Proc Natl Acad Sci U S A , IF:9.412 , 2019 Feb , V116 (8) : P3193-3201 doi: 10.1073/pnas.1811267116
Intercellular cooperation in a fungal plant pathogen facilitates host colonization.
Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Universite de Toulouse, 31326 Castanet-Tolosan, France.; Laboratoire des Interactions Plantes-Microorganismes (LIPM), Institut National de la Recherche Agronomique (INRA), CNRS, Universite de Toulouse, 31326 Castanet-Tolosan, France sylvain.raffaele@inra.fr.
Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.
PMID: 30728304
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Feb , V116 (6) : P2374-2383 doi: 10.1073/pnas.1815238116
Multiomics resolution of molecular events during a day in the life of Chlamydomonas.
Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095.; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095.; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), US Department of Energy, Richland, WA 99352.; Biological Sciences Divison, PNNL, US Department of Energy, Richland, WA 99352.; Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich Heine University, 40225 Dusseldorf, Germany.; Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588.; Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095; sabeeha@chem.ucla.edu.
The unicellular green alga Chlamydomonas reinhardtii displays metabolic flexibility in response to a changing environment. We analyzed expression patterns of its three genomes in cells grown under light-dark cycles. Nearly 85% of transcribed genes show differential expression, with different sets of transcripts being up-regulated over the course of the day to coordinate cellular growth before undergoing cell division. Parallel measurements of select metabolites and pigments, physiological parameters, and a subset of proteins allow us to infer metabolic events and to evaluate the impact of the transcriptome on the proteome. Among the findings are the observations that Chlamydomonas exhibits lower respiratory activity at night compared with the day; multiple fermentation pathways, some oxygen-sensitive, are expressed at night in aerated cultures; we propose that the ferredoxin, FDX9, is potentially the electron donor to hydrogenases. The light stress-responsive genes PSBS, LHCSR1, and LHCSR3 show an acute response to lights-on at dawn under abrupt dark-to-light transitions, while LHCSR3 genes also exhibit a later, second burst in expression in the middle of the day dependent on light intensity. Each response to light (acute and sustained) can be selectively activated under specific conditions. Our expression dataset, complemented with coexpression networks and metabolite profiling, should constitute an excellent resource for the algal and plant communities.
PMID: 30659148
Elife , IF:7.08 , 2019 Feb , V8 doi: 10.7554/eLife.42508
Quantitative insights into the cyanobacterial cell economy.
Laboratory of Adaptive Biotechnologies, Global Change Research Institute CAS, Brno, Czech Republic.; Institut fur Biologie, Fachinstitut fur Theoretische Biologie, Humboldt-Universitat zu Berlin, Berlin, Germany.; Department of Applied Physics, Polytechnic University of Valencia, Valencia, Spain.; Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-Universitat Dusseldorf, Dusseldorf, Germany.; Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russian Federation.
Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.
PMID: 30714903
Conserv Biol , IF:5.405 , 2019 Feb , V33 (1) : P53-65 doi: 10.1111/cobi.13127
Using social-network research to improve outcomes in natural resource management.
School of Biological Sciences, Monash University, Wellington Road, Clayton, VIC, 3800, Australia.; School of Social Sciences, Monash University, Wellington Road, Clayton, VIC, 3800, Australia.; Monash Sustainability Institute, 8 Scenic Boulevard, Clayton, VIC, 3800, Australia.
The conservation and management of natural resources operates in social-ecological systems in which resource users are embedded in social and environmental contexts that influence their management decisions. Characterizing social networks of resource users can be used to inform understanding of social influences on decision making, and social network analysis (SNA) has emerged as a useful technique to explore these relationships. We synthesized how SNA has been used in 85 studies of natural resource management. We considered how social networks and social processes (e.g., interactions between individuals) influence each other and in turn influence social outcomes (e.g., decisions or actions) that affect environmental outcomes (e.g., improved condition). Descriptive methods were used in 58% of the studies to characterize social processes, and 42% of the studies compared multiple networks or multiple points in time to assess social or environmental outcomes. In 4 studies, authors assessed network interventions intended to affect social processes or environmental outcomes. The heterogeneity in case studies, methods, and analyses preclude general lessons. Thus, to structure and further learning about the role of social networks in achieving environmental outcomes, we created a typology that deconstructs social processes, social outcomes, and environmental outcomes into themes and options of social and ecological measures within each. We suggest shifts in research foci toward intervention studies to aid in understanding causality and inform the design of conservation initiatives. There is a need to develop clearer justification and guidance around the proliferation of network measures. The use of SNA in natural resource management is expanding rapidly; thus, now is the time for the conservation community to build a more rigorous evidence base to demonstrate the extent to which social networks can play a role in achieving desired social and environmental outcomes.
