. We then generated a time-course RNA-seq data set to recognize key regulatory genes and regulatory cascades positively regulating AR formation through data analysis and gene network construction, which were followed by experimental validation and characterization. We constructed a multilayered hierarchical gene regulatory network, from which PuMYB40, a typical R2R3-type MYB transcription factor (TF), and its interactive partner, PuWRKY75, as well as their direct targets, PuLRP1 and PuERF003, were identified to function upstream of the known adventitious rooting genes. These regulatory genes were functionally characterized and proved their roles in promoting AR formation in P. ussuriensis. In conclusion, our study unveiled a new hierarchical regulatory network that promoted AR formation in P. ussuriensis, which was activated by short-term LP stimulus and primarily governed by PuMYB40 and PuWRKY75.
PMID: 35514032
Environ Int , IF:9.621 , 2022 Aug , V168 : P107457 doi: 10.1016/j.envint.2022.107457
Storm promotes the dissemination of antibiotic resistome in an urban lagoon through enhancing bio-interactions.
CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.; CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.; Yundang Lake Management Center, Xiamen, Fujian 361004, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.; CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt.; CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia.; CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan.; CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China. Electronic address: ayhu@iue.ac.cn.
Antibiotic-resistance genes (ARGs) and resistant bacteria (ARB) are abundant in stormwater that could cause serious infections, posing a potential threat to public health. However, there is no inference about how stormwater contributes to ARG profiles as well as the dynamic interplay between ARGs and bacteria via vertical gene transfer (VGT) or horizontal gene transfer (HGT) in urban water ecosystems. In this study, the distribution of ARGs, their host communities, and the source and community assembly process of ARGs were investigated in Yundang Lagoon (China) via high-throughput quantitative PCR, 16S rRNA gene amplicon sequencing, and application of SourceTracker before, after and recovering from an extreme precipitation event (132.1 mm). The abundance of ARGs and mobile genetic elements (MGEs) was the highest one day after precipitation and then decreased 2 days after precipitation and so on. Based on SourceTracker and NMDS analysis, the ARG and bacterial communities in lagoon surface water from one day after precipitation were mainly contributed by the wastewater treatment plant (WWTP) influent and effluent. However, the contribution of WWTP to ARG communities was minor 11 days after the precipitation, suggesting that the storm promoted the ARG levels by introducing the input of ARGs, MGEs, and ARB from point and non-point sources, such as sewer overflow and land-applied manure. Based on a novel microbial network analysis framework, the contribution of positive biological interactions between ARGs and MGEs or bacteria was the highest one day after precipitation, indicating a promoted VGT and HGT for ARG dissemination. The microbial networks deconstructed 11 days after precipitation, suggesting the stormwater practices (e.g., tide gate opening, diversion channels, and pumping) alleviated the spread of ARGs. These results advanced our understanding of the distribution and transport of ARGs associated with their source in urban stormwater runoff.
PMID: 35963060
Elife , IF:8.14 , 2022 Jul , V11 doi: 10.7554/eLife.77492
On the flexibility of the cellular amination network in E. coli.
Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.; Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Ammonium (NH4(+)) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine sources and found that several amino acids complement the auxotrophy, either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids beta-alanine, alanine, glycine, and serine as new amine sources and identified d-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.
PMID: 35876664
Environ Pollut , IF:8.071 , 2022 Aug , V307 : P119516 doi: 10.1016/j.envpol.2022.119516
Effects of soil protists on the antibiotic resistome under long term fertilization.
Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China. Electronic address: dongzhu@rcees.ac.cn.; Key Laboratory for Humid Subtropical Ecogeographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871, Frederiksberg, Denmark; Sino-Danish Center for Education and Research, Beijing, China.; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.
PMID: 35609845
Sci Total Environ , IF:7.963 , 2022 Jul : P157496 doi: 10.1016/j.scitotenv.2022.157496
Temperature drives the assembly of Bacillus community in mangrove ecosystem.
Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China.; Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China. Electronic address: liwenjun3@mail.sysu.edu.cn.; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province 350002, PR China. Electronic address: sgzhou@soil.gd.cn.
Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO3-N and NH4-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.
PMID: 35870580
Psychol Med , IF:7.723 , 2022 Aug : P1-12 doi: 10.1017/S003329172200232X
Prospective network analysis of proinflammatory proteins, lipid markers, and depression components in midlife community women.
