Trends Plant Sci , IF:18.313 , 2022 Feb doi: 10.1016/j.tplants.2022.01.008
Transcriptional regulatory network of plant cold-stress responses.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. Electronic address: akido@g.ecc.u-tokyo.ac.jp.; Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan. Electronic address: akys@g.ecc.u-tokyo.ac.jp.
Recent studies have revealed the complex and flexible transcriptional regulatory network involved in cold-stress responses. Focusing on two major signaling pathways that respond to cold stress, we outline current knowledge of the transcriptional regulatory network and the post-translational regulation of transcription factors in the network. Cold-stress signaling pathways are closely associated with other signaling pathways such as those related to the circadian clock, and large amounts of data on their crosstalk and tradeoffs are available. However, it remains unknown how plants sense and transmit cold-stress signals to regulate gene expression. We discuss recent reports on cold-stress sensing and associated signaling pathways that regulate the network. We also emphasize future directions for developing abiotic stress-tolerant crop plants.
PMID: 35210165
Biotechnol Adv , IF:14.227 , 2022 Mar , 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
Bioresour Technol , IF:9.642 , 2022 Mar , V347 : P126724 doi: 10.1016/j.biortech.2022.126724
Simultaneously advanced removal of nitrogen and phosphorus in a biofilter packed with ZVI/PHBV/sawdust composite: Deciphering the succession of dominant bacteria and keystone species.
Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; The Key Laboratory of Water and Sediment Sciences (Peking University), Ministry of Education, Beijing 100871, China. Electronic address: wzwu@pku.edu.cn.
In this study, a biofilter was developed with a ZVI/PHBV/sawdust (ZPS) composite for treating simulative secondary effluent from wastewater treatment plants. Results showed that effluent concentrations of NO3(-)-N and TP in the ZPS biofilter were stable below 2.0 mg/L and 0.1 mg/L, corresponding to 95% NO3(-)-N removal and 99% TP removal, respectively. Microbial community analysis revealed that the transformation of dominant taxa from Dechloromonas to Clostridium sensu stricto_7 from 30 d to 120 d suggested that the ZVI-induced succession of dominant fermentation bacteria ensured the stable carbon supply for denitrification. Co-occurrence network analysis showed that the ZVI directly enhanced the interaction of microbial community. Fe-related bacteria occupied a key position in the rare species, which might maintain the function of iron-mediated organic matter decomposition and denitrification. These findings provide an alternative for advanced removal of nitrogen and phosphorus in biofilters packed with ZPS composites.
PMID: 35065223
Elife , IF:8.14 , 2022 Feb , V11 doi: 10.7554/eLife.73552
Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter.
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.; Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, Mexico City, Mexico.; Swansea University Medical School, Swansea University, Swansea, United Kingdom.; Department of Zoology, University of Oxford, Oxford, United Kingdom.; Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden.; Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand.
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
PMID: 35191377
Food Chem , IF:7.514 , 2022 Mar , V372 : P131118 doi: 10.1016/j.foodchem.2021.131118
Regulatory effect of root restriction on aroma quality of Red Alexandria grape.
Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.; Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Institute of Agro-food Science and Technology/Key Laboratory of Agro-products, Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan 250100, China. Electronic address: fruit@sjtu.edu.cn.
To systematically study the impact of root restriction (RR) on the aroma quality of grape berry, in this study, free and bound compounds were investigated in 'Red Alexandria' grape skin and pulp produced with and without RR during development and ripening. Compared with the control, RR advanced the initiation of free-terpene synthesis and increased their concentrations at 14-18 weeks post-flowering (wpf) by promoting the conversion of bound terpenes to free terpenes. In addition, RR significantly regulated the aromatic series at 14-18 wpf and advanced the date of aroma maturation. Network analyses indicated that the correlations among bound compounds were more conserved than those among free compounds, and the skin network displayed tight coordination compared with the pulp network. Terpenes were highly intercorrelated and played a core role in these networks. Finally, 10 bound compounds in pulp were screened out as indicators of the developmental timing of grape.
PMID: 34600194
J Exp Bot , IF:6.992 , 2022 Mar , V73 (5) : P1277-1287 doi: 10.1093/jxb/erab490
The epigenetic mechanisms regulating floral hub genes and their potential for manipulation.
Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.
PMID: 34752611
Front Plant Sci , IF:5.753 , 2022 , V13 : P827828 doi: 10.3389/fpls.2022.827828
Analysis of Alternative Splicing During the Combinatorial Response to Simultaneous Copper and Iron Deficiency in Arabidopsis Reveals Differential Events in Genes Involved in Amino Acid Metabolism.
Centre for Genomic Regulation, Barcelona, Spain.; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain.
Copper (Cu) and iron (Fe) constitute fundamental nutrients for plant biology but are often limited due to low bioavailability. Unlike responses to single Cu or Fe deprivation, the consequences of simultaneous Cu and Fe deficiency have not yet been fully deciphered. Previously, it was demonstrated that Cu and Fe deficiency applied in combination imposes transcriptome, proteome, and metabolome changes different from those triggered under each deficiency individually. Here, we evaluated the effect of alternative splicing (AS) on the transcriptome of rosette leaves under single and simultaneous Cu and Fe deficiency. Differentially spliced genes (DSGs) and differentially expressed genes (DEGs) coincided in number (2,600 approx.) although the overlapping fraction was minimal (15%). Functional annotation of changes exclusively detected under simultaneous Cu and Fe deficiency revealed that DEGs participated in general stress responses and translation, while DSGs were involved in metabolic reactions, especially amino acid biosynthesis. Interestingly, transcripts encoding central features for tryptophan (Trp) and asparagine (Asn) synthesis - two significantly altered metabolites under simultaneous Cu and Fe deficiency - underwent exclusive intron retention events under the double deficiency. However, transcript and protein amounts for these enzymes did not correlate with Trp and Asn concentration. In consequence, we propose that AS might act as a regulatory mechanism to modify the stability and/or functionality of the enzymes and therefore fine-tune amino acid production during the combinatorial response to simultaneous Cu and Fe deficiency.
