Mol Plant , IF:12.084 , 2020 Jan , V13 (1) : P59-71 doi: 10.1016/j.molp.2019.10.012
Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: jiaoyn@ibcas.ac.cn.
Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs ( approximately 120 million years ago [Ma], approximately 66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.
PMID: 31678615
Proc Natl Acad Sci U S A , IF:9.412 , 2020 Jan , V117 (4) : P2149-2159 doi: 10.1073/pnas.1909915117
Brain-wide functional architecture remodeling by alcohol dependence and abstinence.
Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093.; Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720.; Beckman Institute, California Institute of Technology, Pasadena, CA 91125.; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037.; Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA 92093; olgeorge@ucsd.edu.
Alcohol abuse and alcohol dependence are key factors in the development of alcohol use disorder, which is a pervasive societal problem with substantial economic, medical, and psychiatric consequences. Although our understanding of the neurocircuitry that underlies alcohol use has improved, novel brain regions that are involved in alcohol use and novel biomarkers of alcohol use need to be identified. The present study used a single-cell whole-brain imaging approach to 1) assess whether abstinence from alcohol in an animal model of alcohol dependence alters the functional architecture of brain activity and modularity, 2) validate our current knowledge of the neurocircuitry of alcohol abstinence, and 3) discover brain regions that may be involved in alcohol use. Alcohol abstinence resulted in the whole-brain reorganization of functional architecture in mice and a pronounced decrease in modularity that was not observed in nondependent moderate drinkers. Structuring of the alcohol abstinence network revealed three major brain modules: 1) extended amygdala module, 2) midbrain striatal module, and 3) cortico-hippocampo-thalamic module, reminiscent of the three-stage theory. Many hub brain regions that control this network were identified, including several that have been previously overlooked in alcohol research. These results identify brain targets for future research and demonstrate that alcohol use and dependence remodel brain-wide functional architecture to decrease modularity. Further studies are needed to determine whether the changes in coactivation and modularity that are associated with alcohol abstinence are causal features of alcohol dependence or a consequence of excessive drinking and alcohol exposure.
PMID: 31937658
Elife , IF:7.08 , 2020 Jan , V9 doi: 10.7554/eLife.49658
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification.
School of Life Sciences, University of Dundee, Dundee, United Kingdom.; Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.; Earlham Institute, Norwich Research Park, Norwich, United Kingdom.; James Hutton Institute, Invergowrie, United Kingdom.
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m(6)A). Here we show that m(6)A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m(6)A from 3' untranslated regions is associated with decreased relative transcript abundance and defective RNA 3' end formation. A functional consequence of disrupted m(6)A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode.
PMID: 31931956
mSystems , IF:6.633 , 2020 Jan , V5 (1) doi: 10.1128/mSystems.00423-19
Network Analysis of the Papaya Orchard Virome from Two Agroecological Regions of Chiapas, Mexico.
Plant Pathology Department, University of Florida, Gainesville, Florida, USA.; Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida, USA.; Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.; Departamento de Ingenieria Genetica, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico.; Plant Pathology Department, University of Florida, Gainesville, Florida, USA karengarrett@ufl.edu laura.silvar@cinvestav.mx.; Departamento de Ingenieria Genetica, Cinvestav Unidad Irapuato, Irapuato, Guanajuato, Mexico karengarrett@ufl.edu laura.silvar@cinvestav.mx.
The study of complex ecological interactions, such as those among host, pathogen, and vector communities, can help to explain host ranges and the emergence of novel pathogens. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with genera including Potyvirus, Comovirus, and Tombusvirus (RNA viruses) and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape.IMPORTANCE Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.
PMID: 31937673
Genomics , IF:6.205 , 2020 Jan , V112 (1) : P412-422 doi: 10.1016/j.ygeno.2019.03.004
Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective.
