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
Biotechnol Adv , IF:14.227 , 2022 Jul-Aug , V57 : P107947 doi: 10.1016/j.biotechadv.2022.107947
Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates.
Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: elenaca@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: lisbeth.olsson@chalmers.se.; Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: jan.zrimec@nib.si.; Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden; Science for Life Laboratory, Stockholm, Sweden. Electronic address: aleksej.zelezniak@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: cecilia.geijer@chalmers.se.; Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden. Electronic address: yvonne.nygard@chalmers.se.
The use of renewable plant biomass, lignocellulose, to produce biofuels and biochemicals using microbial cell factories plays a fundamental role in the future bioeconomy. The development of cell factories capable of efficiently fermenting complex biomass streams will improve the cost-effectiveness of microbial conversion processes. At present, inhibitory compounds found in hydrolysates of lignocellulosic biomass substantially influence the performance of a cell factory and the economic feasibility of lignocellulosic biofuels and chemicals. Here, we present and statistically analyze data on Saccharomyces cerevisiae mutants engineered for altered tolerance towards the most common inhibitors found in lignocellulosic hydrolysates: acetic acid, formic acid, furans, and phenolic compounds. We collected data from 7971 experiments including single overexpression or deletion of 3955 unique genes. The mutants included in the analysis had been shown to display increased or decreased tolerance to individual inhibitors or combinations of inhibitors found in lignocellulosic hydrolysates. Moreover, the data included mutants grown on synthetic hydrolysates, in which inhibitors were added at concentrations that mimicked those of lignocellulosic hydrolysates. Genetic engineering aimed at improving inhibitor or hydrolysate tolerance was shown to alter the specific growth rate or length of the lag phase, cell viability, and vitality, block fermentation, and decrease product yield. Different aspects of strain engineering aimed at improving hydrolysate tolerance, such as choice of strain and experimental set-up are discussed and put in relation to their biological relevance. While successful genetic engineering is often strain and condition dependent, we highlight the conserved role of regulators, transporters, and detoxifying enzymes in inhibitor tolerance. The compiled meta-analysis can guide future engineering attempts and aid the development of more efficient cell factories for the conversion of lignocellulosic biomass.
PMID: 35314324
Glob Chang Biol , IF:10.863 , 2022 Jul , V28 (14) : P4323-4341 doi: 10.1111/gcb.16197
Managing for the unexpected: Building resilient forest landscapes to cope with global change.
Centre for Forest Research, Universite du Quebec a Montreal, Montreal, QC, Canada.; Institute for Alpine Environment, Eurac Research, Bozen/Bolzano, Italy.; Institut des Sciences de la Foret Temperee, Universite du Quebec en Outaouais, Ripon, QC, Canada.; Harvard Forest, Harvard University, Petersham, Massachusetts, USA.; Liberal Arts Department, New England Conservatory, Boston, Massachusetts, USA.; Department of Ecology and Evolution, University of Toronto, Toronto, Ontario, Canada.; Forest Sciences and Technology Centre of Catalonia CTFC, Solsona, Spain.
Natural disturbances exacerbated by novel climate regimes are increasing worldwide, threatening the ability of forest ecosystems to mitigate global warming through carbon sequestration and to provide other key ecosystem services. One way to cope with unknown disturbance events is to promote the ecological resilience of the forest by increasing both functional trait and structural diversity and by fostering functional connectivity of the landscape to ensure a rapid and efficient self-reorganization of the system. We investigated how expected and unexpected variations in climate and biotic disturbances affect ecological resilience and carbon storage in a forested region in southeastern Canada. Using a process-based forest landscape model (LANDIS-II), we simulated ecosystem responses to climate change and insect outbreaks under different forest policy scenarios-including a novel approach based on functional diversification and network analysis-and tested how the potentially most damaging insect pests interact with changes in forest composition and structure due to changing climate and management. We found that climate warming, lengthening the vegetation season, will increase forest productivity and carbon storage, but unexpected impacts of drought and insect outbreaks will drastically reduce such variables. Generalist, non-native insects feeding on hardwood are the most damaging biotic agents for our region, and their monitoring and early detection should be a priority for forest authorities. Higher forest diversity driven by climate-smart management and fostered by climate change that promotes warm-adapted species, might increase disturbance severity. However, alternative forest policy scenarios led to a higher functional and structural diversity as well as functional connectivity-and thus to higher ecological resilience-than conventional management. Our results demonstrate that adopting a landscape-scale perspective by planning interventions strategically in space and adopting a functional trait approach to diversify forests is promising for enhancing ecological resilience under unexpected global change stressors.