PMID: 35173758
Front Plant Sci , IF:5.753 , 2022 , V13 : P831204 doi: 10.3389/fpls.2022.831204
Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model.
Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Department of Health Management and Informatics and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.; Division of Plant Sciences and Technology and Biochemistry Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.
Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.
PMID: 35310659
Front Microbiol , IF:5.64 , 2022 , V13 : P795206 doi: 10.3389/fmicb.2022.795206
River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics.
Institut de Chimie des Milieux et Materiaux de Poitiers, UMR CNRS 7285, University of Poitiers, Poitiers, France.; UMR INSERM 1092, Limoges, France.
Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.
PMID: 35222329
Front Microbiol , IF:5.64 , 2022 , V13 : P799819 doi: 10.3389/fmicb.2022.799819
Integrated Analysis of the miRNAome and Transcriptome Reveals miRNA-mRNA Regulatory Networks in Catharanthus roseus Through Cuscuta campestris-Mediated Infection With "Candidatus Liberibacter asiaticus".
National Citrus Engineering Research Center, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China.
Citrus Huanglongbing (HLB) is the most devastating disease of citrus caused by the Gram-negative phloem-limited bacterium "Candidatus Liberibacter asiaticus" (CLas). It can be transmitted by the Asian citrus psyllid "Diaphorina citri," by grafting, and by the holoparasitic dodder. In this study, the non-natural host periwinkle (Catharanthus roseus) was infected via dodder (Cuscuta campestris) from CLas-infected citrus plants, and the asymptomatic leaves (AS) were subjected to transcriptomic and small-RNA profiling. The results were analyzed together with a transcriptome dataset from the NCBI repository that included leaves for which symptoms had just occurred (S) and yellowing leaves (Y). There were 3,675 differentially expressed genes (DEGs) identified in AS, and 6,390 more DEGs in S and further 2109 DEGs in Y. These DEGs were commonly enriched in photosystem, chloroplast, membrane, oxidation-reduction process, metal/zinc ion binding on GO. A total of 14,974 DEGs and 336 DE miRNAs (30 conserved and 301 novel) were identified. Through weighted gene co-expression network and nested network analyses, two critical nested miRNA-mRNA regulatory networks were identified with four conserved miRNAs. The primary miR164-NAC1 network is potentially involved in plant defense responses against CLas from the early infection stage to symptom development. The secondary network revealed the regulation of secondary metabolism and nutrient homeostasis through miR828-MYB94/miR1134-HSF4 and miR827-ATG8 regulatory networks, respectively. The findings discovered new potential mechanisms in periwinkle-CLas interactions, and its confirmation can be done in citrus-CLas system later on. The advantages of periwinkle plants in facilitating the quick establishment and greater multiplication of CLas, and shortening latency for disease symptom development make it a great surrogate for further studies, which could expedite our understanding of CLas pathogenesis.
PMID: 35308338
J Agric Food Chem , IF:5.279 , 2022 Mar , V70 (12) : P3719-3729 doi: 10.1021/acs.jafc.2c00231
Integrated Metabolo-transcriptomics Reveals the Defense Response of Homogentisic Acid in Wheat against Puccinia striiformis f. sp. tritici.
College of Plant Protection, Southwest University, Chongqing 400715, China.
Stripe rust is a widespread and harmful wheat disease caused by Puccinia striiformis f. sp. tritici (Pst) worldwide. Targeted metabolome and transcriptomics analyses of CYR23 infected leaves were performed to identify the differential metabolites and differentially expressed genes related to wheat disease resistance. We observed upregulation of 33 metabolites involved in the primary and secondary metabolism, especially for homogentisic acid (HGA), p-coumaroylagmatine, and saccharopine. These three metabolites were mainly involved in the phenylpropanoid metabolic pathway, hydroxycinnamic acid amides pathway, and saccharopine pathway. Combined with transcriptome data on non-compatible interaction, the synthesis-related genes of these three differential metabolites were all upregulated significantly. The gene regulatory network involved in response to Pst infection was constructed, which revealed that several transcription factor families including WRKYs, MYBs, and bZIPs were identified as potentially hubs in wheat resistance response against Pst. An in vitro test showed that HGA effectively inhibited the germination of stripe rust fungus urediniospores and reduced the occurrence of wheat stripe rust. The results of gene silencing and overexpression of HGA synthesis-related gene 4-hydroxyphenylpyruvate dioxygenase proved that HGA was involved in wheat disease resistance. These results provided a further understanding of the disease resistance of wheat and indicated that HGA can be developed as a potential agent against Pst.
PMID: 35293725
Rice (N Y) , IF:4.783 , 2022 Mar , V15 (1) : P18 doi: 10.1186/s12284-022-00562-8
Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice.
Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qqliu@yzu.edu.cn.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qqliu@yzu.edu.cn.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qfli@yzu.edu.cn.; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China. qfli@yzu.edu.cn.
With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.