Department of life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.; Department of Mathematics, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.; Department of Mathematics, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India. Electronic address: sudeepto.bhattacharya@snu.edu.in.; Department of life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India. Electronic address: ashutosh.bio@gmail.com.
MicroRNAs (miRNAs) and transcription factors (TFs) are the largest families of trans-acting gene regulatory species, which are pivotal players in a complex regulatory network. Recently, extensive research on miRNAs and TFs in agriculture has identified these trans-acting regulatory species, as an effective tool for engineering new crop cultivars to increase yield and quality as well tolerance to environmental stresses but our knowledge of regulatory network is still not sufficient to decipher the exact mechanism. In the current work, stress-specific TF-miRNA-gene network was built for Arabidopsis under drought, cold, salt and waterlogging stress using data from reliable publically available databases; and transcriptome and degradome sequence data analysis by meta-analysis approach. Further network analysis elucidated significantly dense, scale-free, small world and hierarchical backbone of interactions. The various centrality measures highlighted several genes/TF/miRNAs as potential targets for tolerant variety cultivation. This comprehensive regulatory information will accelerate the advancement of current understanding on stress specific transcriptional and post-transcriptional regulatory mechanism and has promising utilizations for experimental biologist who are intended to improve plant crop performance under multiple Abiotic stress environments.
PMID: 30876925
J Exp Bot , IF:5.908 , 2020 Jan doi: 10.1093/jxb/eraa054
A balancing act: how plants integrate nitrogen and water signals.
Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA.; Centro de Genomica y Bioinformatica, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.; International Rice Research Institute, Metro Manila, Philippines.
Nitrogen (N) and Water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic as well as antagonistic effects on key plant traits, such as root architecture and stomata aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N-metabolism affect drought responses, and vice versa. Specifically, perturbing key N-signaling genes may leads to changes in drought responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
PMID: 31990028
Ann Bot , IF:4.005 , 2020 Jan , V125 (1) : P11-28 doi: 10.1093/aob/mcz155
Plants are intelligent, here's how.
Minimal Intelligence Laboratory, Universidad de Murcia, Murcia, Spain.; Biological Intelligence Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.; Laboratory of Plant Cognition and Electrophysiology, Federal University of Pelotas, Pelotas - RS, Brazil.; Institute of Molecular Plant Science, Kings Buildings, University of Edinburgh, Edinburgh, UK.
HYPOTHESES: The drive to survive is a biological universal. Intelligent behaviour is usually recognized when individual organisms including plants, in the face of fiercely competitive or adverse, real-world circumstances, change their behaviour to improve their probability of survival. SCOPE: This article explains the potential relationship of intelligence to adaptability and emphasizes the need to recognize individual variation in intelligence showing it to be goal directed and thus being purposeful. Intelligent behaviour in single cells and microbes is frequently reported. Individual variation might be underpinned by a novel learning mechanism, described here in detail. The requirements for real-world circumstances are outlined, and the relationship to organic selection is indicated together with niche construction as a good example of intentional behaviour that should improve survival. Adaptability is important in crop development but the term may be complex incorporating numerous behavioural traits some of which are indicated. CONCLUSION: There is real biological benefit to regarding plants as intelligent both from the fundamental issue of understanding plant life but also from providing a direction for fundamental future research and in crop breeding.
PMID: 31563953
Planta , IF:3.39 , 2020 Jan , V251 (2) : P43 doi: 10.1007/s00425-019-03335-8
Systematic identification of genes associated with plant growth-defense tradeoffs under JA signaling in Arabidopsis.
State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China.; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No. 94 Weijin Road, Tianjin, 300071, People's Republic of China. fanzj@nankai.edu.cn.
