Multiplex Decomposition of Non-Markovian Dynamics and the Hidden Layer Reconstruction Problem

Elements composing complex systems usually interact in several different ways and as such the interaction architecture is well modelled by a multiplex network. However often this architecture is hidden, as one usually only has experimental access to an aggregated projection. A fundamental challenge is thus to determine whether the hidden underlying architecture of complex systems is better modelled as a single interaction layer or results from the aggregation and interplay of multiple layers. Here we show that using local information provided by a random walker navigating the aggregated network one can decide in a robust way if the underlying structure is a multiplex or not and, in the former case, to determine the most probable number of hidden layers. As a byproduct, we show that the mathematical formalism also provides a principled solution for the optimal decomposition and projection of complex, non-Markovian dynamics into a Markov switching combination of diffusive modes. We validate the proposed methodology with numerical simulations of both (i) random walks navigating hidden multiplex networks (thereby reconstructing the true hidden architecture) and (ii) Markovian and non-Markovian continuous stochastic processes (thereby reconstructing an effective multiplex decomposition where each layer accounts for a different diffusive mode). We also state and prove two existence theorems guaranteeing that an exact reconstruction of the dynamics in terms of these hidden jump-Markov models is always possible for arbitrary finite-order Markovian and fully non-Markovian processes. Finally, we showcase the applicability of the method to experimental recordings from (i) the mobility dynamics of human players in an online multiplayer game and (ii) the dynamics of RNA polymerases at the single-molecule level.Comment: 40 pages, 24 figure

Genetic Markers in Long-Term Survivors of Glioblastoma Multiforme

Scope: Genistein from foods or supplements is metabolized by the gut microbiota and the human body, thereby releasingmany different metabolites into systemic circulation. The order of their appearance in plasma and the possible influence of food format are still unknown. This study compared the nutrikinetic profiles of genistein metabolites. Methods and results: In a randomized cross-over trial, 12 healthy young volunteers were administered a single dose of 30mggenistein provided as a genistein tablet, a genistein tablet in low fat milk, and soy milk containing genistein glycosides. A high mass resolution LC-LTQ-Orbitrap FTMS platform detected and quantified in human plasma: free genistein, seven of its phase-II metabolites and 15 gut-derived metabolites. Interestingly, a novel metabolite, genistein-4- glucuronide-7-sulfate (G-4 G7S) was identified. Nutrikinetic analysis using population-based modeling revealed the order of appearance of five genistein phase II metabolites in plasma: (1) genistein-4,7-diglucuronide, (2) genistein-7-sulfate, (3) genistein-4--sulfate-7-glucuronide, (4) genistein-4-glucuronide, and (5) genistein-7-glucuronide, independent of the food matrix. Conclusion: The conjugated genistein metabolites appear in a distinct order in human plasma. The specific early appearance of G-4 ,7-diG suggests a multistep formation process for the mono and hetero genistein conjugates, involving one or two deglucuronidation steps

The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics

Flavonoids are secondary metabolites present in all terrestrial plants. The flavonoid pathway has been extensively studied, and many of the involved genes and metabolites have been described in the literature. Despite this extensive knowledge, the functioning of the pathway in vivo is still poorly understood. Here, we study the flavonoid pathway using both experiments and mathematical models. We measured flavonoid metabolite dynamics in two tissues, hypocotyls and cotyledons, during tomato seedling development. Interestingly, the same backbone of interactions leads to very different accumulation patterns in the different tissues. Initially, we developed a mathematical model with constant enzyme concentrations that described the metabolic networks separately in both tissues. This model was unable to fit the measured flavonoid dynamics in the hypocotyls, even if we allowed unrealistic parameter values. This suggested us to investigate the effect of transcript abundance on flavonoid accumulation. We found that the expression of candidate flavonoid genes varies considerably with time. Variation in transcript abundance results in enzymatic variation, which could have a large effect on metabolite accumulation. Candidate transcript abundance was included in the mathematical model as representative for enzyme concentration. We fitted the resulting model to the flavonoid dynamics in the cotyledons, and tested it by applying it to the data from hypocotyls. When transcript abundance is included, we are indeed able to explain flavonoid dynamics in both tissues. Importantly, this is possible under the biologically relevant restriction that the enzymatic properties estimated by the model are conserved between the tissues

Effects of Triazole Derivatives on Strigolactone Levels and Growth Retardation in Rice

We previously discovered a lead compound for strigolactone (SL) biosynthesis inhibitors, TIS13 (2,2-dimethyl-7-phenoxy-4-(1H-1,2,4-triazol-1-yl)heptan-3-ol). Here, we carried out a structure-activity relationship study of TIS13 to discover more potent and specific SL biosynthesis inhibitor because TIS13 has a severe side effect at high concentrations, including retardation of the growth of rice seedlings. TIS108, a new TIS13 derivative, was found to be a more specific SL biosynthesis inhibitor than TIS13. Treatment of rice seedlings with TIS108 reduced SL levels in both roots and root exudates in a concentration-dependent manner and did not reduce plant height. In addition, root exudates of TIS108-treated rice seedlings stimulated Striga germination less than those of control plants. These results suggest that TIS108 has a potential to be applied in the control of root parasitic weeds germination

Genetic variation in strigolactone production and tillering in rice and its effect on Striga hermonthica infection