PMID: 35303197
BMC Med Res Methodol , IF:4.615 , 2022 Mar , V22 (1) : P62 doi: 10.1186/s12874-022-01544-6
Individual-specific networks for prediction modelling - A scoping review of methods.
Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria.; Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.; BIO3 Laboratory for Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium.; Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France.; BIO3 Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liege, Liege, Belgium.; Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria. georg.heinze@meduniwien.ac.at.
BACKGROUND: Recent advances in biotechnology enable the acquisition of high-dimensional data on individuals, posing challenges for prediction models which traditionally use covariates such as clinical patient characteristics. Alternative forms of covariate representations for the features derived from these modern data modalities should be considered that can utilize their intrinsic interconnection. The connectivity information between these features can be represented as an individual-specific network defined by a set of nodes and edges, the strength of which can vary from individual to individual. Global or local graph-theoretical features describing the network may constitute potential prognostic biomarkers instead of or in addition to traditional covariates and may replace the often unsuccessful search for individual biomarkers in a high-dimensional predictor space. METHODS: We conducted a scoping review to identify, collate and critically appraise the state-of-art in the use of individual-specific networks for prediction modelling in medicine and applied health research, published during 2000-2020 in the electronic databases PubMed, Scopus and Embase. RESULTS: Our scoping review revealed the main application areas namely neurology and pathopsychology, followed by cancer research, cardiology and pathology (N = 148). Network construction was mainly based on Pearson correlation coefficients of repeated measurements, but also alternative approaches (e.g. partial correlation, visibility graphs) were found. For covariates measured only once per individual, network construction was mostly based on quantifying an individual's contribution to the overall group-level structure. Despite the multitude of identified methodological approaches for individual-specific network inference, the number of studies that were intended to enable the prediction of clinical outcomes for future individuals was quite limited, and most of the models served as proof of concept that network characteristics can in principle be useful for prediction. CONCLUSION: The current body of research clearly demonstrates the value of individual-specific network analysis for prediction modelling, but it has not yet been considered as a general tool outside the current areas of application. More methodological research is still needed on well-founded strategies for network inference, especially on adequate network sparsification and outcome-guided graph-theoretical feature extraction and selection, and on how networks can be exploited efficiently for prediction modelling.
PMID: 35249534
Front Genet , IF:4.599 , 2021 , V12 : P780599 doi: 10.3389/fgene.2021.780599
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.
Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.; National Institute of Animal Science, Rural Development Administration, Jeonju, South Korea.; ICAR-National Institute for Plant Biotechnology, New Delhi, India.; Agricultural Education Division, Indian Council of Agricultural Research, New Delhi, India.
Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.
PMID: 35198001
Plant Physiol Biochem , IF:4.27 , 2022 May , V178 : P40-54 doi: 10.1016/j.plaphy.2022.02.024
Evolutionary and functional characterisation of glutathione peroxidases showed splicing mediated stress responses in Maize.
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India. Electronic address: MG.Mallikarjuna@icar.gov.in.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.; ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.; Department of Genetics and Plant Breeding, University of Agricultural Sciences, GKVK, Bengaluru, 560065, India.; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
Maize (Zea mays L) is an important cereal with extensive adaptability and multifaceted usages. However, various abiotic and biotic stresses limit the productivity of maize across the globe. Exposure of plant to stresses disturb the balance between reactive oxygen species (ROS) production and scavenging, which subsequently increases cellular damage and death of plants. Tolerant genotypes have evolved higher output of scavenging antioxidative defence compounds (ADCs) during stresses as one of the protective mechanisms. The glutathione peroxidases (GPXs) are the broad class of ADCs family. The plant GPXs catalyse the reduction of hydrogen peroxide (H2O2), lipid hydroperoxides and organic hydroperoxides to the corresponding alcohol, and facilitate the regulation of stress tolerance mechanisms. The present investigation was framed to study the maize GPXs using evolutionary and functional analyses. Seven GPX genes with thirteen splice-variants and sixty-three types of cis-acting elements were identified through whole-genome scanning in maize. Evolutionary analysis of GPXs in monocots and dicots revealed mixed and lineage-specific grouping patterns in phylogeny. The expression of ZmGPX splice variants was studied in drought and waterlogging tolerant (L1621701) and sensitive (PML10) genotypes in root and shoot tissues. Further, the differential expression of splice variants of ZmGPX1, ZmGPX3, ZmGPX6 and ZmGPX7 and regulatory network analysis suggested the splicing and regulatory elements mediated stress responses. The present investigation suggests targeting the splicing machinery of GPXs as an approach to enhance the stress tolerance in maize.
PMID: 35276595
Tree Physiol , IF:4.196 , 2022 Mar , V42 (3) : P664-683 doi: 10.1093/treephys/tpab114
SMRT and Illumina RNA sequencing reveal the complexity of terpenoid biosynthesis in Zanthoxylum armatum.
College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.; College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China.; Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China.; Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.
