Annu Rev Plant Biol , IF:19.54 , 2020 Apr , V71 : P303-326 doi: 10.1146/annurev-arplant-050718-100221
Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models.
Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA; email: tclark@bnl.gov, schwend@bnl.gov.; Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA; email: theobald1214@gmail.com, jamorgan@purdue.edu.
Mathematical modeling of plant metabolism enables the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In the many studies using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For (13)C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.
PMID: 32017600
J Pineal Res , IF:14.528 , 2020 Apr : Pe12659 doi: 10.1111/jpi.12659
Melatonin confers cadmium tolerance by modulating critical heavy metal chelators and transporters in radish plants.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing, China.; School of Agriculture and Environment, The UWA's Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.; College of Life Science, Nanjing Agricultural University, Nanjing, China.
Cadmium (Cd) is an environmental pollutant that causes health hazard to living organisms. Melatonin (MT) has emerged as a ubiquitous pleiotropic molecule capable of coordinating heavy metal (HM) stresses in plants. However, it remains unclear how melatonin mediates Cd homeostasis and detoxification at transcriptional and/or post-transcriptional levels in radish. Herein, the activities of five key antioxidant enzymes were increased, while root and shoot Cd contents were dramatically decreased by melatonin. A combined small RNA and transcriptome sequencing analysis showed that 14 differentially expressed microRNAs (DEMs) and 966 differentially expressed genes (DEGs) were shared between the Cd and Cd + MT conditions. In all, 23 and ten correlated miRNA-DEG pairs were identified in Con vs. Cd and Con vs. Cd + MT comparisons, respectively. Several DEGs encoding yellow stripe 1-like (YSL), heavy metal ATPases (HMA), and ATP-binding cassette (ABC) transporters were involved in Cd transportation and sequestration in radish. Root exposure to Cd(2+) induced several specific signaling molecules, which consequently trigger some HM chelators, transporters, and antioxidants to achieve reactive oxygen species (ROS) scavenging and detoxification and eliminate Cd toxicity in radish plants. Notably, transgenic analysis revealed that overexpression of the RsMT1 (Metallothionein 1) gene could enhance Cd tolerance of tobacco plants, indicating that the exogenous melatonin confers Cd tolerance, which might be attributable to melatonin-mediated upregulation of RsMT1 gene in radish plants. These results could contribute to dissecting the molecular basis governing melatonin-mediated Cd stress response in plants and pave the way for high-efficient genetically engineering low-Cd-content cultivars in radish breeding programs.
PMID: 32323337
Proc Natl Acad Sci U S A , IF:9.412 , 2020 Apr , V117 (14) : P8187-8195 doi: 10.1073/pnas.1913688117
ENO regulates tomato fruit size through the floral meristem development network.
Centro de Investigacion en Biotecnologia Agroalimentaria,Universidad de Almeria, 04120 Almeria, Spain.; Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.; Instituto de Biologia Molecular y Celular de Plantas, Universitat Politecnica de Valencia-Consejo Superior de Investigaciones Cientificas, 46022 Valencia, Spain.; Genome Research Group, Thunen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.; Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), AgroParisTech, CNRS, Universite Paris-Saclay, 78026 Versailles, France.; Centro de Investigacion en Biotecnologia Agroalimentaria,Universidad de Almeria, 04120 Almeria, Spain; rlozano@ual.es.
A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato (Solanum lycopersicum), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signaling pathway have led to a significant increase in fruit size generating enlarged meristems that lead to flowers with extra organs and bigger fruits. In this work, by combining mapping-by-sequencing and CRISPR/Cas9 genome editing methods, we isolated EXCESSIVE NUMBER OF FLORAL ORGANS (ENO), an AP2/ERF transcription factor which regulates floral meristem activity. Thus, the ENO gene mutation gives rise to plants that yield larger multilocular fruits due to an increased size of the floral meristem. Genetic analyses indicate that eno exhibits synergistic effects with mutations at the LOCULE NUMBER (encoding SlWUS) and FASCIATED (encoding SlCLV3) loci, two central players in the evolution of fruit size in the domestication of cultivated tomatoes. Our findings reveal that an eno mutation causes a substantial expansion of SlWUS expression domains in a flower-specific manner. In vitro binding results show that ENO is able to interact with the GGC-box cis-regulatory element within the SlWUS promoter region, suggesting that ENO directly regulates SlWUS expression domains to maintain floral stem-cell homeostasis. Furthermore, the study of natural allelic variation of the ENO locus proved that a cis-regulatory mutation in the promoter of ENO had been targeted by positive selection during the domestication process, setting up the background for significant increases in fruit locule number and fruit size in modern tomatoes.