PMID: 29738621
Genes (Basel) , IF:3.759 , 2019 Feb , V10 (2) doi: 10.3390/genes10020139
An Integrative Systems Perspective on Plant Phosphate Research.
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK. ishan.ajmera@nottingham.ac.uk.; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK. charlie.hodgman@nottingham.ac.uk.; School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0 QF, UK. chungui.lu@ntu.ac.uk.
The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards. This work introduces integrative systems approaches as a way to represent and understand this complexity, so that meaningful links can be established between genotype, environment, crop traits and yield. It aims to provide a large set of pointers to potential genes and research practice, with a view to encouraging members of the plant-phosphate research community to adopt such approaches so that, together, we can aid efforts in global food security.
PMID: 30781872
J R Soc Interface , IF:3.748 , 2019 Feb , V16 (151) : P20180731 doi: 10.1098/rsif.2018.0731
Fashion and art cycles are driven by counter-dominance signals of elite competition: quantitative evidence from music styles.
1 Section for Science of Complex Systems, CeMSIIS, Medical University of Vienna , Spitalgasse 23, 1090 Vienna , Austria.; 2 Complexity Science Hub Vienna , Josefstaedter Strasse 39, 1080 Vienna , Austria.; 3 Department of Marketing and Retail Management, Surrey Business School, University of Surrey, Guildford GU2 7XH , UK.; 4 Santa Fe Institute , 1399 Hyde Park Road, Santa Fe, NM 85701 , USA.; 5 IIASA , Schlossplatz 1, 2361 Laxenburg , Austria.
Human symbol systems such as art and fashion styles emerge from complex social processes that govern the continuous re-organization of modern societies. They provide a signalling scheme that allows members of an elite to distinguish themselves from the rest of society. Efforts to understand the dynamics of art and fashion cycles have been placed on 'bottom-up' and 'top-down' theories. According to 'top-down' theories, elite members signal their superior status by introducing new symbols (e.g. fashion styles), which are adopted by low-status groups. In response to this adoption, elite members would need to introduce new symbols to signal their status. According to many 'bottom-up' theories, style cycles evolve from lower classes and follow an essentially random pattern. We propose an alternative explanation based on counter-dominance signalling (CDS). In CDS, elite members want others to imitate their symbols; changes only occur when outsider groups successfully challenge the elite by introducing signals that contrast those endorsed by the elite. We investigate these mechanisms using a dynamic network approach on data containing almost 8 million music albums released between 1956 and 2015. The network systematically quantifies artistic similarities of competing musical styles and their changes over time. We formulate empirical tests for whether new symbols are introduced by current elite members (top-down), randomness (bottom-up) or by peripheral groups through counter-dominance signals. We find clear evidence that CDS drives changes in musical styles. This provides a quantitative, completely data-driven answer to a century-old debate about the nature of the underlying social dynamics of fashion cycles.
PMID: 30958188
BMC Plant Biol , IF:3.497 , 2019 Feb , V19 (Suppl 1) : P53 doi: 10.1186/s12870-019-1640-2
The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development.
The Siberian Branch of the Russian Academy of Sciences (IC&G SB RAS), The Institute of Cytology and Genetics, Novosibirsk, Russia. ad@bionet.nsc.ru.; Novosibirsk State University (NSU), Novosibirsk, Russia. ad@bionet.nsc.ru.; The Siberian Branch of the Russian Academy of Sciences (IC&G SB RAS), The Institute of Cytology and Genetics, Novosibirsk, Russia.; Novosibirsk State University (NSU), Novosibirsk, Russia.; School of Life Science, Immanuel Kant Federal Baltic University, Kaliningrad, Russia.; Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
BACKGROUND: The variation in structure and function of gene regulatory networks (GRNs) participating in organisms development is a key for understanding species-specific evolutionary strategies. Even the tiniest modification of developmental GRN might result in a substantial change of a complex morphogenetic pattern. Great variety of trichomes and their accessibility makes them a useful model for studying the molecular processes of cell fate determination, cell cycle control and cellular morphogenesis. Nowadays, a large number of genes regulating the morphogenesis of A. thaliana trichomes are described. Here we aimed at a study the evolution of the GRN defining the trichome formation, and evaluation its importance in other developmental processes. RESULTS: In study of the evolution of trichomes formation GRN we combined classical phylogenetic analysis with information on the GRN topology and composition in major plants taxa. This approach allowed us to estimate both times of evolutionary emergence of the GRN components which are mainly proteins, and the relative rate of their molecular evolution. Various simplifications of protein structure (based on the position of amino acid residues in protein globula, secondary structure type, and structural disorder) allowed us to demonstrate the evolutionary associations between changes in protein globules and speciations/duplications events. We discussed their potential involvement in protein-protein interactions and GRN function. CONCLUSIONS: We hypothesize that the divergence and/or the specialization of the trichome-forming GRN is linked to the emergence of plant taxa. Information about the structural targets of the protein evolution in the GRN may predict switching points in gene networks functioning in course of evolution. We also propose a list of candidate genes responsible for the development of trichomes in a wide range of plant species.