Sichuan pepper (Zanthoxylum armatum DC) is a popular spice and is often prescribed in traditional Chinese medicine to treat vomiting, diarrhea, ascariasis and eczema, among other conditions. Volatile oils from Z. armatum leaves contain active ingredients, with terpenoids being one of the main components. In the present study, the combination of sequencing data of Z. armatum from PacBio single molecule real time (SMRT) and Illumina RNA sequencing (RNA-Seq) platforms facilitated an understanding of the gene regulatory network of terpenoid biosynthesis in pepper leaves. The leaves of three developmental stages from two Z. armatum cultivars, 'Rongchangwuci' (WC) and 'Zhuye' (ZY), were selected as test materials to construct sequencing libraries. A total of 143,122 predictions of unique coding sequences, 105,465 simple sequence repeats, 20,145 transcription factors and 4719 long non-coding RNAs (lncRNAs) were identified, and 142,829 transcripts were successfully annotated. The occurrence of alternative splicing events was verified by reverse transcription PCR, and quantitative real-time PCR was used to confirm the expression pattern of six randomly selected lncRNAs. A total of 96,931 differentially expressed genes were filtered from different samples. According to functional annotation, a total of 560 candidate genes were involved in terpenoid synthesis, of which 526 were differentially expressed genes (DEGs). To identify the key genes involved in terpenoid biosynthesis, the module genes in different samples, including structural and transcription factors genes, were analyzed using the weighted gene co-expression network method, and the co-expression network of genes was constructed. Thirty-one terpenoids were identified by gas chromatography-mass spectrometry. The correlation between 18 compounds with significantly different contents and genes with high connectivity in the module was jointly analyzed in both cultivars, yielding 12 candidate DEGs presumably involved in the regulation of terpenoid biosynthesis. Our findings showed that full-length transcriptome SMRT and Illumina RNA-Seq can play an important role in studying organisms without reference genomes and elucidating the gene regulation of a biosynthetic pathway.
PMID: 34448876
Genes (Basel) , IF:4.096 , 2022 Feb , V13 (2) doi: 10.3390/genes13020374
Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize.
State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China.; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China.
BACKGROUND: Maize mesophyll (M) cells play important roles in various biological processes such as photosynthesis II and secondary metabolism. Functional differentiation occurs during M-cell development, but the underlying mechanisms for regulating M-cell development are largely unknown. RESULTS: We conducted single-cell RNA sequencing (scRNA-seq) to profile transcripts in maize leaves. We then identified coregulated modules by analyzing the resulting pseudo-time-series data through gene regulatory network analyses. WRKY, ERF, NAC, MYB and Heat stress transcription factor (HSF) families were highly expressed in the early stage, whereas CONSTANS (CO)-like (COL) and ERF families were highly expressed in the late stage of M-cell development. Construction of regulatory networks revealed that these transcript factor (TF) families, especially HSF and COL, were the major players in the early and later stages of M-cell development, respectively. Integration of scRNA expression matrix with TF ChIP-seq and Hi-C further revealed regulatory interactions between these TFs and their targets. HSF1 and COL8 were primarily expressed in the leaf bases and tips, respectively, and their targets were validated with protoplast-based ChIP-qPCR, with the binding sites of HSF1 being experimentally confirmed. CONCLUSIONS: Our study provides evidence that several TF families, with the involvement of epigenetic regulation, play vital roles in the regulation of M-cell development in maize.
PMID: 35205426
BMC Genomics , IF:3.969 , 2022 Feb , V23 (1) : P125 doi: 10.1186/s12864-022-08345-7
Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance.
Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China.; Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China. qyx2011@ahnu.edu.cn.
BACKGROUND: As one of the largest transcription factor families in plants, the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is involved in various biological processes and plays significant roles in plant growth, development and responses to various stresses. Although identification and characterization of AP2/ERF superfamily genes have been accomplished in many plant species, very little is known regarding the structure and function of AP2/ERF genes in maize. RESULTS: In this study, a total of 214 genes encoding ZmAP2/ERF proteins with complete AP2/ERF domain were eventually identified according to the AGPv4 version of the maize B73 genome. Based on the number of AP2/ERF domain and similarities of amino acid sequences among AP2/ERF proteins from Arabidopsis, rice and maize, all 214 putative ZmAP2/ERF proteins were categorized into three distinct families, including the AP2 family (44), the ERF family (166) and the RAV family (4), respectively. Among them, the ERF family was further subdivided into two diverse subfamilies, including the DREB and ERF subfamilies with 61 and 105 members, respectively. Further, based on phylogenetic analysis, the members of DREB and ERF subfamilies were subdivided into four (Group I-IV) and eight (Group V-XII) groups, respectively. The characteristics of exon-intron structure of these putative ZmAP2/ERF genes and conserved protein motifs of their encoded ZmAP2/ERF proteins were also presented respectively, which was in accordance with the results of group classification. Promoter analysis suggested that ZmAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Gene duplication and synteny analysis revealed that tandem or segmental duplication and purifying selection might play significant roles in evolution and functional differentiation of AP2/ERF superfamily genes among three various gramineous species (maize, rice and sorghum). Using RNA-seq data, transcriptome analysis indicated that the majority of ZmAP2/ERF genes displayed differential expression patterns at different developmental stages of maize. In addition, the following analyses of co-expression network among ZmAP2/ERF genes and protein protein interaction between ZmAP2 and ZmERF proteins further enabled us to understand the regulatory relationship among members of the AP2/ERF superfamily in maize. Furthermore, by quantitative real-time PCR analysis, twenty-seven selected ZmAP2/ERF genes were further confirmed to respond to three different abiotic stresses, suggesting their potential roles in various abiotic stress responses. Collectively, these results revealed that these ZmAP2/ERF genes play essential roles in abiotic stress tolerance. CONCLUSIONS: Taken together, the present study will serve to present an important theoretical basis for further exploring the function and regulatory mechanism of ZmAP2/ERF genes in the growth, development, and adaptation to abiotic stresses in maize.