PMID: 35429213
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
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
Sci Total Environ , IF:7.963 , 2022 Sep , V838 (Pt 3) : P156426 doi: 10.1016/j.scitotenv.2022.156426
The combined effect of an integrated reclaimed water system on the reduction of antibiotic resistome.
Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China.; Beijing BHZQ Environmental Engineering Technology Co., LTD, Beijing 100176, China.; Engineering Research Center of Ministry of Education on Groundwater Pollution Control and Remediation, College of Water Sciences, Beijing Normal University, Beijing 100875, China. Electronic address: chen.haiyang@bnu.edu.cn.
The reuse of urban reclaimed water is conducive to alleviate the current serious shortage of water resources. However, antibiotic resistance genes (ARGs) in reclaimed water have received widespread attention due to their potential risks to public health. Deciphering the fate of ARGs in reclaimed water benefits the development of effective strategies to control resistome risk and guarantees the safety of water supply of reclaimed systems. In this study, the characteristics of ARGs in an integrated reclaimed water system (sewage treatment plant-constructed wetland, STP-CW) in Beijing (China) have been identified using metagenomic assembly-based analysis, as well as the combined effect of the STP-CW system on the reduction of antibiotic resistome. Results showed a total of 29 ARG types and 813 subtypes were found in the reclaimed water system. As expected, the STP-CW system improved the removal of ARGs, and about 58% of ARG subtypes were removed from the effluent of the integrated STP-CW system, which exceeded 43% for the STP system and 37% for the CW system. Although the STP-CW system had a great removal on ARGs, abundant and diverse ARGs were still found in the downstream river. Importantly, network analysis revealed the co-occurrence of ARGs, mobile genetic elements and virulence factors in the downstream water, implying potential resistome dissemination risk in the environment. Source identification with SourceTracker showed the STP-effluent was the largest contributor of ARGs in the downstream river, with a contribution of 45%. Overall, the integrated STP-CW system presented a combined effect on the reduction of antibiotic resistome, however, the resistome dissemination risk was still non-negligible in the downstream reclaimed water. This study provides a comprehensive analysis on the fate of ARGs in the STP-CW-river system, which would benefit the development of effective strategies to control resistome risk for the reuse of reclaimed water.
PMID: 35660592
Comput Struct Biotechnol J , IF:7.271 , 2022 , V20 : P3234-3247 doi: 10.1016/j.csbj.2022.06.033
REGENOMICS: A web-based application for plant REGENeration-associated transcriptOMICS analyses.
Department of Chemistry, Seoul National University, Seoul 08826, South Korea.; School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.; Research Center for Plant Plasticity, Seoul National University, Seoul 08826, South Korea.; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, South Korea.; Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea.
In plants, differentiated somatic cells exhibit an exceptional ability to regenerate new tissues, organs, or whole plants. Recent studies have unveiled core genetic components and pathways underlying cellular reprogramming and de novo tissue regeneration in plants. Although high-throughput analyses have led to key discoveries in plant regeneration, a comprehensive organization of large-scale data is needed to further enhance our understanding of plant regeneration. Here, we collected all currently available transcriptome datasets related to wounding responses, callus formation, de novo organogenesis, somatic embryogenesis, and protoplast regeneration to construct REGENOMICS, a web-based application for plant REGENeration-associated transcriptOMICS analyses. REGENOMICS supports single- and multi-query analyses of plant regeneration-related gene-expression dynamics, co-expression networks, gene-regulatory networks, and single-cell expression profiles. Furthermore, it enables user-friendly transcriptome-level analysis of REGENOMICS-deposited and user-submitted RNA-seq datasets. Overall, we demonstrate that REGENOMICS can serve as a key hub of plant regeneration transcriptome analysis and greatly enhance our understanding on gene-expression networks, new molecular interactions, and the crosstalk between genetic pathways underlying each mode of plant regeneration. The REGENOMICS web-based application is available at http://plantregeneration.snu.ac.kr.
PMID: 35832616
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 Jul , 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
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 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
J Fungi (Basel) , IF:5.816 , 2022 Jun , V8 (6) doi: 10.3390/jof8060631
Leaf-Associated Epiphytic Fungi of Gingko biloba, Pinus bungeana and Sabina chinensis Exhibit Delicate Seasonal Variations.
Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.; School of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 102616, China.; State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa 999078, Macao.; Xiongan Institute of Innovation, Baoding 071000, China.
Plant-leaf surface on Earth harbors complex microbial communities that influence plant productivity and health. To gain a detailed understanding of the assembly and key drivers of leaf microbial communities, especially for leaf-associated fungi, we investigated leaf-associated fungal communities in two seasons for three plant species at two sites by high-throughput sequencing. The results reveal a strong impact of growing season and plant species on fungal community composition, exhibiting clear temporal patterns in abundance and diversity. For the deciduous tree Gingko biloba, the number of enriched genera in May was much higher than that in October. The number of enriched genera in the two evergreen trees Pinus bungeana and Sabina chinensis was slightly higher in October than in May. Among the genus-level biomarkers, the abundances of Alternaria, Cladosporium and Filobasidium were significantly higher in October than in May in the three tree species. Additionally, network correlations between the leaf-associated fungi of G. biloba were more complex in May than those in October, containing extra negative associations, which was more obvious than the network correlation changes of leaf-associated fungi of the two evergreen plant species. Overall, the fungal diversity and community composition varied significantly between different growing seasons and host plant species.
PMID: 35736114
Front Pharmacol , IF:5.81 , 2022 , V13 : P904190 doi: 10.3389/fphar.2022.904190
Integrating Metabolomics and Network Analysis for Exploring the Mechanism Underlying the Antidepressant Activity of Paeoniflorin in Rats With CUMS-Induced Depression.
School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.; Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China.; Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China.
Background: Paeoniflorin (PF) represents the major bioactive constituent of the traditional Chinese medicine plant Paeonia suffruticosa (Ranunculaceae), which has a long history as a folk medicine in Asian. Paeoniflorin, a bitter pinene monoterpene glycoside, has antidepressant effects, but its potential therapeutic mechanism has not been thoroughly explored. Methods: Experimental depression in rats was established by the chronic unpredictable mild stress (CUMS) combined with orphan method, and the efficacy of paeoniflorin on depression was evaluated by the sucrose preference test and open field test. The antidepressant mechanism of paeoniflorin was investigated by metabolomic and network pharmacology. The relevant pathways of biomarkers highlighted in metabolomics were explored, and the possible targets of paeoniflorin in the treatment of depression were further revealed through network analysis. The binding activity of paeoniflorin to key targets was verified by molecular docking. Results: Metabolomics showed that rats with CUMS-induced depression had urine metabolic disorders, which were reversed by paeoniflorin through the regulation of metabolic pathways. Metabolites that play a key role in the function of paeoniflorin include citric acid, thiamine monophosphate, gluconolactone, 5-hydroxyindoleacetic acid and stachyose. Key predicted targets are SLC6A4, TNF, IL6 and SLC6A3. An important metabolic pathway is the Citrate cycle (TCA cycle). Conclusion: Network integrative analysis in this study showed that paeoniflorin could improve depressive-like symptoms in model rats with CUMS-induced depression and overall correct the disordered metabolic profile through multiple metabolic pathways.
PMID: 35770096
Front Plant Sci , IF:5.753 , 2022 , V13 : P899177 doi: 10.3389/fpls.2022.899177
Gene Co-expression Network Analysis of the Comparative Transcriptome Identifies Hub Genes Associated With Resistance to Aspergillus flavus L. in Cultivated Peanut (Arachis hypogaea L.).
College of Agriculture, Nanjing Agricultural University, Nanjing, China.; The Shennong Laboratory, Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Science, Zhengzhou, China.; Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou, China.; Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, China.; National Centre for Plant Breeding, Xinxiang, China.; Key Laboratory of Detection for Mycotoxins, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China.; Department of Horticulture, Ghazi University, Dera Ghazi Khan, Pakistan.