PMID: 32179669
New Phytol , IF:8.512 , 2020 Apr doi: 10.1111/nph.16627
Gene regulatory network and its constituent transcription factors that control nitrogen-deficiency responses in rice.
Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.; Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.; Graduate School of Agricultural Science, Tohoku University, Aoba 468-1, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan.
Increase in the nitrogen (N)-use efficiency and optimization of N response in crop species are urgently needed. Although transcription factor-based genetic engineering is a promising approach for achieving these goals, transcription factors that play key roles in the response to N deficiency have not been studied extensively. Here, we performed RNA-seq analysis of root samples of 20 Asian rice (Oryza sativa) accessions with differential nutrient uptake. Data obtained from plants exposed to N-replete and N-deficient conditions were subjected to coexpression analysis and machine learning-based pathway inference to dissect the gene regulatory network required for the response to N deficiency. Four transcription factors, including members of the G2-like and bZIP families, were predicted to function as key regulators of gene transcription within the network in response to N deficiency. Cotransfection assays validated inferred novel regulatory pathways, and further analyses using genome-edited knockout lines suggested that these transcription factors are important for N-deficiency responses in planta. Many of the N deficiency-responsive genes, including those encoding key regulators within the network, were coordinately regulated by transcription factors belonging to different families. Transcription factors identified in this study could be valuable for the modification of N response and metabolism.
PMID: 32343414
BMC Med , IF:6.782 , 2020 Apr , V18 (1) : P99 doi: 10.1186/s12916-020-01558-1
Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis.
University of Groningen, University Medical Center Groningen, University Center Psychiatry (UCP) Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), Hanzeplein 1, 9713 GZ, Groningen, The Netherlands. j.burger@uva.nl.; University of Amsterdam, Institute for Advanced Study, Amsterdam, The Netherlands. j.burger@uva.nl.; University of Groningen, University Medical Center Groningen, University Center Psychiatry (UCP) Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.; Harvard University, Department of Psychiatry, Massachusetts General Hospital, .Cambridge, MA, USA.; University of Amsterdam, Institute for Advanced Study, Amsterdam, The Netherlands.
BACKGROUND: The past decades of research have seen an increase in statistical tools to explore the complex dynamics of mental health from patient data, yet the application of these tools in clinical practice remains uncommon. This is surprising, given that clinical reasoning, e.g., case conceptualizations, largely coincides with the dynamical system approach. We argue that the gap between statistical tools and clinical practice can partly be explained by the fact that current estimation techniques disregard theoretical and practical considerations relevant to psychotherapy. To address this issue, we propose that case conceptualizations should be formalized. We illustrate this approach by introducing a computational model of functional analysis, a framework commonly used by practitioners to formulate case conceptualizations and design patient-tailored treatment. METHODS: We outline the general approach of formalizing idiographic theories, drawing on the example of a functional analysis for a patient suffering from panic disorder. We specified the system using a series of differential equations and simulated different scenarios; first, we simulated data without intervening in the system to examine the effects of avoidant coping on the development of panic symptomatic. Second, we formalized two interventions commonly used in cognitive behavioral therapy (CBT; exposure and cognitive reappraisal) and subsequently simulated their effects on the system. RESULTS: The first simulation showed that the specified system could recover several aspects of the phenomenon (panic disorder), however, also showed some incongruency with the nature of panic attacks (e.g., rapid decreases were not observed). The second simulation study illustrated differential effects of CBT interventions for this patient. All tested interventions could decrease panic levels in the system. CONCLUSIONS: Formalizing idiographic theories is promising in bridging the gap between complexity science and clinical practice and can help foster more rigorous scientific practices in psychotherapy, through enhancing theory development. More precise case conceptualizations could potentially improve intervention planning and treatment outcomes. We discuss applications in psychotherapy and future directions, amongst others barriers for systematic theory evaluation and extending the framework to incorporate interactions between individual systems, relevant for modeling social learning processes. With this report, we hope to stimulate future efforts in formalizing clinical frameworks.