PMID: 35151253
Plants (Basel) , IF:3.935 , 2022 Feb , V11 (4) doi: 10.3390/plants11040510
Metabolic Circuits in Sap Extracts Reflect the Effects of a Microbial Biostimulant on Maize Metabolism under Drought Conditions.
Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa.; International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa.
The use of microbial biostimulants in the agricultural sector is increasingly gaining momentum and drawing scientific attention to decode the molecular interactions between the biostimulants and plants. Although these biostimulants have been shown to improve plant health and development, the underlying molecular phenomenology remains enigmatic. Thus, this study is a metabolomics work to unravel metabolic circuits in sap extracts from maize plants treated with a microbial biostimulant, under normal and drought conditions. The biostimulant, which was a consortium of different Bacilli strains, was applied at the planting stage, followed by drought stress application. The maize sap extracts were collected at 5 weeks after emergence, and the extracted metabolites were analyzed on liquid chromatography-mass spectrometry platforms. The acquired data were mined using chemometrics and bioinformatics tools. The results showed that under both well-watered and drought stress conditions, the application of the biostimulant led to differential changes in the profiles of amino acids, hormones, TCA intermediates, phenolics, steviol glycosides and oxylipins. These metabolic changes spanned several biological pathways and involved a high correlation of the biochemical as well as structural metabolic relationships that coordinate the maize metabolism. The hypothetical model, postulated from this study, describes metabolic events induced by the microbial biostimulant for growth promotion and enhanced defences. Such understanding of biostimulant-induced changes in maize sap pinpoints to the biochemistry and molecular mechanisms that govern the biostimulant-plant interactions, which contribute to ongoing efforts to generate actionable knowledge of the molecular and physiological mechanisms that define modes of action of biostimulants.
PMID: 35214843
Plants (Basel) , IF:3.935 , 2022 Mar , V11 (5) doi: 10.3390/plants11050677
Uncovering the Gene Regulatory Network of Maize Hybrid ZD309 under Heat Stress by Transcriptomic and Metabolomic Analysis.
Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.; National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
Maize is an important cereal crop but is sensitive to heat stress, which significantly restricts its grain yield. To explore the molecular mechanism of maize heat tolerance, a heat-tolerant hybrid ZD309 and its parental lines (H39_1 and M189) were subjected to heat stress, followed by transcriptomic and metabolomic analyses. After six-day-heat treatment, the growth of ZD309 and its parental lines were suppressed, showing dwarf stature and rolled leaf compared with the control plants. ZD309 exhibited vigorous growth; however, M189 displayed superior heat tolerance. By transcriptomic and metabolomic analysis, hundreds to thousands of differentially expressed genes (DEGs) and metabolites (DEMs) were identified. Notably, the female parent H39 shares more DEGs and DEMs with the hybrid ZD309, indicating more genetic gain derived from the female instead of the male. A total of 299 heat shock genes detected among three genotypes were greatly aggregated in sugar transmembrane transporter activity, plasma membrane, photosynthesis, protein processing in the endoplasmic reticulum, cysteine, and methionine metabolism. A total of 150 heat-responsive metabolites detected among three genotypes were highly accumulated, including jasmonic acid, amino acids, sugar, flavonoids, coumarin, and organic acids. Integrating transcriptomic and metabolomic assays revealed that plant hormone signal transduction, cysteine, and methionine metabolism, and alpha-linolenic acid metabolism play crucial roles in heat tolerance in maize. Our research will be facilitated to identify essential heat tolerance genes in maize, thereby contributing to breeding heat resistance maize varieties.
PMID: 35270147
Am J Drug Alcohol Abuse , IF:3.829 , 2022 Jan : P1-9 doi: 10.1080/00952990.2021.2012185
Cocaine use disorder criteria in a clinical sample: an analysis using item response theory, factor and network analysis.
Department of Clinical and Experimental Psychology, University of Huelva, Huelva, Spain.; Research Center for Natural Resources, Health and The Environment, University of Huelva, Huelva, Spain.
BACKGROUND: The conceptualization of substance use disorders (SUDs) was modified in successive editions of the DSM. Dimensionality and inclusion/exclusion of several criteria was studied using various analytic approaches. OBJECTIVE: The study aimed to deepen our knowledge of the interrelationships between the diagnostic criteria for cocaine use disorder (CUD), applying three different analytical techniques: factor analysis, Item Response Theory (IRT) models, and network analysis. METHODS: 425 (85.4% male) outpatients were evaluated for CUD using the Substance Dependence Severity Scale. Confirmatory Factor Analysis, 2-parameter logistic model (IRT) and network analysis were applied to analyze the relationships between the diagnostic criteria. RESULTS: The results show that "legal problems" criterion is not congruent with the CUD measure on three analyses. Also, network analysis suggests the usefulness of the "craving" criterion. The criterion "quit/control" is the one that presents the best centrality indices and expected influence, showing strong relationships with the criteria of "craving," "tolerance," "neglect roles" and "activities given up." CONCLUSIONS: Network analysis appears to be a useful and complementary technique to factor analysis and IRT for understanding CUD. The "quit/control" criterion emerges as a central criterion to understand CUD.
PMID: 35100067
Gene , IF:3.688 , 2022 Apr , V819 : P146233 doi: 10.1016/j.gene.2022.146233
Different gene co-expression patterns of aortic intima-media and adventitia in thoracic aortic aneurysm.
Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: lcx_pumc@163.com.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China.; Department of Neurosurgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.; Department of Vascular Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No 1. Shuaifuyuan, Dongcheng District, Beijing, China. Electronic address: yuehongzheng@yahoo.com.