PMID: 30813891
J Pharm Biomed Anal , IF:3.209 , 2019 Feb , V164 : P231-240 doi: 10.1016/j.jpba.2018.10.035
Nuclear magnetic resonance-based metabolomics approach to evaluate preventive and therapeutic effects of Gastrodia elata Blume on chronic atrophic gastritis.
Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.; Center of Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China. Electronic address: wang.junsong@gmail.com.
Chronic atrophic gastritis (CAG) is one of the most common digestive system diseases worldwide which defined by WHO as initial step of cancer. Gastrodia elata Blume (GEB) is a traditional herbal with multiple pharmacological activities which was widely used in Asian countries. This study aims to explore the preventive and therapeutical effects of Gastrodia elata Blume on auto-immune induced CAG in rats. Tissues of stomachs were collected and submitted to (1)H NMR-based metabolomics analysis and histopathological inspection. The biochemical indexes of MDA, SOD, GSH, NO and XOD were measured. Gastrodia elata Blume could apparently ameliorate the damaged gastric glands and the biochemical parameters, enhance gastric acid secretion, and significantly relieve the inflammation of the stomach. Orthogonal signal correction-partial least squares-discriminant analysis (OSC-PLS-DA) of NMR profiles and correlation network analysis revealed that Gastrodia elata Blume could effectively treat CAG via regulating energy and purine metabolisms, and by anti-oxidation and anti-inflammation effects.
PMID: 30391812
R Soc Open Sci , IF:2.647 , 2019 Feb , V6 (2) : P180719 doi: 10.1098/rsos.180719
Contact chains of cattle farms in Great Britain.
Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK.; College of Engineering, Mathematics and Physical Sciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK.; Animal and Plant Health Agency, Woodchester Park, Nympsfield, Stonehouse GL10 3UJ, UK.
Network analyses can assist in predicting the course of epidemics. Time-directed paths or 'contact chains' provide a measure of host-connectedness across specified timeframes, and so represent potential pathways for spread of infections with different epidemiological characteristics. We analysed networks and contact chains of cattle farms in Great Britain using Cattle Tracing System data from 2001 to 2015. We focused on the potential for between-farm transmission of bovine tuberculosis, a chronic infection with potential for hidden spread through the network. Networks were characterized by scale-free type properties, where individual farms were found to be influential 'hubs' in the network. We found a markedly bimodal distribution of farms with either small or very large ingoing and outgoing contact chains (ICCs and OCCs). As a result of their cattle purchases within 12-month periods, 47% of British farms were connected by ICCs to more than 1000 other farms and 16% were connected to more than 10 000 other farms. As a result of their cattle sales within 12-month periods, 66% of farms had OCCs that reached more than 1000 other farms and 15% reached more than 10 000 other farms. Over 19 000 farms had both ICCs and OCCs reaching more than 10 000 farms for two or more years. While farms with more contacts in their ICCs or OCCs might play an important role in disease spread, farms with extensive ICCs and OCCs might be particularly important by being at higher risk of both acquiring and disseminating infections.
PMID: 30891255
J Theor Biol , IF:2.327 , 2019 Feb , V463 : P155-166 doi: 10.1016/j.jtbi.2018.12.014
Reducing the complexity of mathematical models for the plant circadian clock by distributed delays.
Graduate School of Science and Engineering, Ritsumeikan University, Noji-higashi, Kusatsu, Shiga 525-8577, Japan. Electronic address: isao@fc.ritsumei.ac.jp.; College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK. Electronic address: O.E.Akman@exeter.ac.uk.; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK. Electronic address: James.Locke@slcu.cam.ac.uk.
A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.
PMID: 30550861
Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz , IF:1.059 , 2019 Feb , V62 (2) : P140-149 doi: 10.1007/s00103-018-2862-4
[A social network analysis regarding geographic variation for patients with depression in Germany].
Zentralinstitut fur die kassenarztliche Versorgung in Deutschland, Salzufer 8, 10587, Berlin, Deutschland. cgerber@zi.de.; Zentralinstitut fur die kassenarztliche Versorgung in Deutschland, Salzufer 8, 10587, Berlin, Deutschland.