PMID: 32264914
Plant Cell Environ , IF:6.362 , 2020 Apr , V43 (4) : P1084-1101 doi: 10.1111/pce.13721
Plasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responses.
Noble Research Institute LLC, Ardmore, Oklahoma.; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.; Bredesen Center for Interdisciplinary Studies, University of Tennessee Knoxville, Knoxville, Tennessee.
Necrotrophic fungi constitute the largest group of plant fungal pathogens that cause heavy crop losses worldwide. Phymatotrichopsis omnivora is a broad host, soil-borne necrotrophic fungal pathogen that infects over 2,000 dicotyledonous plants. The molecular basis of such broad host range is unknown. We conducted cell biology and transcriptomic studies in Medicago truncatula (susceptible), Brachypodium distachyon (resistant/nonhost), and Arabidopsis thaliana (partially resistant) to understand P. omnivora virulence mechanisms. We performed defence gene analysis, gene enrichments, and correlational network studies during key infection stages. We identified that P. omnivora infects the susceptible plant as a traditional necrotroph. However, it infects the partially resistant plant as a hemi-biotroph triggering salicylic acid-mediated defence pathways in the plant. Further, the infection strategy in partially resistant plants is determined by the host responses during early infection stages. Mutant analyses in A. thaliana established the role of small peptides PEP1 and PEP2 in defence against P. omnivora. The resistant/nonhost B. distachyon triggered stress responses involving sugars and aromatic acids. Bdwat1 mutant analysis identified the role of cell walls in defence. This is the first report that describes the plasticity in infection strategies of P. omnivora providing insights into broad host range.
PMID: 31930733
Development , IF:5.611 , 2020 Apr , V147 (8) doi: 10.1242/dev.186130
Specification and regulation of vascular tissue identity in the Arabidopsis embryo.
Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands.; Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia.; Institute of Cytology and Genetics, Novosibirsk, 630090, Russia.; Institute of Biotechnology, HiLIFE/Organismal and Evolurionary Biology Research Programma, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland.; Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.; Max Planck Institute for Developmental Biology, Cell Biology, Tubingen, 72076, Germany.; Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands dolf.weijers@wur.nl.
Development of plant vascular tissues involves tissue identity specification, growth, pattern formation and cell-type differentiation. Although later developmental steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we found that vascular identity was specified in the 16-cell embryo. After a transient precursor state, however, there was no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We found that, although an AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP)-dependent auxin response was required, it was not sufficient for tissue specification. We therefore used a large-scale enhanced yeast one-hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of candidate regulators suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, can modulate vascular gene expression by tuning MP output through direct interaction. Our work uncovers components of a gene regulatory network that controls the initial specification of vascular tissue identity.
PMID: 32198154
Neuroimage Clin , IF:4.35 , 2020 Apr , V27 : P102264 doi: 10.1016/j.nicl.2020.102264
Functional brain network characteristics are associated with epilepsy severity in childhood absence epilepsy.
Department of Electrical Engineering, Eindhoven University of Technology, De Rondom 70, Eindhoven, Netherlands,; School for Mental Health and Neuroscience, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands.; School for Mental Health and Neuroscience, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Neurology, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Behavioral Sciences, Epilepsy Center Kempenhaeghe, Sterkselseweg 65, Heeze, Netherlands.; School for Mental Health and Neuroscience, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands.; Department of Electrical Engineering, Eindhoven University of Technology, De Rondom 70, Eindhoven, Netherlands,; Department of Neurology, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Behavioral Sciences, Epilepsy Center Kempenhaeghe, Sterkselseweg 65, Heeze, Netherlands.; School for Mental Health and Neuroscience, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Neurology, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands.; Department of Behavioral Sciences, Epilepsy Center Kempenhaeghe, Sterkselseweg 65, Heeze, Netherlands.; Department of Electrical Engineering, Eindhoven University of Technology, De Rondom 70, Eindhoven, Netherlands,; School for Mental Health and Neuroscience, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands; Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, Netherlands. Electronic address: jacobus.jansen@mumc.nl.