BACKGROUND: Due to permanent aortic dilation, thoracic aortic aneurysm (TAA) is a life-threatening disease. Once ruptured, TAA has a high lethality and disability rate. Although studies have focused on transcriptomic alterations in TAA, more detailed analysis is still lacking, especially the different aortic intima-media and adventitia roles. This study aimed to identify the different co-expression patterns between the aortic intima-media and the adventitia underlying the aortic dilation. METHODS: We analyzed the gene expression profiles obtained from Gene Expression Omnibus (GEO, GSE26155) database. With a false discovery rate (FDR) < 0.05 and |log2FC| >/= 1, 56 and 33 differential genes in the intima-media and adventitia, respectively, between the non-dilated and dilated status. Gene ontology (GO) and gene set enrichment analysis revealed that degranulation and activation of neutrophils play an essential role in the intima-media of dilated aortas. Through weighted gene co-expression network analysis (WGCNA), we identified essential co-expressed modules and hub genes to explore the biological functions of the dysregulated genes. RESULTS: Functional pathway analysis suggested that lipid metabolism, C-C motif chemokine pathways were significantly enriched in the adventitia, whereas ribosome proteins and related mRNA translation pathways were closely related to intima and media. Furthermore, the ssGSEA analysis indicated that macrophages, helper T cells, and neutrophils were higher in the intima-media of the dilated thoracic aorta. Finally, we validated the critical findings of the study with the murine model of TAA. CONCLUSION: This study identified and verified hub genes and pathways in aortic intima-media and adventitia prominently associated with aortic dilation, providing practical understanding in the perspective of searching for new molecular targets.
PMID: 35121027
J Plant Physiol , IF:3.549 , 2022 Apr , V271 : P153666 doi: 10.1016/j.jplph.2022.153666
Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau.
Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China. Electronic address: xqzhao@nwipb.cas.cn.; Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China. Electronic address: sxxu@nwipb.cas.cn.
There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.
PMID: 35303514
Fungal Genet Biol , IF:3.495 , 2022 Apr , V159 : P103673 doi: 10.1016/j.fgb.2022.103673
Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta.
Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN, United States. Electronic address: zhan3437@umn.edu.; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States.; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States. Electronic address: schillin@umn.edu.
Brown rot fungi dominate the carbon degradation of northern terrestrial conifers. These fungi adapted unique genetic inventories to degrade lignocellulose and to rapidly release a large quantity of carbohydrates for fungal catabolism. We know that brown rot involves "two-step" gene regulation to delay most hydrolytic enzyme expression until after harsh oxidative pretreatments. This implies the crucial role of concise gene regulation to brown rot efficacy, but the underlying regulatory mechanisms remain uncharacterized. Here, using the combined transcriptomic and enzyme analyses we investigated the roles of carbon catabolites in controlling gene expression in model brown rot fungus Rhodonia placenta. We identified co-regulated gene regulons as shared transcriptional responses to no-carbon controls, glucose, cellobiose, or aspen wood (Populus sp.). We found that cellobiose, a common inducing catabolite for fungi, induced expression of main chain-cleaving cellulases in GH5 and GH12 families (cellobiose vs. no-carbon > 4-fold, Padj < 0.05), whereas complex aspen was a universal inducer for Carbohydrate Active Enzymes (CAZymes) expression. Importantly, we observed the attenuated glucose-mediated repression effects on cellulases expression, but not on hemicellulases and lignin oxidoreductases, suggesting fungi might have adapted diverged regulatory routes to boost cellulase production for the fast carbohydrate release. Using carbon regulons, we further predicted the cis- and trans-regulatory elements and assembled a network model of the distinctive regulatory machinery of brown rot. These results offer mechanistic insights into the energy efficiency traits of a common group of decomposer fungi with enormous influence on the carbon cycle.
PMID: 35150839
Brain Sci , IF:3.394 , 2022 Mar , V12 (3) doi: 10.3390/brainsci12030378
A Preliminary Report of Network Electroencephalographic Measures in Primary Progressive Apraxia of Speech and Aphasia.
Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA.; Department of Neurology, Mayo Clinic, Scottsdale, AZ 85259, USA.; Department of Radiology, Mayo Clinic, Rochester, MN 55905, USA.
The objective of this study was to characterize network-level changes in nonfluent/agrammatic Primary Progressive Aphasia (agPPA) and Primary Progressive Apraxia of Speech (PPAOS) with graph theory (GT) measures derived from scalp electroencephalography (EEG) recordings. EEGs of 15 agPPA and 7 PPAOS patients were collected during relaxed wakefulness with eyes closed (21 electrodes, 10-20 positions, 256 Hz sampling rate, 1-200 Hz bandpass filter). Eight artifact-free, non-overlapping 1024-point epochs were selected. Via Brainwave software, GT weighted connectivity and minimum spanning tree (MST) measures were calculated for theta and upper and lower alpha frequency bands. Differences in GT and MST measures between agPPA and PPAOS were assessed with Wilcoxon rank-sum tests. Of greatest interest, Spearman correlations were computed between behavioral and network measures in all frequency bands across all patients. There were no statistically significant differences in GT or MST measures between agPPA and PPAOS. There were significant correlations between several network and behavioral variables. The correlations demonstrate a relationship between reduced global efficiency and clinical symptom severity (e.g., parkinsonism, AOS). This preliminary, exploratory study demonstrates potential for EEG GT measures to quantify network changes associated with degenerative speech-language disorders.