Cultivated peanut (Arachis hypogaea L.), a cosmopolitan oil crop, is susceptible to a variety of pathogens, especially Aspergillus flavus L., which not only vastly reduce the quality of peanut products but also seriously threaten food safety for the contamination of aflatoxin. However, the key genes related to resistance to Aspergillus flavus L. in peanuts remain unclear. This study identifies hub genes positively associated with resistance to A. flavus in two genotypes by comparative transcriptome and weighted gene co-expression network analysis (WGCNA) method. Compared with susceptible genotype (Zhonghua 12, S), the rapid response to A. flavus and quick preparation for the translation of resistance-related genes in the resistant genotype (J-11, R) may be the drivers of its high resistance. WGCNA analysis revealed that 18 genes encoding pathogenesis-related proteins (PR10), 1-aminocyclopropane-1-carboxylate oxidase (ACO1), MAPK kinase, serine/threonine kinase (STK), pattern recognition receptors (PRRs), cytochrome P450, SNARE protein SYP121, pectinesterase, phosphatidylinositol transfer protein, and pentatricopeptide repeat (PPR) protein play major and active roles in peanut resistance to A. flavus. Collectively, this study provides new insight into resistance to A. flavus by employing WGCNA, and the identification of hub resistance-responsive genes may contribute to the development of resistant cultivars by molecular-assisted breeding.
PMID: 35812950
Front Plant Sci , IF:5.753 , 2022 , V13 : P915400 doi: 10.3389/fpls.2022.915400
Dynamic Transcriptome-Based Weighted Gene Co-expression Network Analysis Reveals Key Modules and Hub Genes Associated With the Structure and Nutrient Formation of Endosperm for Wax Corn.
Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China.
The endosperm of corn kernel consists of two components, a horny endosperm, and a floury endosperm. In the experiment, a kind of floury endosperm corn was identified. The result of phenotypic trait analysis and determination of amino acid content showed that the floury endosperm filled with the small, loose, and scattered irregular spherical shape starch granules and contained higher content of amino acid. The starch biochemical properties are similar between floury corns and regular flint corn. By using dynamically comparative transcriptome analysis of endosperm at 20, 25, and 30 DAP, a total of 113.42 million raw reads and 50.508 thousand genes were obtained. By using the weighted gene co-expression network analysis, 806 genes and six modules were identified. And the turquoise module with 459 genes was proved to be the key module closely related to the floury endosperm formation. Nine zein genes in turquoise module, including two zein-alpha A20 (Zm00001d019155 and Zm00001d019156), two zein-alpha A30 (Zm00001d048849 and Zm00001d048850), one 50 kDa gamma-zein (Zm00001d020591), one 22 kDa alpha-zein 14 (Zm00001d048817), one zein-alpha 19D1 (Zm00001d030855), one zein-alpha 19B1 (Zm00001d048848), and one FLOURY 2 (Zm00001d048808) were identified closely related the floury endosperm formation. Both zein-alpha 19B1 (Zm00001d048848) and zein-alpha A30 (Zm00001d048850) function as source genes with the highest expression level in floury endosperm. These results may provide the supplementary molecular mechanism of structure and nutrient formation for the floury endosperm of maize.
PMID: 35755662
Front Plant Sci , IF:5.753 , 2022 , V13 : P923136 doi: 10.3389/fpls.2022.923136
New Advances in the Regulation of Leaf Senescence by Classical and Peptide Hormones.
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China.
Leaf senescence is the last stage of leaf development, manifested by leaf yellowing due to the loss of chlorophyll, along with the degradation of macromolecules and facilitates nutrient translocation from the sink to the source tissues, which is essential for the plants' fitness. Leaf senescence is controlled by a sophisticated genetic network that has been revealed through the study of the molecular mechanisms of hundreds of senescence-associated genes (SAGs), which are involved in multiple layers of regulation. Leaf senescence is primarily regulated by plant age, but also influenced by a variety of factors, including phytohormones and environmental stimuli. Phytohormones, as important signaling molecules in plant, contribute to the onset and progression of leaf senescence. Recently, peptide hormones have been reported to be involved in the regulation of leaf senescence, enriching the significance of signaling molecules in controlling leaf senescence. This review summarizes recent advances in the regulation of leaf senescence by classical and peptide hormones, aiming to better understand the coordinated network of different pathways during leaf senescence.
PMID: 35837465
Front Plant Sci , IF:5.753 , 2022 , V13 : P896945 doi: 10.3389/fpls.2022.896945
R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses.
Institute of Biosciences and Bioresources, National Research Council (CNR), Bari, Italy.; Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy.