BACKGROUND: Worldwide there is an acute requirement for an early and needs-based treatment for patients with depression. The successful treatment of depression requires the collaborative care of all healthcare providers. AIM: The aim of this work was to identify virtual networks of physicians treating patients with depression in Germany. We identified specialists who are involved in the care of patients with depression, including geographic variations. METHODS: The analyses were based on claims data of physician practices and psychotherapists in Germany. The data of 18- to 79-year-old patients with depression during 2016 were analysed. Methods and algorithms related to the network analysis were taken from mathematical graph theory. In addition, analyses were stratified by geographical areas (17 associations of statutory health insurance physicians). RESULTS: The analyses presented an opportunity to generate maps illustrating patient sharing networks within the 17 associations. The analyses demonstrated that general practitioners, psychiatrists and neurologists play a major role in the treatment of patients with depression. It was also shown that different cooperation and cost structures varied by geographical area. Complete-coverage networking of all physicians was shown in Schleswig-Holstein. By contrast Rhineland-Palatinate had four distinct areas. CONCLUSION: In the future, differences in healthcare processes and cooperation between physicians might become more visible through network analyses. This would create opportunities for cooperation and coordination between different practitioners of higher quality.
PMID: 30570671
Br J Health Psychol , 2019 Feb , V24 (1) : P215-236 doi: 10.1111/bjhp.12350
The centrality of health behaviours: A network analytic approach.
Faculty of Psychology, Philipps University of Marburg, Germany.; Coller School of Management, Recanati Business School, Tel Aviv University, Israel.; School of Psychological Sciences, Tel Aviv University, Israel.
OBJECTIVES: Since behavioural risk factors are the foremost causes of disability and premature mortality, developing new perspectives for understanding them is of utmost importance. This paper describes an innovative approach that conceptualizes health-related behaviours as nodes in a weighted network. DESIGN & METHODS: Using self-reported data from a representative sample (n = 374), a network of 37 health behaviours was analysed, with the aim of identifying 'central' nodes, that is, behaviours that are likely to co-occur with others and potentially influence them. RESULTS: In line with conservation of resources theory, the analysis indicated that behaviours related to basic physiological needs (nutrition and sleep) were most central. Behaviour centrality also varied across subpopulations: Periodic medical examinations, eating meals regularly, and sleep hygiene were more central among high- compared to low-socio-economic status participants; behaviours related to supportive social relationships and sun protection were more central among women compared to men. CONCLUSION: By emphasizing behavioural connectivity, the approach applied herein has identified core health behaviours with potentially high impact on healthy lifestyle behaviours. Statement of Contribution What is already known on this subject? Many health behaviours are related to each other. Engagement in one health behaviour can affect engagement in other behaviours. What does this study add? Health behaviour can be viewed and analysed as a network. Sleep and nutrition behaviours are the most central behaviours in the network. Centrality varies as a function of socio-economic status and gender.
PMID: 30549157
Res Social Adm Pharm , 2019 Feb , V15 (2) : P182-192 doi: 10.1016/j.sapharm.2018.04.010
Communication networks of medication management in an ambulatory care setting.
Drake University College of Pharmacy and Health Sciences, Fitch Hall, 2507 University Ave. Des Moines, IA, 50311, USA. Electronic address: andrea.kjos@drake.edu.; Drake University College of Pharmacy and Health Sciences, Cline Hall, 2507 University Ave. Des Moines, IA, 50311, USA. Electronic address: ginelle.bryant@drake.edu.
BACKGROUND: Systems approaches in healthcare address complexities of care related to medication safety. Adverse drug events can be prevented by communication between providers. Thus, methods that depict the structures and processes of communications are foundational for prevention efforts. Social network analysis is a methodology applied in healthcare settings to describe and quantify communication patterns. Knowledge of the structures and processes surrounding medication management communications will be useful to explain and intervene on related quality or safety outcomes. OBJECTIVES: The aim of this study was to use social network analysis as a tool to describe the communication structures and processes of medication management for patients on warfarin therapy in an ambulatory care setting. METHOD: A longitudinal, roster-based assessment was used for the social network analysis. Data were collected from electronic medical records and coded using a fixed-list format. Information was collected regarding who was involved as well as frequency and type of communications. The analysis followed 16 subjects at one internal medicine clinic over six months. RESULTS: Structurally, communications were unidirectional and most often connected actors from different groups. Most communications were directed from nursing staff to patients. Central actors were a pharmacist, several nursing staff and one prescriber. Difference in processes were identified by characterizing communications according to level of impact on patient safety. Moderate impact communications corresponded to focused connections between providers. Further, the pharmacist was measured as the most prominent gatekeeper in moderate impact communications compared to an advanced registered nurse practitioner for low impact communications. CONCLUSIONS: Medication management reflected a unidirectional and interdisciplinary communication structure that maintained process variation according to the potential impact on patient safety. The level of influence of the pharmacist as a connector in the network rose in conjunction with the level of potential impact the communication had on patient safety.
PMID: 29699776