While cognitive impairments are not generally considered to be part of the childhood absence epilepsy (CAE) syndrome, some recent studies report cognitive, mainly attentional, deficits. Here we set out to investigate the whole brain functional network of children with CAE and controls. Furthermore, the possible relation of the functional network abnormalities with epilepsy and neurocognitive characteristics is studied. Seventeen children with childhood CAE (aged 9.2+/-2.1 years) and 15 controls (aged 9.8+/-1.8 years) were included. Resting state functional MRI was acquired to study the functional network. Using graph theoretical analysis, three global metrics of the functional network were investigated: the characteristic path length, the clustering coefficient, and the small-worldness. A multivariable linear regression model including age, sex, and subject motion as covariates was used to investigate group differences in the graph metrics. Subsequently, relations of the graph metrics with epilepsy and neurocognitive characteristics were assessed. Longer path lengths, weaker clustering and a lower small-world network topology were observed in children with CAE compared to controls. Moreover, longer path lengths were related to a longer duration of CAE and a higher number of absence seizure per hour. Clustering and small-worldness were not significantly related to epilepsy or neurocognitive characteristics. The organization of the functional network of children with CAE is less efficient compared to controls, and is related to disease duration. These preliminary findings suggest that CAE is associated with alterations in the functional network.
PMID: 32387851
Mol Plant Pathol , IF:4.326 , 2020 Apr , V21 (4) : P527-540 doi: 10.1111/mpp.12914
Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae.
Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore.; Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea.; School of Chemical Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
Xanthomonas oryzae pv. oryzae (Xoo) is a vascular pathogen that causes leaf blight in rice, leading to severe yield losses. Since the usage of chemical control methods has not been very promising for the future disease management, it is of high importance to systematically gain new insights about Xoo virulence and pathogenesis, and devise effective strategies to combat the rice disease. To do this, we reconstructed a genome-scale metabolic model of Xoo (iXOO673) and validated the model predictions using culture experiments. Comparison of the metabolic architecture of Xoo and other plant pathogens indicated that the Entner-Doudoroff pathway is a more common feature in these bacteria than previously thought, while suggesting some of the unique virulence mechanisms related to Xoo metabolism. Subsequent constraint-based flux analysis allowed us to show that Xoo modulates fluxes through gluconeogenesis, glycogen biosynthesis, and degradation pathways, thereby exacerbating the leaf blight in rice exposed to nitrogenous fertilizers, which is remarkably consistent with published experimental literature. Moreover, model-based interrogation of transcriptomic data revealed the metabolic components under the diffusible signal factor regulon that are crucial for virulence and survival in Xoo. Finally, we identified promising antibacterial targets for the control of leaf blight in rice by using gene essentiality analysis.
PMID: 32068953
Cogn Neurodyn , IF:3.925 , 2020 Apr , V14 (2) : P215-228 doi: 10.1007/s11571-019-09562-9
The dynamic properties of a brain network during working memory based on the algorithm of cross-frequency coupling.
State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300130 China.grid.412030.40000 0000 9226 1013
Working memory (WM) refers to a memory system with limited energy for short-term maintenance and plays an important role in cognitive functions. At present, research regarding WM mostly focuses on the coordination between neural signals in the signal microelectrode channel. However, how neural signals coordinate the coding of WM at the network level is rarely studied. Cross-frequency coupling (CFC) reflects the coordinated effect between different frequency components (e.g., theta and gamma) of local field potentials (LFPs) during WM. In this study, we try to map the changes that occur in the brain networks during WM at the level of CFC between theta-gamma of LFPs. First, a 16-channel brain network by using the CFC between theta-gamma of LFPs during WM was constructed. Then, the dynamic properties of the brain network during WM were analyzed based on graph theory. Experimental results show that the LFPs power increased at the WM state than at resting stat, but decreased across learning; the CFC between theta-gamma increased with learning days and phase-amplitude coupling (PAC) in the WM state was higher than that in free choice state and rest state; the changes of average degree, average shortest path length and global efficiency had significant difference on learning days. We can indicate that the CFC between theta-gamma in the network plays an important role in the WM formation. Furthermore, correct storage of WM information will not change local information transmission and the small-world attribute, while, it can increase the network connection and efficiency of information transmission.