MAIN CONCLUSION: Co-expression and regulatory networks yield important insights into the growth-defense tradeoffs mechanism under jasmonic acid (JA) signals in Arabidopsis. Elevated defense is commonly associated with growth inhibition. However, a comprehensive atlas of the genes associated with the plant growth-defense tradeoffs under JA signaling is lacking. To gain an insight into the dynamic architecture of growth-defense tradeoffs, a coexpression network analysis was employed on publicly available high-resolution transcriptomes of Arabidopsis treated with coronatine (COR), a mimic of jasmonoyl-l-isoleucine. The genes involved in JA-mediated growth-defense tradeoffs were systematically revealed. Promoter enrichment analysis revealed the core regulatory module in which the genes underwent rapid activation, sustained upregulation after COR treatment, and mediated the growth-defense tradeoffs. Several transcription factors (TFs), including RAP2.6L, MYB44, WRKY40, and WRKY18, were identified as instantly activated components associated with pathogen and insect resistance. JA might rapidly activate RAV1 and KAN1 to repress brassinosteroid (BR) response genes, upregulate KAN1, the C2H2 TF families ZF2, ZF3, ZAT6, and STZ/ZAT10 to repress the biosynthesis, transport, and signaling of auxin to arrest growth. Independent datasets and preserved analyses validated the reproducibility of the results. Our study provided a comprehensive snapshot of genes that respond to JA signals and provided valuable resources for functional studies on the genetic modification of breeding population that exhibit robust growth and defense simultaneously.
PMID: 31907627
Plant Mol Biol , IF:3.302 , 2020 Jan , V102 (1-2) : P73-88 doi: 10.1007/s11103-019-00932-9
Identification of transcription factors that bind to the 5'-UTR of the barley PHO2 gene.
Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland. apacak@amu.edu.pl.
In barley and other higher plants, phosphate homeostasis is maintained by a regulatory network involving the PHO2 (PHOSPHATE2) encoding ubiquitin-conjugating (UBC) E2 enzyme, the PHR1 (PHOSPHATE STARVATION RESPONSE 1) transcription factor (TF), IPS1 (INDUCED BYPHOSPHATESTARVATION1) RNA, and miR399. During phosphate ion (Pi) deprivation, PHR1 positively regulates MIR399 expression, after transcription and processing mature miR399 guides the Ago protein to the 5'-UTR of PHO2 transcripts. Non-coding IPS1 RNA is highly expressed during Pi starvation, and the sequestration of miR399 molecules protects PHO2 mRNA from complete degradation. Here, we reveal new cis- and trans-regulatory elements that are crucial for efficient PHO2 gene expression in barley. We found that the 5'-UTR of PHO2 contains two PHR1 binding sites (P1BSs) and one Pi-responsive PHO element. Using a yeast one-hybrid (Y1H) assay, we identified two candidate proteins that might mediate this transcriptional regulation: a barley PHR1 ortholog and a TF containing an uncharacterized MYB domain. Additional results classified this new potential TF as belonging to the APL (ALTERED PHLOEM DEVELOPMENT) protein family, and we observed its nuclear localization in barley protoplasts. Pi starvation induced the accumulation of barley APL transcripts in both the shoots and roots. Interestingly, the deletion of the P1BS motif from the first intron of the barley 5'-UTR led to a significant increase in the transcription of a downstream beta-glucuronidase (GUS) reporter gene in tobacco leaves. Our work extends the current knowledge about putative cis- and trans-regulatory elements that may affect the expression of the barley PHO2 gene.
PMID: 31745747
Int J Environ Res Public Health , IF:2.849 , 2020 Jan , V17 (2) doi: 10.3390/ijerph17020596
A Framework to Understand the Progression of Cardiovascular Disease for Type 2 Diabetes Mellitus Patients Using a Network Approach.
Complex Systems Research Group, Faculty of Engineering, The University of Sydney, Darlington, NSW 2008, Australia.; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia.