Department of Health Care Policy, Harvard Medical School, Boston, MA, USA.; Department of Psychology, The Pennsylvania State University, State College, PA, USA.
BACKGROUND: Vulnerability theories propose that suboptimal levels of lipid markers and proinflammatory proteins predict future heightened depression. Scar models posit the reverse association. However, most studies that tested relationships between non-specific immune/endocrine markers and depression did not separate temporal inferences between people and within-person and how different immunometabolism markers related to unique depression symptoms. We thus used cross-lagged prospective network analyses (CLPN) to investigate this topic. METHODS: Community midlife women (n = 2224) completed the Center for Epidemiologic Studies-Depression scale and provided biomarker samples across five time-points spanning 9 years. CLPN identified significant relations (edges) among components (nodes) of depression (depressed mood, somatic symptoms, interpersonal issues), lipid markers [insulin, fasting glucose, triglycerides, low-density lipoprotein-cholesterol (LDL), high-density lipoprotein-cholesterol (HDL)], and proinflammatory proteins [C-reactive protein (CRP), fibrinogen], within and across time-points. All models adjusted for age, estradiol, follicle-stimulating hormone, and menopausal status. RESULTS: In within-person temporal networks, higher CRP and HDL predicted all three depression components (d = 0.131-2.112). Increased LDL preceded higher depressed mood and interpersonal issues (v. somatic symptoms) (d = 0.251-0.327). Elevated triglycerides predicted more somatic symptoms (v. depressed mood and interpersonal problems) (d = 0.131). More interpersonal problems forecasted elevated fibrinogen and LDL levels (d = 0.129-0.331), and stronger somatic symptoms preceded higher fibrinogen levels (d = 0.188). CONCLUSIONS: Results supported both vulnerability and scar models. Long-term dysregulated immunometabolism systems, social disengagement, and related patterns are possible mechanistic accounts. Cognitive-behavioral therapies that optimize nutrition and physical activity may effectively target depression.
PMID: 35924730
J Exp Bot , IF:6.992 , 2022 Jul doi: 10.1093/jxb/erac300
Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Rua do Matao, 277, 05508-090, Sao Paulo, Brazil.; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.; VIB Metabolomics Core, 9052 Ghent, Belgium.; Joint BioEnergy Institute, Emeryville, CA 94608, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes 10, E-41012, Seville, Spain.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, 370, 05508-020, Sao Paulo, Brazil.
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant (with reduced CAD activity) was analyzed. In the WT, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
PMID: 35788296
J Environ Manage , IF:6.789 , 2022 Oct , V319 : P115694 doi: 10.1016/j.jenvman.2022.115694
Optimization of vegetable waste composting and the exploration of microbial mechanisms related to fungal communities during composting.
Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China. Electronic address: wangweiping119@126.com.
The application of additives to regulate the microbial functional composition during composting has attracted much research attention. However, little is known about the succession and role of the fungal community in the laboratory-scale composting of vegetable waste supplemented with pig manure and microbial agents. The purpose of this study was to identify effective additives for improving vegetable waste composting performance and product quality, and to analyze the microbial community succession during composting. The results showed that the combined addition of pig manure and microbial agents (T2 treatment) accelerated the pile temperature increase, enhanced total organic carbon degradation (23.36%), and promoted the maturation of the compost. Furthermore, the T2 treatment increased the activities of most enzymes, reshaped the microbial community, and reduced the relative abundance of potential animal (1.60%) and plant (0.095%) pathogens. The relative abundance of Firmicutes (71.23%) increased with the combined addition of pig manure and microbial agents in the thermophilic stage. In the middle and late stages, Saccharomonospora, Aspergillus, and Thermomyces, which were related to C/N and total phosphorus, were enriched in the T2 treatment. Network analysis demonstrated that the complexity and stability of the fungal network were more evidently increased in the T2 treatment, and Saccharomonospora, Aspergillus, and Microascus were identified as keystone taxa. The keystone taxa associated with extracellular enzymes contributed significantly to compost maturation. These results provide a reference for the application of additives to improve compost safety in pilot-scale composting.
PMID: 35841778
Neuroimage , IF:6.556 , 2022 Aug , V256 : P119246 doi: 10.1016/j.neuroimage.2022.119246
Diurnal variations of resting-state fMRI data: A graph-based analysis.
Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA; Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA. Electronic address: ffaraha2@jhu.edu.; Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA.; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA; Department of Psychology, University of California, Berkeley, CA, USA.; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.; Institute for Simulation and Training, University of Central Florida, Orlando, FL, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland; Department of Psychology of Individual Differences, Psychological Diagnosis, and Psychometrics, Institute of Psychology, University of Social Sciences and Humanities, Warsaw, Poland.; Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland. Electronic address: magda.fafrowicz@uj.edu.pl.
Circadian rhythms (lasting approximately 24 h) control and entrain various physiological processes, ranging from neural activity and hormone secretion to sleep cycles and eating habits. Several studies have shown that time of day (TOD) is associated with human cognition and brain functions. In this study, utilizing a chronotype-based paradigm, we applied a graph theory approach on resting-state functional MRI (rs-fMRI) data to compare whole-brain functional network topology between morning and evening sessions and between morning-type (MT) and evening-type (ET) participants. Sixty-two individuals (31 MT and 31 ET) underwent two fMRI sessions, approximately 1 hour (morning) and 10 h (evening) after their wake-up time, according to their declared habitual sleep-wake pattern on a regular working day. In the global analysis, the findings revealed the effect of TOD on functional connectivity (FC) patterns, including increased small-worldness, assortativity, and synchronization across the day. However, we identified no significant differences based on chronotype categories. The study of the modular structure of the brain at mesoscale showed that functional networks tended to be more integrated with one another in the evening session than in the morning session. Local/regional changes were affected by both factors (i.e., TOD and chronotype), mostly in areas associated with somatomotor, attention, frontoparietal, and default networks. Furthermore, connectivity and hub analyses revealed that the somatomotor, ventral attention, and visual networks covered the most highly connected areas in the morning and evening sessions: the latter two were more active in the morning sessions, and the first was identified as being more active in the evening. Finally, we performed a correlation analysis to determine whether global and nodal measures were associated with subjective assessments across participants. Collectively, these findings contribute to an increased understanding of diurnal fluctuations in resting brain activity and highlight the role of TOD in future studies on brain function and the design of fMRI experiments.
PMID: 35477020
Plant J , IF:6.417 , 2022 Jul doi: 10.1111/tpj.15905
Unsupervised and semi-supervised learning: the next frontier in machine learning for plant systems biology.
Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100094, China.; National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China.
Advances in high-throughput omics technologies are leading plant biology research into the era of big data. Machine learning (ML) performs an important role in plant systems biology because of its excellent performance and wide application in the analysis of big data. However, to achieve ideal performance, supervised ML algorithms require large numbers of labeled samples as training data. In some cases, it is impossible or prohibitively expensive to obtain enough labeled training data; here, the paradigms of unsupervised learning (UL) and semi-supervised learning (SSL) play an indispensable role. In this review, we first introduce the basic concepts of ML techniques, as well as some representative UL and SSL algorithms, including clustering, dimensionality reduction, self-supervised learning (self-SL), positive-unlabeled (PU) learning and transfer learning. We then review recent advances and applications of UL and SSL paradigms in both plant systems biology and plant phenotyping research. Finally, we discuss the limitations and highlight the significance and challenges of UL and SSL strategies in plant systems biology.
PMID: 35821601
Plant J , IF:6.417 , 2022 Aug doi: 10.1111/tpj.15928
A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid.
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2 s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.
PMID: 35912411
Plant J , IF:6.417 , 2022 Jul , V111 (2) : P546-566 doi: 10.1111/tpj.15838
CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice.
UMR DIADE, Universite de Montpellier, IRD, CIRAD, 911 Avenue Agropolis, 34394, Montpellier cedex 5, France.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, 69007, France.; National Key Laboratory for Plant Cell Biotechnology, LMI RICE2, Agricultural Genetic Institute, 11300, Hanoi, Vietnam.; CIRAD, UMR AGAP, F-34398, Montpellier, France.; UMR AGAP, Universite de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.; University of Science and Technology of Hanoi, LMIRICE2, Vietnam Academy of Science and Technology, 11300, Hanoi, Vietnam.; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium.; VIB Center for Plant Systems Biology, 9052, Ghent, Belgium.; Czech Advanced Technology and Research Institute, Centre of Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Olomouc, Czech Republic.; Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain-Centre de Recherche, Route d'Ennezat, Chappes, France.