PMID: 32226563
J Ethnopharmacol , IF:3.69 , 2020 Apr , V251 : P112415 doi: 10.1016/j.jep.2019.112415
Medicinal plants for gastrointestinal diseases among the Kuki-Chin ethnolinguistic groups across Bangladesh, India, and Myanmar: A comparative and network analysis study.
Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea.; Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea. Electronic address: ydkim@hallym.ac.kr.
ETHNOPHARMACOLOGICAL RELEVANCE: The Kuki-Chin is a composite ethnolinguistic group made up of many distinct groups and subgroups that are linked by a common history, culture, and population distribution in the Kuki-Chin region, shared geopolitically by Bangladesh, India, and Myanmar. This region is shown to be in a hotspot of digestive disease activity based on official reports and in concordance with data from related ethnopharmacological field surveys. Our work provides a comparative analysis of medicinal plant knowledge for the treatment of gastrointestinal diseases (GAS-Ds) among the Kuki-Chin ethnic groups found across the three countries. AIM OF THE STUDY: The objectives were (1) to identify the medicinal plants and herbal therapies for the treatment of GAS-Ds reported in related Kuki-Chin ethnobotanical publications, (2) to find the similarities and differences in medicinal plant knowledge among the country-affiliated groups by comparing plant and disease information, and (3) to determine significant plant taxa and their pattern(s) of use as digestive disease herbal remedies by analyzing disease-plant networks. MATERIALS AND METHODS: Secondary data were gathered from 34 related studies through internet search of ethnobotanical information from field studies published in journals, reports, books, and dissertations/theses. These data represented 22 Kuki-Chin ethnolinguistic groups inhabiting 23 districts across six states comprising the Kuki-Chin region: the Chittagong Division (Bangladesh); Mizoram, Assam, Manipur, and Tripura States (India); and Chin State (Myanmar). Scientific names of plants and digestive diseases collated from secondary sources were validated and standardized following the Plant List and the International Classification of Primary Care Second Edition, respectively. RESULTS AND DISCUSSION: A total of 482 species in 330 genera and 118 families of vascular plants were recorded for the treatment of 29 standardized GAS-Ds. On the basis of the number of use-reports, regional native species Phyllanthus emblica, Centella asiatica, and Aegle marmelos, as well as the non-natives Carica papaya, Portulaca oleracea, and Psidium guajava were found to be the most preferred. Comparative analysis of medicinal species showed that groups in India revealed the highest number of medicinal plant taxa, followed by those in Bangladesh and Myanmar. The most prevalent GAS-Ds were shown to be abdominal pain epigastric, gastroenteritis presumed infections, and diarrhoea, as supported by the number of use-reports and medicinal taxa used for their treatment, and their informant consensus factor values. Analyses of disease-plant networks graphically showed both GAS-Ds distribution patterns in the region and potential medicinal plant (group) candidates for further studies. CONCLUSION: Overall, this study revealed an astonishingly rich diversity of medicinal plants used to treat digestive diseases among the Kuki-Chin. A comparative analysis showed variations and remarkable distinctions in medicinal plant knowledge among country-affiliated groups, as likely influenced by external sociocultural factors and geopolitical barriers, as well as the availability of ethnobotanical data. The use of network analysis reflected not only shared common affinities and patterns of plant use based on the taxonomic composition and species selection, but also disease prevalence and distribution patterns. The information found here can hopefully spur interest among future researchers and policy makers to better improve both the (ethno) medicinal research capacity and healthcare system in the region.
PMID: 31917280
Am J Bot , IF:3.038 , 2020 Apr , V107 (4) : P628-638 doi: 10.1002/ajb2.1451
Trait integration and functional differentiation among co-existing plant species.
Department of Sustainable Resources Management, State University of New York College of Environmental Sciences and Forestry, 320 Bray Hall, 1 Forestry Dr., Syracuse, NY, 13210, USA.; U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA.; U.S. Environmental Protection Agency, Western Ecology Division, 200 SW 35th, Corvallis, OR, 97331, USA.; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR, 97331, USA.