MYB transcription factors (TFs) represent one of the biggest TF families in plants, being involved in various specific plant processes, such as responses to biotic and abiotic stresses. The implication of MYB TFs in the tolerance mechanisms to abiotic stress is particularly interesting for crop breeding, since environmental conditions can negatively affect growth and productivity. Wheat is a worldwide-cultivated cereal, and is a major source of plant-based proteins in human food. In particular, durum wheat plays an important role in global food security improvement, since its adaptation to hot and dry conditions constitutes the base for the success of wheat breeding programs in future. In the present study, a genome-wide identification of R2R3-MYB TFs in durum wheat was performed. MYB profile search and phylogenetic analyses based on homology with Arabidopsis and rice MYB TFs led to the identification of 233 R2R3-TdMYB (Triticum durum MYB). Three Poaceae-specific MYB clusters were detected, one of which had never been described before. The expression of eight selected genes under different abiotic stress conditions, revealed that most of them responded especially to salt and drought stress. Finally, gene regulatory network analyses led to the identification of 41 gene targets for three TdR2R3-MYBs that represent novel candidates for functional analyses. This study provides a detailed description of durum wheat R2R3-MYB genes and contributes to a deeper understanding of the molecular response of durum wheat to unfavorable climate conditions.
PMID: 35795353
Front Microbiol , IF:5.64 , 2022 , V13 : P884765 doi: 10.3389/fmicb.2022.884765
The Seasonal Patterns, Ecological Function and Assembly Processes of Bacterioplankton Communities in the Danjiangkou Reservoir, China.
International Joint Laboratory of Watershed Ecological Security and Collaborative Innovation Center of Water Security for Water Source Region of Middle Route Project of South-North Water Diversion in Henan Province, School of Water Resource and Environmental Engineering, Nanyang Normal University, Nanyang, China.; Ecological Complexity and Modelling Laboratory, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States.; Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China.
As the water source for the Middle Route Project of the South-to-North Water Diversion Project (MR-SNWD) of China, the Danjiangkou Reservoir (DJR) is in the process of ecosystem reassembly, but the composition, function, and assembly mechanisms of bacterioplankton communities are not yet clear. In this study, the composition, distribution characteristics and influencing factors of bacterioplankton communities were analyzed by high-throughput sequencing (HTS); PICRUSt2 was used to predict community function; a molecular ecological network was used to analyze bacterioplankton interactions; and the assembly process of bacterioplankton communities was estimated with a neutral model. The results indicated that the communities, function and interaction of bacterioplankton in the DJR had significant annual and seasonal variations and that the seasonal differences were greater than that the annual differences. Excessive nitrogen (N) and phosphorus (P) nutrients in the DJR are the most important factors affecting water quality in the reservoir, N and P nutrients are the main factors affecting bacterial communities. Season is the most important factor affecting bacterioplankton N and P cycle functions. Ecological network analysis indicated that the average clustering coefficient and average connectivity of the spring samples were lower than those of the autumn samples, while the number of modules for the spring samples was higher than that for the autumn samples. The neutral model explained 66.3%, 63.0%, 63.0%, and 70.9% of the bacterioplankton community variations in samples in the spring of 2018, the autumn of 2018, the spring of 2019, and the autumn of 2019, respectively. Stochastic processes dominate bacterioplankton community assembly in the DJR. This study revealed the composition, function, interaction, and assembly of bacterioplankton communities in the DJR, providing a reference for the protection of water quality and the ecological functions of DJR bacterioplankton.
PMID: 35783417
Front Microbiol , IF:5.64 , 2022 , V13 : P854216 doi: 10.3389/fmicb.2022.854216
Living and Dead Microorganisms in Mediating Soil Carbon Stocks Under Long-Term Fertilization in a Rice-Wheat Rotation.
Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.; College of Forestry, Hebei Agricultural University, Baoding, China.; Institute of Plant Protection and Soil Fertility, Hubei Academy of Agricultural Sciences, Wuhan, China.
Although soil microorganism is an active area of research, we are still in the early stages of understanding how living microorganisms influence the accumulations of soil microbial residues under different agricultural practices. Based on a 39-year fertilization experiment, we characterized the soil microbiota and correlated their compositions to soil microbial residues, which are indicated by amino sugars under a rice-wheat rotation. In the present study, fertilization regimes and crop season all exerted significant impacts on the compositions of soil microbial communities and their residues, although no significant difference in the microbial residues was found between soil depth (0-10 cm vs. 10-20 cm). Compared within fertilization regimes, the long-term fertilization, especially the application of organic manure, stimulated the accumulations of carbon (C) and nitrogen in soils and microbial residues. Upland soils in wheat season accumulated more microbial residues, particularly in fungal residues, than paddy soils in rice season. Our results suggested that the long-term application of organic manure favored the growth of soil microbial communities, and then increased the contents of microbial residues, particularly in fungal residues, leading to an enlargement of soil C pools. The keystone taxa Pseudaleuria identified by network analysis showed a significantly positive potential in soil C sequestration by increasing the accumulation of fungal residues. Thus, this study revealed the strong and close connections between microbial communities and their residues, and provided evidence about the critical role of keystone taxa in regulating C sequestration.