In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
PMID: 35596715
Front Cardiovasc Med , IF:6.05 , 2022 , V9 : P920399 doi: 10.3389/fcvm.2022.920399
Hub Genes Identification, Small Molecule Compounds Prediction for Atrial Fibrillation and Diagnostic Model Construction Based on XGBoost Algorithm.
Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
Background: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia and engenders significant global health care burden. The underlying mechanisms of AF is remained to be revealed and current treatment options for AF have limitations. Besides, a detection system can help identify those at risk of developing AF and will enable personalized management. Materials and Methods: In this study, we utilized the robust rank aggregation method to integrate six AF microarray datasets from the Gene Expression Omnibus database, and identified a set of differentially expressed genes between patients with AF and controls. Potential compounds were identified by mining the Connectivity Map database. Functional modules and closely-interacted clusters were identified using weighted gene co-expression network analysis and protein-protein interaction network, respectively. The overlapped hub genes were further filtered. Subsequent analyses were performed to analyze the function, biological features, and regulatory networks. Moreover, a reliable Machine Learning-based diagnostic model was constructed and visualized to clarify the diagnostic features of these genes. Results: A total of 156 upregulated and 34 downregulated genes were identified, some of which had not been previously investigated. We showed that mitogen-activated protein kinase and epidermal growth factor receptor inhibitors were likely to mitigate AF based on Connectivity Map analysis. Four genes, including CXCL12, LTBP1, LOXL1, and IGFBP3, were identified as hub genes. CXCL12 was shown to play an important role in regulation of local inflammatory response and immune cell infiltration. Regulation of CXCL12 expression in AF was analyzed by constructing a transcription factor-miRNA-mRNA network. The Machine Learning-based diagnostic model generated in this study showed good efficacy and reliability. Conclusion: Key genes involving in the pathogenesis of AF and potential therapeutic compounds for AF were identified. The biological features of CXCL12 in AF were investigated using integrative bioinformatics tools. The results suggested that CXCL12 might be a biomarker that could be used for distinguishing subsets of AF, and indicated that CXCL12 might be an important intermediate in the development of AF. A reliable Machine Learning-based diagnostic model was constructed. Our work improved understanding of the mechanisms of AF predisposition and progression, and identified potential therapeutic avenues for treatment of AF.
PMID: 35911532
Int J Mol Sci , IF:5.923 , 2022 Jul , V23 (15) doi: 10.3390/ijms23158520
Proteomics Evidence of a Systemic Response to Desiccation in the Resurrection Plant Haberlea rhodopensis.
Agrobioinstitute, Agricultural Academy Bulgaria, 1164 Sofia, Bulgaria.; Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; Laboratoire de Physiologie Cellulaire et Vegetale, University Grenoble Alpes, CNRS, INRAE, CEA, 38054 Grenoble, France.; Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.; Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, L-4362 Esch-sur-Alzette, Luxembourg.; Laboratoire de Biologie a Grande Echelle, Institut de Recherches en Technologies et Sciences pour le Vivant, CEA, Universite Grenoble Alpes INSERM, 38054 Grenoble, France.; Department of Biochemistry, Faculty of Biology, Sofia University, 1164 Sofia, Bulgaria.
Global warming and drought stress are expected to have a negative impact on agricultural productivity. Desiccation-tolerant species, which are able to tolerate the almost complete desiccation of their vegetative tissues, are appropriate models to study extreme drought tolerance and identify novel approaches to improve the resistance of crops to drought stress. In the present study, to better understand what makes resurrection plants extremely tolerant to drought, we performed transmission electron microscopy and integrative large-scale proteomics, including organellar and phosphorylation proteomics, and combined these investigations with previously published transcriptomic and metabolomics data from the resurrection plant Haberlea rhodopensis. The results revealed new evidence about organelle and cell preservation, posttranscriptional and posttranslational regulation, photosynthesis, primary metabolism, autophagy, and cell death in response to desiccation in H. rhodopensis. Different protective intrinsically disordered proteins, such as late embryogenesis abundant (LEA) proteins, thaumatin-like proteins (TLPs), and heat shock proteins (HSPs), were detected. We also found a constitutively abundant dehydrin in H. rhodopensis whose phosphorylation levels increased under stress in the chloroplast fraction. This integrative multi-omics analysis revealed a systemic response to desiccation in H. rhodopensis and certain targets for further genomic and evolutionary studies on DT mechanisms and genetic engineering towards the improvement of drought tolerance in crops.