PREMISE: Determining which traits characterize strategies of coexisting species is important to developing trait-based models of plant communities. First, global dimensions may not exist locally. Second, the degree to which traits and trait spectra constitute independent dimensions of functional variation at various scales continues to be refined. Finally, traits may be associated with existing categorical groupings. METHODS: We assessed trait integration and differentiation across 57 forest understory plant species in Douglas-fir forests of western Oregon, United States. We combined measurements for a range of traits with literature-based estimates of seed mass and species groupings. We used network analysis and nonmetric multidimensional scaling ordination (NMS) to determine the degree of integration. RESULTS: We observed a strong leaf economics spectrum (LES) integrated with stem but not root traits. However, stem traits and intrinsic water-use efficiency integrated LES and root traits. Network analyses indicated a modest grouping of a priori trait dimensions. NMS indicated that multivariate differences among species were related primarily to (1) rooting depth and plant height vs. specific root length, (2) the LES, and (3) leaf size vs. seed mass. These differences were related to species groupings associated with growth and life form, leaf lifespan and seed dispersal mechanisms. CONCLUSIONS: The strategies of coexisting understory plant species could not be reduced to a single dimension. Yet, species can be characterized efficiently and effectively for trait-based studies of plant communities by measuring four common traits: plant height, specific leaf area, leaf size, and seed mass.
PMID: 32236958
Dev Biol , IF:2.895 , 2020 Apr , V460 (1) : P32-39 doi: 10.1016/j.ydbio.2018.10.024
Of mice and plants: Comparative developmental systems biology.
Computational Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, the Netherlands. Electronic address: k.h.w.j.tentusscher@uu.nl.
Multicellular animals and plants represent independent evolutionary experiments with complex multicellular bodyplans. Differences in their life history, a mobile versus sessile lifestyle, and predominant embryonic versus postembryonic development, have led to the evolution of highly different body plans. However, also many intriguing parallels exist. Extension of the vertebrate body axis and its segmentation into somites bears striking resemblance to plant root growth and the concomittant prepatterning of lateral root competent sites. Likewise, plant shoot phyllotaxis displays similarities with vertebrate limb and digit patterning. Additionally, both plants and animals use complex signalling systems combining systemic and local signals to fine tune and coordinate organ growth across their body. Identification of these striking examples of convergent evolution provides support for the existence of general design principles: the idea that for particular patterning demands, evolution is likely to arrive at highly similar developmental patterning mechanisms. Furthermore, focussing on these parallels may aid in identifying core mechanistic principles, often obscured by the highly complex nature of multiscale patterning processes.
PMID: 30395805
Comput Biol Chem , IF:1.85 , 2020 Apr , V85 : P107188 doi: 10.1016/j.compbiolchem.2019.107188
Comparative analysis of salt responsive gene regulatory networks in rice and Arabidopsis.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address: huangji@njau.edu.cn.
By using the available expression datasets of mRNAs and small RNAs, we constructed and compared the salt-responsive gene regulatory networks (GRNs) involving both transcriptional and post-transcriptional regulations between model plants rice and Arabidopsis. The salt-responsive GRNs involve the transcription factors (TFs), microRNAs (miRNAs) and their target genes. Here we describe 552 miRNA-target interactions (MTIs), 95 up-regulated TF-target interactions (TTIs) and 56 down-regulated TTIs in rice, while 332 MTIs, 138 up-regulated and 4 down-regulated TTIs in Arabidopsis. Interestingly, we observed the networks in rice are more complicated where target genes were enriched in rice development and growth, while more stress-related genes were detected in Arabidopsis networks. With the construction and comparison of GRNs between rice and Arabidopsis in response to salt stress, we can basically describe the differences of salt responsive mechanisms in two species: rice tends to respond slower and chooses to manipulate its development and growth to avoid salt stress, while Arabidopsis prefers to trigger a serious salt-defending genes to protect itself from stress. Our work provides the foundation for further exploring the molecular basis of plant salt response and the potential breeding practice by engineering the critical components in the networks in improving plant salt tolerance.
PMID: 31954202
Future Gener Comput Syst , 2020 Apr doi: 10.1016/j.future.2020.04.004
A network-based method with privacy-preserving for identifying influential providers in large healthcare service systems.
School of Engineering and Technology, China University of Geosciences (Beijing), China.; Department of Mathematics and Applications, University of Naples Federico II, Italy.