PMID: 35326334
Virus Res , IF:3.303 , 2022 Apr , V311 : P198704 doi: 10.1016/j.virusres.2022.198704
Complex small RNA-mediated regulatory networks between viruses/viroids/satellites and host plants.
Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China.; Chinese Academy of Inspection and Quarantine, Beijing 100176, China. Electronic address: zhusf@caiq.org.cn.
Host plants deploy the small RNA (sRNA)-directed RNA silencing pathway to resist invasion by acellular microorganisms (viruses/viroids/satellites), and, in turn, this pathway is exploited by pathogenic agents to create an environment conducive to infection. Previous known sRNA-RNA systems consist of host endogenous microRNAs (miRNAs) mediating the regulation of host mRNAs and virus/viroid/satellite-derived small interfering RNAs (vsiRNAs) targeting their genomic RNAs. However, more in-depth explorations have substantially expanded the understanding of the complexity of sRNA-RNA regulatory networks. Here, we review some recently discovered sRNA-mediated regulatory systems. Specifically, in addition to virus-encoded proteins acting as virulence factors, vsiRNAs can serve as important pathogenic determinants targeting host mRNAs and noncoding RNAs to promote virus/viroid/satellite infection and trigger symptoms that may be side effects of infection. Additionally, virus-activated but host-derived siRNAs (vasiRNAs) regulate endogenous plant gene expression related to virus resistance or pathogenicity. The inhibitory effect of miRNAs on plant endogenous mRNAs and viral RNAs (vRNAs) has also been identified. Furthermore, siRNA-based interregulation occurring between viruses and their parasite satellite RNAs (satRNAs) enables coexisting virus-satRNA-plant homoeostasis. Thus, the underlying mechanisms of plant-virus/viroid/satellite competition and symbiosis are largely obscured by these diverse sRNA-RNA combinations. Guided by the intricate regulatory network-based principle at the RNA level, practically applicable and feasible strategies have been developed for the management of plant viruses/viroids/satellites for which effective control measures are lacking.
PMID: 35139407
Brain Struct Funct , IF:3.27 , 2022 Apr , V227 (3) : P741-762 doi: 10.1007/s00429-021-02435-0
A hands-on tutorial on network and topological neuroscience.
Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands.; Institut Des Maladies Neurodegeneratives, UMR 5293, Universite de Bordeaux, CNRS, Bordeaux Neurocampus, 146 Rue Leo Saignat, 33000, Bordeaux, France.; Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Psychiatry, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands.; Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Anatomy and Neurosciences, Amsterdam UMC, De Boelelaan 1117, Amsterdam, The Netherlands. f.nobregasantos@amsterdamumc.nl.; Institute for Advanced Studies, University of Amsterdam, Oude Turfmarkt 147, 1012 GC, Amsterdam, The Netherlands. f.nobregasantos@amsterdamumc.nl.
The brain is an extraordinarily complex system that facilitates the optimal integration of information from different regions to execute its functions. With the recent advances in technology, researchers can now collect enormous amounts of data from the brain using neuroimaging at different scales and from numerous modalities. With that comes the need for sophisticated tools for analysis. The field of network neuroscience has been trying to tackle these challenges, and graph theory has been one of its essential branches through the investigation of brain networks. Recently, topological data analysis has gained more attention as an alternative framework by providing a set of metrics that go beyond pairwise connections and offer improved robustness against noise. In this hands-on tutorial, our goal is to provide the computational tools to explore neuroimaging data using these frameworks and to facilitate their accessibility, data visualisation, and comprehension for newcomers to the field. We will start by giving a concise (and by no means complete) overview of the field to introduce the two frameworks and then explain how to compute both well-established and newer metrics on resting-state functional magnetic resonance imaging. We use an open-source language (Python) and provide an accompanying publicly available Jupyter Notebook that uses the 1000 Functional Connectomes Project dataset. Moreover, we would like to highlight one part of our notebook dedicated to the realistic visualisation of high order interactions in brain networks. This pipeline provides three-dimensional (3-D) plots of pairwise and higher-order interactions projected in a brain atlas, a new feature tailor-made for network neuroscience.
PMID: 35142909
PeerJ , IF:2.984 , 2022 , V10 : Pe12965 doi: 10.7717/peerj.12965
Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.).
College of Agronomy, Shenyang Agricultural University, Shenyang, China.; Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China.
Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by (60)Co gamma-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.
PMID: 35251782
Prev Vet Med , IF:2.67 , 2022 Feb , V199 : P105556 doi: 10.1016/j.prevetmed.2021.105556
Preventive effect of on-farm biosecurity practices against highly pathogenic avian influenza (HPAI) H5N6 infection on commercial layer farms in the Republic of Korea during the 2016-17 epidemic: A case-control study.
Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea. Electronic address: shanuar@korea.kr.; Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea.; Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Farm Animal Clinical Training and Research Center, Seoul National University, Pyeongchang, 25354, Republic of Korea.; Department of Computer and Information Science, Korea University, Seojong, 30019, Republic of Korea.