PMID: 35955654
Int J Mol Sci , IF:5.923 , 2022 Aug , V23 (16) doi: 10.3390/ijms23168986
Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery.
Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.; Center for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.; Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China.; Department of Food Science, Aarhus University, 8200 Aarhus, Denmark.; Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada.
Celery (Apium graveolens L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chlorophyll and carotenoid-related genes in celery and six representative species. Significantly, different contents and gene expression patterns were found among three celery varieties. In total, 237 and 290 chlorophyll and carotenoid-related genes were identified in seven species. No notable gene expansion of chlorophyll biosynthesis was detected in examined species. However, the gene encoding zeta-carotene desaturase (ZDS) enzyme in carotenoid was expanded in celery. Comparative genomics and RNA-seq analyses revealed 16 and 5 key genes, respectively, regulating chlorophyll and carotenoid. An intriguing finding is that chlorophyll and carotenoid-related genes were coordinately regulated by transcriptional factors, which could be distinctively classified into positive- and negative-regulation groups. Six CONSTANS (CO)-like transcription factors co-regulated chlorophyll and carotenoid-related genes were identified in celery. In conclusion, this study provides new insights into the regulation of chlorophyll and carotenoid by transcription factors.
PMID: 36012264
Int J Mol Sci , IF:5.923 , 2022 Aug , V23 (15) doi: 10.3390/ijms23158665
Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis.
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.; Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea.; Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093, USA.; USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA.
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
PMID: 35955798
Front Plant Sci , IF:5.753 , 2022 , V13 : P941380 doi: 10.3389/fpls.2022.941380
Identification and Functional Prediction of Poplar Root circRNAs Involved in Treatment With Different Forms of Nitrogen.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
Circular RNAs (circRNAs) are a class of noncoding RNA molecules with ring structures formed by covalent bonds and are commonly present in organisms, playing an important regulatory role in plant growth and development. However, the mechanism of circRNAs in poplar root responses to different forms of nitrogen (N) is still unclear. In this study, high-throughput sequencing was used to identify and predict the function of circRNAs in the roots of poplar exposed to three N forms [1 mM NO3 (-) (T1), 0.5 mM NH4NO3 (T2, control) and 1 mM NH4 (+) (T3)]. A total of 2,193 circRNAs were identified, and 37, 24 and 45 differentially expressed circRNAs (DECs) were screened in the T1-T2, T3-T2 and T1-T3 comparisons, respectively. In addition, 30 DECs could act as miRNA sponges, and several of them could bind miRNA family members that play key roles in response to different N forms, indicating their important functions in response to N and plant growth and development. Furthermore, we generated a competing endogenous RNA (ceRNA) regulatory network in poplar roots treated with three N forms. DECs could participate in responses to N in poplar roots through the ceRNA regulatory network, which mainly included N metabolism, amino acid metabolism and synthesis, response to NO3 (-) or NH4 (+) and remobilization of N. Together, these results provide new insights into the potential role of circRNAs in poplar root responses to different N forms.
PMID: 35874008
Front Microbiol , IF:5.64 , 2022 , V13 : P949152 doi: 10.3389/fmicb.2022.949152
Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice.
Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan.; Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh.
Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.
PMID: 35983324
Environ Sci Pollut Res Int , IF:4.223 , 2022 Aug , V29 (37) : P56291-56308 doi: 10.1007/s11356-022-19816-5
The drivers of collaborative innovation of the comprehensive utilization technologies of coal fly ash in China: a network analysis.
College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.; School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China. heartchang@126.com.; College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China. wujing@nankai.edu.cn.