PMID: 35756033
Transbound Emerg Dis , IF:5.005 , 2022 Jul , V69 (4) : Pe717-e733 doi: 10.1111/tbed.14389
Molecular identification and genetic diversity of Bartonella spp. in 24 bat species from Thailand.
Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.; Veterinary Pathobiology Graduate Program, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.; The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.; Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.; Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.; Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Songkhla, Thailand.; Sai Yok National Park, Department of National Parks, Wildlife and Plant Conservation, Kanchanaburi, Thailand.
The study of bacterial zoonoses has been under-pursued despite the fact that bacteria cause the majority of zoonotic diseases, of which 70% have a wildlife origin. More Bartonella species are being identified as the cause of human diseases, and several of them have been linked to domestic and wild animals. Bats are outstanding reservoirs for Bartonella species because of their wide distribution, mobility, roosting behaviour, and long life span. Here, we carried out a PCR-based survey on bats that were collected from 19 sampling sites in eight provinces of Thailand from February 2018 to April 2021. Bartonella infection was investigated in a total of 459 bats that belong to 24 different bat species (21 species of which had never been previously studied in Thailand). PCR diagnostics revealed that 115 out of 459 (25.5%) blood samples tested positive for Bartonella. The nucleotide identities of the Bartonella 16S rRNA sequences in this study were between 95.78-99.66% identical to those of known zoonotic species (Bartonella ancashensis, Bartonella henselae, Bartonella bacilliformis and Bartonella australis) as well as to an unidentified Bartonella spp. In addition, the citrate synthase (gltA) and RNA polymerase-beta subunit (rpoB) genes of Bartonella were sequenced and analyzed in positive samples. The gltA and rpoB gene sequences from Hipposideros gentilis and Rhinolophus coelophyllus bat samples showed low nucleotide identity (<95%) compared to those of the currently deposited sequences in the GenBank database, indicating the possibility of new Bartonella species. The phylogenetic inference and genetic diversity were generated and indicated a close relationship with other Bartonella species previously discovered in Asian bats. Overall, the current study demonstrates the primary evidence pointing to a potential novel Bartonella species in bats. This discovery also contributes to our current understanding of the geographical distribution, genetic diversity, and host ranges of bat-related Bartonella.
PMID: 34755483
Front Genet , IF:4.599 , 2022 , V13 : P921096 doi: 10.3389/fgene.2022.921096
Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development.
State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.; National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.; Hainan Yazhou Bay Seed Laboratory, Sanya, China.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
PMID: 35754813
Plant Dis , IF:4.438 , 2022 Jul , V106 (7) : P1882-1889 doi: 10.1094/PDIS-09-21-1974-RE
Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases.
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China.
Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.
PMID: 35021874
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121533
Particle-Based Imaging Tools Revealing Water Flows in Maize Nodal Vascular Plexus.
Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Institute of Computational Mathematics and Mathematical Geophysics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Department of Mechanics and Mathematics, Novosibirsk State University, 630090 Novosibirsk, Russia.; Kutateladze Institute of Thermophysics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.
In plants, water flows are the major driving force behind growth and play a crucial role in the life cycle. To study hydrodynamics, methods based on tracking small particles inside water flows attend a special place. Thanks to these tools, it is possible to obtain information about the dynamics of the spatial distribution of the flux characteristics. In this paper, using contrast-enhanced magnetic resonance imaging (MRI), we show that gadolinium chelate, used as an MRI contrast agent, marks the structural characteristics of the xylem bundles of maize stem nodes and internodes. Supplementing MRI data, the high-precision visualization of xylem vessels by laser scanning microscopy was used to reveal the structural and dimensional characteristics of the stem vascular system. In addition, we propose the concept of using prototype "Y-type xylem vascular connection" as a model of the elementary connection of vessels within the vascular system. A Reynolds number could match the microchannel model with the real xylem vessels.