In data science, networks provide a useful abstraction of the structure of many complex systems, ranging from social systems and computer networks to biological networks and physical systems. Healthcare service systems are one of the main social systems that can also be understood using network-based approaches, for example, to identify and evaluate influential providers. In this paper, we propose a network-based method with privacy-preserving for identifying influential providers in large healthcare service systems. First, the provider-interacting network is constructed by employing publicly available information on locations and types of healthcare services of providers. Second, the ranking of nodes in the generated provider-interacting network is conducted in parallel on the basis of four nodal influence metrics. Third, the impact of the top-ranked influential nodes in the provider-interacting network is evaluated using three indicators. Compared with other research work based on patient-sharing networks, in this paper, the provider-interacting network of healthcare service providers can be roughly created according to the locations and the publicly available types of healthcare services, without the need for personally private electronic medical claims, thus protecting the privacy of patients. The proposed method is demonstrated by employing Physician and Other Supplier Data CY 2017, and can be applied to other similar datasets to help make decisions for the optimization of healthcare resources in the response to public health emergencies.
PMID: 32296253
Proc Math Phys Eng Sci , 2020 Apr , V476 (2236) : P20190724 doi: 10.1098/rspa.2019.0724
A framework for second-order eigenvector centralities and clustering coefficients.
Department of Mathematics and Statistics, University of Strathclyde, Glasgow G1 1XH, UK.; School of Mathematics, University of Edinburgh, Edinburgh EH9 3FD, UK.; School of Mathematics, Gran Sasso Science Institute, 67100 L'Aquila, Italy.
We propose and analyse a general tensor-based framework for incorporating second-order features into network measures. This approach allows us to combine traditional pairwise links with information that records whether triples of nodes are involved in wedges or triangles. Our treatment covers classical spectral methods and recently proposed cases from the literature, but we also identify many interesting extensions. In particular, we define a mutually reinforcing (spectral) version of the classical clustering coefficient. The underlying object of study is a constrained nonlinear eigenvalue problem associated with a cubic tensor. Using recent results from nonlinear Perron-Frobenius theory, we establish existence and uniqueness under appropriate conditions, and show that the new spectral measures can be computed efficiently with a nonlinear power method. To illustrate the added value of the new formulation, we analyse the measures on a class of synthetic networks. We also give computational results on centrality and link prediction for real-world networks.
PMID: 32398932
J Clin Psychol , 2020 Apr , V76 (4) : P787-800 doi: 10.1002/jclp.22916
A network analysis of borderline personality disorder symptoms and disordered eating.
Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia.; School of Psychology, Deakin University, Geelong, Victoria, Australia.; Centre for Social and Early Emotional Development, Deakin University, Burwood, Victoria, Australia.; Eating Disorders Program, The Melbourne Clinic, Richmond, Victoria, Australia.
OBJECTIVE: The current study used network analysis to explore associations between specific groupings of borderline personality disorder (BPD) and eating disorder (ED) symptoms, and other transdiagnostic variables including insecure attachment, rejection sensitivity, emotion dysregulation, a theory of mind, and emotion recognition. METHOD: Network analysis was undertaken on self-report data from 753 adults (81.5% women), of whom 109 reported a lifetime ED diagnosis. RESULTS: Comorbidity between BPD and ED symptoms was only partially conceptualized through the transdiagnostic variables. The centrality indices from the network analysis indicated that emotion dysregulation and abandonment were the most central elements in the network. Conversely, the theory of mind and emotion recognition had very few connections with the other transdiagnostic variables in the network. DISCUSSION: The findings provide empirical insight into the nature of the observed co-occurrence between BPD and ED symptoms and serve to improve clinical decision-making regarding psychological interventions for both problem sets.
PMID: 31953849
Biophys Rev , 2020 Apr , V12 (2) : P377-384 doi: 10.1007/s12551-020-00665-w
Application of information theory in systems biology.
Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan. uda@bioreg.kyushu-u.ac.jp.
Over recent years, new light has been shed on aspects of information processing in cells. The quantification of information, as described by Shannon's information theory, is a basic and powerful tool that can be applied to various fields, such as communication, statistics, and computer science, as well as to information processing within cells. It has also been used to infer the network structure of molecular species. However, the difficulty of obtaining sufficient sample sizes and the computational burden associated with the high-dimensional data often encountered in biology can result in bottlenecks in the application of information theory to systems biology. This article provides an overview of the application of information theory to systems biology, discussing the associated bottlenecks and reviewing recent work.
PMID: 32144740