Coal consumption brings a lot of coal fly ash (CFA). It requires interdisciplinary efforts in research, policy, and practice to improve the utilization of CFA. Although there have been a lot of achievements in technological innovation, the utilization of CFA is still difficult to match its output. So, it is urgent to explore how to guide its effective innovation. This paper uses social network analysis to discuss the characteristics of the collaborative innovation network of CFA comprehensive utilization technology in China. Then, this paper uses regression analysis to explore the differences in innovation performance under different research and development (R&D) backgrounds. The results show that (1) based on the network-level indicators, the collaborative innovation scale has an obvious trend of expanding. Partnerships increased from 20 to 574. Meanwhile, the network shows obvious scale-free and "small-world" characteristics, indicating that innovation resources are concentrated in a few organizations. (2) Based on the node-level indicators, the major contributor has shifted from universities and research institutions to enterprises. Enterprises account for the highest proportion (73%) and have the highest centrality (8.3). The betweenness centrality of the universities is 265, and only 14% of the organizations are universities which means universities play an important role in connecting different organizations in the network, but their participation in the collaborative innovation is insufficient. (3) Based on the collaborative relationship-level indicators, the cooperation is lack of depth. Only a small number of organizations, especially enterprises, have stable partners, showing the characteristic of "low cooperation width and high cooperation depth," which means fewer partners but more frequently collaborative innovation. (4) Based on the innovation performance, the innovation performance under the category of cooperative R&D, especially industry-academy cooperation, is better than that of independent R&D. But, industry-academy cooperation only occupied 43% of collaborative relationships in the network. Finally, this paper puts forward suggestions for governments from five aspects: decentralization, defining roles of enterprise and university, encouraging collaboration, changing the idea of the patent application, and promoting deeper cooperation.
PMID: 35334046
BMC Plant Biol , IF:4.215 , 2022 Jul , V22 (1) : P359 doi: 10.1186/s12870-022-03751-1
Transcriptome and co-expression network analyses of key genes and pathways associated with differential abscisic acid accumulation during maize seed maturation.
National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China.; National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China. wangwei@henau.edu.cn.; National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China. wuxiaolin@henau.edu.cn.
BACKGROUND: Currently, mechanical maize kernel harvesting has not been fully utilized in developing countries including China, partly due to the absence of suitable cultivars capable of rapid desiccation during seed maturation. The initiation of rapid desiccation during seed maturation is regulated by abscisic acid (ABA). For further characterization of ABA-regulated key genes and cellular events, it is necessary to perform transcriptome analysis of maize developing embryos. The ABA synthesis-deficient mutant (vp5) and normal maize (Vp5) seeds are suitable materials for such purpose. RESULTS: In the present work, developing vp5 and Vp5 embryos were compared by ABA content and transcriptome analyses. Quantitative analysis revealed the significant difference in ABA synthesis between both genotypes. From 29 days after pollination (DAP), ABA content increased rapidly in Vp5 embryos, but decreased gradually in vp5 embryos. At 36 DAP, ABA level in vp5 decreased to 1/4 that of Vp5, suggesting that the differential ABA levels would affect seed maturation. Comparative transcriptomic analysis has found 1019 differentially expressed genes (DEGs) between both genotypes, with the most DEGs (818) at 36 DAP. Further, weighted correlation network analysis (WGCNA) revealed eight DEGs co-expression modules. Particularly, a module was negatively correlated with ABA content in vp5 embryos. The module was mainly involved in metabolic and cellular processes, and its hub genes encoded thiamine, NPF proteins, calmodulin, metallothionein etc. Moreover, the expression of a set of key genes regulated by ABA was further verified by RT-qPCR. The results of the present work suggested that because of ABA deficiency, the vp5 seeds maintained strong metabolic activities and lacked dormancy initiation during seed maturation. CONCLUSION: Transcriptome and WGCNA analyses revealed significant ABA-related changes in metabolic pathways and DEGs between vp5 and Vp5 during seed maturation. The results would provide insights for elucidating the molecular mechanism of ABA signaling and developing high dehydration tolerance maize suitable for mechanical harvesting.
PMID: 35869440
Front Psychol , 2022 , V13 : P983698 doi: 10.3389/fpsyg.2022.983698
The need for social network analysis for the investigation of affective variables in second language acquisition.
School of Foreign Languages, Hunan University of Arts and Science, Changde, China.; Lyceum of the Philippines University-Batangas, Batangas, Philippines.
Considering the inherent developmental nature of language learners' affective variables (e.g., their motivation, grit, foreign language enjoyment, and boredom), nuances of the development of these constructs need to be approached from a complex dynamic systems theory (CDST) perspective. Among the qualitative research methodologies compatible with the CDST is the social network analysis (SNA) with the interconnectedness and interdependence of systems within a social network at its core. In this article, an overall introduction to SNA is presented first and then followed by a review of the limited existing literature on second language acquisition (SLA) studies. Then, I argue why this innovative research method is suitable to investigate the dynamic nature of L2 learners' affective variables in the social network of classroom learning. I also suggest several relevant research questions that can potentially be formulated and answered using the SNA. The article ends with conclusive remarks on the need for a more extensive use of innovative CDST-compatible research methods such as SNA in the prospective SLA line of research.