PMID: 35736684
Biosystems , IF:1.973 , 2022 Jul , V219 : P104732 doi: 10.1016/j.biosystems.2022.104732
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis.
School of Engineering, University of Warwick, CV4 7AL, Coventry, UK. Electronic address: M.Foo@warwick.ac.uk.; Institute of Computational Biology, Helmholtz Munich, 85764, Neuherberg, Germany; Department of Translational Psychiatry, Max Planck Institute of Psychiatry, International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany. Electronic address: leander.dony@helmholtz-munich.de.; Centre for Computational Science and Mathematical Modelling, Coventry University, CV1 2JH, Coventry, UK. Electronic address: Fei.He@coventry.ac.uk.
Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback control circuits, an accurate model that is able to capture the vital dynamical behaviour of the pathogen-infected plant is required. In this study, using a data-driven modelling approach, we develop and compare four dynamical models (i.e. linear, Michaelis-Menten with Hill coefficient (Hill Function), standard S-System and extended S-System) of a pathogen-infected plant gene regulatory network (GRN). These models are then assessed across several criteria, i.e. ease of identifying the type of gene regulation, the predictive capability, Akaike Information Criterion (AIC) and the robustness to parameter uncertainty to determine its viability of balancing between biological complexity and accuracy when modelling the pathogen-infected plant GRN. Using our defined ranking score, we obtain the following insights to the modelling of GRN. Our analyses show that despite commonly used and provide biological relevance, the Hill Function model ranks the lowest while the extended S-System model ranks highest in the overall comparison. Interestingly, the performance of the linear model is more consistent throughout the comparison, making it the preferred model for this pathogen-infected plant GRN when considering data-driven modelling approach.
PMID: 35781035
J Comput Biol , IF:1.479 , 2022 Jul , V29 (7) : P752-768 doi: 10.1089/cmb.2021.0600
Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum.
Department of Statistics, University of Oxford, Oxford, United Kingdom.; Department of Plant Sciences, University of Oxford, Oxford, United Kingdom.; Department of the Mathematical Institute, University of Oxford, Oxford, United Kingdom.
Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For this bacterium, gene expression data are available, but functional gene annotation is less well developed than for other model organisms. More annotations could lead to a better understanding of the pathways for growth, plant colonization, and nitrogen fixation in R. leguminosarum. In this study, we present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or to a prioritized list of genes for further study.
PMID: 35588362
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
Energy Nexus , 2022 Jun , V6 : P100080 doi: 10.1016/j.nexus.2022.100080
Plant-Based Natural Bioactive Compounds 2,4-Ditert-Butylphenolas: A Potential Candidates Against SARS-Cov-2019.
Department of Botany, Periyar University, Periyar Palkalai Nagar, Salem 636011, Tamil Nadu, India.; Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous) Chennai 600 042.; Department of Biotechnology, Rathinam College of Arts and Science(Autonomous), Coimbatore 641021, Tamil Nadu, India.; Department of Botany, Thiru Kolanjiyapper Government Arts College, Virudhachalam, Cuddalore 606001, Tamil Nadu, India.; Department of Biotechnology, St Joseph's College (Arts & Science), Kovur, Chennai, Tamil Nadu, India.; Department of Botany, Shri Sakthikailassh Women's college, Salem 636003, Tamil Nadu, India.
The novel coronavirus 2019 is spreading around the world and causing serious concern. However, there is limited information about novel coronavirus that hinders the design of effective drug. Bioactive compounds are rich source of chemo preventive ingredients. In our present research focuses on identifying and recognizing bioactive chemicals in Lantana camara, by evaluating their potential toward new coronaviruses and confirming the findings using molecular docking, ADMET, network analysis and dynamics investigations.. The spike protein receptor binding domain were docked with 25 identified compounds and 2,4-Ditertbutyl-phenol (-6.3kcal/mol) shows highest docking score, its interactions enhances the increase in binding and helps to identify the biological activity. The ADME/toxicity result shows that all the tested compounds can serve as inhibitors of the enzymes CYP1A2 and CYP2D6. In addition, Molecular dynamics simulations studies with reference inhibitors were carried out to test the stability. This study identifies the possible active molecules against the receptor binding domain of spike protein, which can be further exploited for the treatment of novel coronavirus 2019. The results of the toxicity risk for phytocompounds and their active derivatives showed a moderate to good drug score.
PMID: 35578668