Highly pathogenic avian influenza virus (HPAIv) H5N6 has destructive consequences on the global poultry production system. Recently, a growing number of layer farms have been heavily damaged from the HPAIv epidemic due to the increased virulence of the virus and the intensification of the production system. Therefore, stakeholders should implement effective preventive practices at the farm level that are aligned with contingency measures at the national level to minimize poultry losses. However, numerous biosecurity protocols for layer farm workers to follow have been developed, impeding efficient prevention and control. Furthermore, the effectiveness of biosecurity practices varies with the geographical condition and inter-farm contact structures. Hence, the objective of our study was to examine the preventive effect of five biosecurity actions commonly practiced at layer farms in the Republic of Korea against HPAIv H5N6: (i) fence installation around a farm, ii) rodent control inside a farm; iii) disinfection booth for visitors for disinfection protocols, iv) an anterior room in the sheds before entering the bird area and v) boots changes when moving between sheds in the same farm. We conducted a case-control study on 114 layer case farms and 129 layer control farms during the 2016-17 HPAI epidemic. The odds ratios for five on-farm biosecurity practices implemented in those study groups were estimated as a preventive effect on the HPAI infection with covariates, including seven geographical conditions and three network metrics using Bayesian hierarchical logistic regression and geographical location weighted logistic regression. The results showed that the use of a disinfection booth for personnel reduced the odds of HPAIv H5N6 infection (adjusted odds ratio [AOR] = 0.002, 95 % credible interval [CrI] = 0.00007 - 0.025) with relatively small spatial variation (minimum AOR - maximum AOR: 0.084-0.263). Changing boots between sheds on the same farm reduced the odds of HPAIv H5N6 infection (AOR = 0.160, 95 % CrI = 0.024-0.852) with relatively wide spatial variation (minimum AOR - maximum AOR = 0.270-0.688). Therefore, enhanced personnel biosecurity protocols at the farm of entry for layer farms is recommended to effectively prevent and respond to HPAIv H5N6 infection under different local condition. Our study provides an important message for layer farmers to effectively implement on-farm biosecurity actions against HPAIv H5N6 infection at their farms by setting priorities based on their spatial condition and network position.
PMID: 34896940
STAR Protoc , 2022 Mar , V3 (1) : P101208 doi: 10.1016/j.xpro.2022.101208
Gene coexpression analysis in Arabidopsis thaliana based on public microarray data.
Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.; biobank.cy Center of Excellence in Biobanking and Biomedical Research, University of Cyprus, 2029 Nicosia, Cyprus.
Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach. For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).
PMID: 35243384
STAR Protoc , 2022 Mar , V3 (1) : P101175 doi: 10.1016/j.xpro.2022.101175
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.; Department of Computer Science, Western University, London, ON N6A 5B7, Canada.; Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA.
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).
PMID: 35243369
J Transp Geogr , 2022 Feb , V99 : P103265 doi: 10.1016/j.jtrangeo.2021.103265
Global shipping network dynamics during the COVID-19 pandemic's initial phases.
Department of Operations and Technology, Kuhne Logistics University (KLU), Hamburg, Germany.
Catastrophic incidents can significantly disrupt supply chains, but most of these disruptions remain localized. It was not until the onset of COVID-19 that a disruption in our lifetimes achieved a global magnitude. In order to contain the pandemic, governments around the world resorted to closing borders, shutting down manufacturing plants, and imposing lockdowns, which resulted in disrupted production capabilities and weakened consumer spending. The effects of these measures have been clearly visible in global transport networks, where disruptions ripple through the system and serve as a precursor to the disruptions in the broader economy. In this study, we use liner shipping schedule cancellations, a form of serious transport network disruption, as distress signals of the pandemic's impact on global supply chains. Our study applies a three-stage approach and provides insights into operator behaviors when under distress. We show that the pandemic challenged service network integrity and that network disruptions first clustered in Asia before rippling along main trade routes. Agile liner shipping operations, aided by planned service suspensions, prevented the collapse of the global maritime transport networks and indicated the maritime industry's ability to withstand even major catastrophic incidents.
PMID: 35035126
J Biomol Struct Dyn , 2022 Mar , V40 (4) : P1719-1735 doi: 10.1080/07391102.2020.1832577
Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection.
Department of Centre for Advanced Research (CFAR), Faculty of Medicine, King George's Medical University (KGMU), Lucknow, India.
SARS-CoV-2 is the etiological agent of COVID-19 and responsible for more than 6 million cases globally, for which no vaccine or antiviral is available. Therefore, this study was planned to investigate the antiviral role of the active constituents against spike glycoprotein of SARS-CoV-2 as well as its host ACE2 receptor. Structure-based drug design approach has been used to elucidate the antiviral activity of active constituents present in traditional medicinal plants from Ayurveda. Further, parameters like drug-likeness, pharmacokinetics, and toxicity were determined to ensure the safety and efficacy of active constituents. Gene network analysis was performed to investigate the pathways altered during COVID-19. The prediction of drug-target interactions was performed to discover novel targets for active constituents. The results suggested that amarogentin, eufoliatorin, alpha-amyrin, caesalpinins, kutkin, beta-sitosterol, and belladonnine are the top-ranked molecules have the highest affinity towards both the spike glycoprotein and ACE2. Most active constituents have passed the criteria of drug-likeness and demonstrated good pharmacokinetic profile with minimum predicted toxicity level. Gene network analysis confirmed that G-protein coupled receptor, protein kinase B signaling, protein secretion, peptidyl-serine phosphorylation, nuclear transport, apoptotic pathway, tumor necrosis factor, regulation of angiotensin level, positive regulation of ion transport, and membrane protein proteolysis were altered during COVID-19. The target prediction analysis revealed that most active constituents target the same pathways which are found to be altered during COVID-19. Collectively, our data encourages the use of active constituents as a potential therapy for COVID-19. However, further studies are ongoing to confirm its efficacy against disease. Communicated by Ramaswamy H. Sarma.
PMID: 33073699