PMID: 36003100
J Clin Psychol , 2022 Aug doi: 10.1002/jclp.23432
Using theory to guide exploratory network analyses.
Mississippi State University, Mississippi State, Mississippi, USA.; Murray State University, Murray, Kentucky, USA.; The New School for Social Research, New York, New York, USA.
The use of exploratory network analysis has increased in psychopathology research over the past decade. A benefit of exploratory network analysis is the wealth of information it can provide; however, a single analysis may generate more inferences than what can be discussed in one manuscript (e.g., centrality indices of each node). This necessitates that authors choose which results to discuss in further detail and which to omit. Without a guide for this process, the likelihood of a biased interpretation is high. We propose that the integration of theory throughout the research process makes the interpretation of exploratory networks more manageable for the researcher and more likely to result in an interpretation that advances science. The goals of this paper are to differentiate between exploratory and confirmatory network analyses, discuss the utility of exploratory work, and provide a practical framework that uses theory as a guide to interpret exploratory network analyses.
PMID: 35999793
Radiol Phys Technol , 2022 Aug doi: 10.1007/s12194-022-00670-6
Reproducibility of functional connectivity metrics estimated from resting-state functional MRI with differences in days, coils, and global signal regression.
Department of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.; Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko Minami, Higashi-ku, Nagoya, Aichi, 461-8673, Japan. ebagarinao@met.nagoya-u.ac.jp.; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan. ebagarinao@met.nagoya-u.ac.jp.; Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko Minami, Higashi-ku, Nagoya, Aichi, 461-8673, Japan.; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan.; Department of Neurology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.; Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.; Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.; Department of Radiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.; Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.; Department of Neurology, Aichi Medical University, Nagakute, Aichi, Japan.
In multisite studies, differences in imaging acquisition systems could affect the reproducibility of the results when examining changes in brain function using resting-state functional magnetic resonance imaging (rs-fMRI). This is also important for longitudinal studies, in which changes in equipment settings can occur. This study examined the reproducibility of functional connectivity (FC) metrics estimated from rs-fMRI data acquired using scanner receiver coils with different numbers of channels. This study involved 80 rs-fMRI datasets from 20 healthy volunteers scanned in two independent imaging sessions using both 12- and 32-channel coils for each session. We used independent component analysis (ICA) to evaluate the FC of canonical resting-state networks (RSNs) and graph theory to calculate several whole-brain network metrics. The effect of global signal regression (GSR) as a preprocessing step was also considered. Comparisons within and between receiver coils were performed. Irrespective of the GSR, RSNs derived from rs-fMRI data acquired using the same receiver coil were reproducible, but not from different receiver coils. However, both the GSR and the channel count of the receiver coil have discernible effects on the reproducibility of network metrics estimated using whole-brain network analysis. The data acquired using the 32-channel coil tended to have better reproducibility than those acquired using the 12-channel coil. Our findings suggest that the reproducibility of FC metrics estimated from rs-fMRI data acquired using different receiver coils showed some level of dependence on the preprocessing method and the type of analysis performed.
PMID: 35960494
Heliyon , 2022 Jul , V8 (7) : Pe09929 doi: 10.1016/j.heliyon.2022.e09929
Psychometric assessment of the Bangla version of the Bergen Social Media Addiction Scale.
Department of Psychology, University of Chittagong, Chattogram 4331, Bangladesh.; Department of Economics, University of Chittagong, Chattogram 4331, Bangladesh.
Recently, researchers have raised their concern about problematic engagement in social media use that significantly impacted users' mental health and daily lives. Therefore, it is important to have a psychometrically sound assessment tool to assess social media addiction. The present study aimed to assess the reliability and validity of the Bangla version of the Bergen Social Media Addiction Scale (BSMAS) for assessing social media addiction among young Bangladeshi adults. In this study, we utilized secondary data that contained information from 577 Bangladeshi university students. Exploratory factor analysis explored a single latent factor, and confirmatory factor analyses supported this structure. Discrimination indices of items in both classical test theory (CTT) and item response theory (IRT) approach suggested that items could discriminate between low scorers and high scorers in this scale. This scale has good internal consistency, composite, and IRT reliability. Multigroup CFA and differential item functioning bias results suggested this scale would be assessed the same construct across gender and usage duration groups (5 h and more vs less than 5 h). Network analysis results suggested relapse following salience as the core symptoms of social media addiction among young Bangladeshi adults. Overall, results suggested the Bangla BSMAS as a psychometrically sound tool to assess symptoms of social media addiction among young Bangladeshi adults. This scale has practical utility to mental health practitioners as this scale provides information about the core symptoms of social media addiction.