The prevalence of chronic disease comorbidity has increased worldwide. Comorbidity-i.e., the presence of multiple chronic diseases-is associated with adverse health outcomes in terms of mobility and quality of life as well as financial burden. Understanding the progression of comorbidities can provide valuable insights towards the prevention and better management of chronic diseases. Administrative data can be used in this regard as they contain semantic information on patients' health conditions. Most studies in this field are focused on understanding the progression of one chronic disease rather than multiple diseases. This study aims to understand the progression of two chronic diseases in the Australian health context. It specifically focuses on the comorbidity progression of cardiovascular disease (CVD) in patients with type 2 diabetes mellitus (T2DM), as the prevalence of these chronic diseases in Australians is high. A research framework is proposed to understand and represent the progression of CVD in patients with T2DM using graph theory and social network analysis techniques. Two study cohorts (i.e., patients with both T2DM and CVD and patients with only T2DM) were selected from an administrative dataset obtained from an Australian health insurance company. Two baseline disease networks were constructed from these two selected cohorts. A final disease network from two baseline disease networks was then generated by weight adjustments in a normalized way. The prevalence of renal failure, fluid and electrolyte disorders, hypertension and obesity was significantly higher in patients with both CVD and T2DM than patients with only T2DM. This showed that these chronic diseases occurred frequently during the progression of CVD in patients with T2DM. The proposed network-based model may potentially help the healthcare provider to understand high-risk diseases and the progression patterns between the recurrence of T2DM and CVD. Also, the framework could be useful for stakeholders including governments and private health insurers to adopt appropriate preventive health management programs for patients at a high risk of developing multiple chronic diseases.
PMID: 31963383
Epilepsy Res , IF:2.208 , 2020 Jan , V159 : P106255 doi: 10.1016/j.eplepsyres.2019.106255
Emerging roles of network analysis for epilepsy.
Department of Neurology, Department of Biomedical Engineering, University of Michigan, United States. Electronic address: William.stacey@umich.edu.; Department of Mathematics and Statistics, Center of Systems Neuroscience, Boston University, United States.; Department of Biomedical Engineering, Johns Hopkins University, United States.; Department of Neurological Surgery, University of Pittsburgh, United States.; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, United States.; Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, NIH, United States.; Department of Neurology, Department of Biomedical Engineering, University of Michigan, United States.; Department of Bioengineering, University of Pennsylvania, United States.; Department of Biomedical Engineering, University of California, Irvine, United States.; Department of Pediatrics, University of California, Irvine, United States; Department of Child Neurology, Children's Hospital of Orange County, CA, United States.; Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.
In recent years there has been increasing interest in applying network science tools to EEG data. At the 2018 American Epilepsy Society conference in New Orleans, LA, the yearly session of the Engineering and Neurostimulation Special Interest Group focused on emerging, translational technologies to analyze seizure networks. Each speaker demonstrated practical examples of how network tools can be utilized in clinical care and provide additional data to help care for patients with intractable epilepsy. The groups presented advances using tools from functional connectivity, control theory, and graph theory to analyze human EEG data. These tools have great potential to augment clinical interpretation of EEG signals.
PMID: 31855828
Heliyon , 2020 Jan , V6 (1) : Pe03030 doi: 10.1016/j.heliyon.2019.e03030
Optimal control of a discrete age-structured model for tuberculosis transmission.
Department of Mathematics, Faculty of Science and Technology, Universitas Airlangga, Surabaya 60115, Indonesia.; Department of Mathematics, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia.
In this present paper, a discrete age-structured model of tuberculosis (TB) transmission is formulated and analyzed. The existence and stability of the model equilibriums are discussed based on the basic reproduction ratio. A sensitivity analysis of the model parameters is determined. We then apply the optimal control strategy for controlling the transmission of TB in child and adult populations. The control variables are TB prevention, chemoprophylaxis of latent TB, and active TB treatment efforts. The optimal controls are then derived analytically using the Pontryagin Maximum Principle. Various intervention strategies are performed numerically to investigate the impact of the interventions. We used the incremental cost-effectiveness ratios (ICER) to assess the benefit of each one the control strategies.
PMID: 31909242