PMID: 35874067
Appl Netw Sci , 2022 , V7 (1) : P50 doi: 10.1007/s41109-022-00476-w
Exploring the raison d'etre behind metric selection in network analysis: a systematic review.
School of Energy, Geosciences, Infrastructure and Society, Heriot-Watt University, William Arrol Building, Room W.A. 3.36/3.37, 2 Third Gait, Currie, Edinburgh, EH14 4AS UK.grid.9531.e0000000106567444
Network analysis is a useful tool to analyse the interactions and structure of graphs that represent the relationships among entities, such as sectors within an urban system. Connecting entities in this way is vital in understanding the complexity of the modern world, and how to navigate these complexities during an event. However, the field of network analysis has grown rapidly since the 1970s to produce a vast array of available metrics that describe different graph properties. This diversity allows network analysis to be applied across myriad research domains and contexts, however widespread applications have produced polysemic metrics. Challenges arise in identifying which method of network analysis to adopt, which metrics to choose, and how many are suitable. This paper undertakes a structured review of literature to provide clarity on raison d'etre behind metric selection and suggests a way forward for applied network analysis. It is essential that future studies explicitly report the rationale behind metric choice and describe how the mathematics relates to target concepts and themes. An exploratory metric analysis is an important step in identifying the most important metrics and understanding redundant ones. Finally, where applicable, one should select an optimal number of metrics that describe the network both locally and globally, so as to understand the interactions and structure as holistically as possible. Supplementary Information: The online version contains supplementary material available at 10.1007/s41109-022-00476-w.
PMID: 35854964
Int J Psychol , 2022 Aug , V57 (4) : P511-523 doi: 10.1002/ijop.12831
Positive and negative social contacts with immigrants from different groups: Investigating the role of group appraisal and opportunity for contact using network analysis.
Bob Shapell School of Social Work, Tel Aviv University, Tel Aviv, Israel.; Department of Criminology, Bar Ilan University, Ramat Gan, Israel.
What can enhance positive inter-group contacts in a world of mass immigration is a subject high on the theoretical and practical agenda. However, there is a lack of research examining how contacts with different immigrant groups are related to characteristics of the group, as perceived by the receiving society. Using Threat-Benefit Theory (Tartakovsky & Walsh, 2016a, 2016b, 2019, 2020), the present study examines how different domains of positive and negative appraisal of a specific immigrant group may relate to contacts with group members. Using a representative sample of 1600 adults in the majority of the Jewish population in Israel, we applied network analysis to examine relationships between threat-benefit appraisal, opportunities for contact and levels of positive and negative contacts with four immigrant groups: diaspora immigrants from Ethiopia, Western countries and the former Soviet Union and asylum seekers. Levels of contact were related to particular domains of appraisal, which differed across immigrant groups. However, opportunities for contact had a stronger association with contact than the appraisal. Results point to a theoretical need to develop nuanced models related to inter-group contact, which consider particular characteristics of the immigrant group as perceived by the local population.
PMID: 35001368
Public Underst Sci , 2022 Aug , V31 (6) : P732-750 doi: 10.1177/09636625211070150
Does China have a public debate on genetically modified organisms? A discourse network analysis of public debate on Weibo.
Wageningen University, The Netherlands.; Teagasc-Irish Agriculture and Food Development Authority, Ireland.; Heidelberg University, Germany.
We examine stakeholder participation in the online debate on genetically modified organisms in China and assess how the debate has changed over time. Therefore, we compare messages posted between 2013 and 2020 on the Chinese microblog website Weibo by using discourse network analysis. Our findings reveal strong opposition to genetically modified crops, along with the existence of two competing coalitions of supporters and opponents. We further observe an increasing number of posts supporting genetically modified organisms by the public in recent years. Consequently, there is an indication that the positions of stakeholders have changed over time. We discuss the policy implications for China and draw conclusions for other countries.
PMID: 35086388