Tillering in cereals is a complex process in the regulation of which also signals from the roots in the form of strigolactones play an important role. The strigolactones are signalling molecules that are secreted into the rhizosphere where they act as germination stimulants for root parasitic plants and hyphal branching factors for arbuscular mycorrhizal fungi. On the other hand, they are also transported from the roots to the shoot where they inhibit tillering or branching. In the present study, the genetic variation in strigolactone production and tillering phenotype was studied in twenty rice varieties collected from all over the world and correlated with S. hermonthica infection. Rice cultivars like IAC 165, IAC 1246, Gangweondo and Kinko produced high amounts of the strigolactones orobanchol, 2′-epi-5-deoxystrigol and three methoxy-5-deoxystrigol isomers and displayed low amounts of tillers. These varieties induced high S. hermonthica germination, attachment, emergence as well as dry biomass. In contrast, rice cultivars such as Super Basmati, TN 1, Anakila and Agee displayed high tillering in combination with low production of the aforementioned strigolactones. These varieties induced only low S. hermonthica germination, attachment, emergence and dry biomass. Statistical analysis across all the varieties confirmed a positive correlation between strigolactone production and S. hermonthica infection and a negative relationship with tillering. These results show that genetic variation in tillering capacity is the result of genetic variation in strigolactone production and hence could be a helpful tool in selecting rice cultivars that are less susceptible to S. hermonthica infection

Influence of gestational age at initiation of antihypertensive therapy: secondary analysis of CHIPS trial data (control of hypertension in pregnancy study)

For hypertensive women in CHIPS (Control of Hypertension in Pregnancy Study), we assessed whether the maternal benefits of tight control could be achieved, while minimizing any potentially negative effect on fetal growth, by delaying initiation of antihypertensive therapy until later in pregnancy. For the 981 women with nonsevere, chronic or gestational hypertension randomized to less-tight (target diastolic blood pressure, 100 mm Hg), or tight (target, 85 mm Hg) control, we used mixed-effects logistic regression to examine whether the effect of less-tight (versus tight) control on major outcomes was dependent on gestational age at randomization, adjusting for baseline factors as in the primary analysis and including an interaction term between gestational age at randomization and treatment allocation. Gestational age was considered categorically (quartiles) and continuously (linear or quadratic form), and the optimal functional form selected to provide the best fit to the data based on the Akaike information criterion. Randomization before (but not after) 24 weeks to less-tight (versus tight) control was associated with fewer babies with birth weight 48 hours (Pinteraction=0.354). For the mother, less-tight (versus tight) control was associated with more severe hypertension at all gestational ages but particularly so before 28 weeks (Pinteraction=0.076). In women with nonsevere, chronic, or gestational hypertension, there seems to be no gestational age at which less-tight (versus tight) control is the preferred management strategy to optimize maternal or perinatal outcomes

Rice APC/CTE controls tillering by mediating the degradation of MONOCULM 1

Rice MONOCULM 1 (MOC1) and its orthologues LS/LAS (lateral suppressor in tomato and Arabidopsis) are key promoting factors of shoot branching and tillering in higher plants. However, the molecular mechanisms regulating MOC1/LS/LAS have remained elusive. Here we show that the rice tiller enhancer (te) mutant displays a drastically increased tiller number. We demonstrate that TE encodes a rice homologue of Cdh1, and that TE acts as an activator of the anaphase promoting complex/cyclosome (APC/C) complex. We show that TE coexpresses with MOC1 in the axil of leaves, where the APC/CTE complex mediates the degradation of MOC1 by the ubiquitin–26S proteasome pathway, and consequently downregulates the expression of the meristem identity gene Oryza sativa homeobox 1, thus repressing axillary meristem initiation and formation. We conclude that besides having a conserved role in regulating cell cycle, APC/CTE has a unique function in regulating the plant-specific postembryonic shoot branching and tillering, which are major determinants of plant architecture and grain yield

How do nitrogen and phosphorus deficiencies affect strigolactone production and exudation?

Plants exude strigolactones (SLs) to attract symbiotic arbuscular mycorrhizal fungi in the rhizosphere. Previous studies have demonstrated that phosphorus (P) deficiency, but not nitrogen (N) deficiency, significantly promotes SL exudation in red clover, while in sorghum not only P deficiency but also N deficiency enhances SL exudation. There are differences between plant species in SL exudation under P- and N-deficient conditions, which may possibly be related to differences between legumes and non-legumes. To investigate this possibility in detail, the effects of N and P deficiencies on SL exudation were examined in Fabaceae (alfalfa and Chinese milk vetch), Asteraceae (marigold and lettuce), Solanaceae (tomato), and Poaceae (wheat) plants. In alfalfa as expected, and unexpectedly in tomato, only P deficiency promoted SL exudation. In contrast, in Chinese milk vetch, a leguminous plant, and in the other non-leguminous plants examined, N deficiency as well as P deficiency enhanced SL exudation. Distinct reductions in shoot P levels were observed in plants grown under N deficiency, except for tomato, in which shoot P level was increased by N starvation, suggesting that the P status of the shoot regulates SL exudation. There seems to be a correlation between shoot P levels and SL exudation across the species/families investigated

Over-expression of the IGI1 leading to altered shoot-branching development related to MAX pathway in Arabidopsis

Shoot branching and growth are controlled by phytohormones such as auxin and other components in Arabidopsis. We identified a mutant (igi1) showing decreased height and bunchy branching patterns. The phenotypes reverted to the wild type in response to RNA interference with the IGI1 gene. Histochemical analysis by GUS assay revealed tissue-specific gene expression in the anther and showed that the expression levels of the IGI1 gene in apical parts, including flowers, were higher than in other parts of the plants. The auxin biosynthesis component gene, CYP79B2, was up-regulated in igi1 mutants and the IGI1 gene was down-regulated by IAA treatment. These results indicated that there is an interplay regulation between IGI1 and phytohormone auxin. Moreover, the expression of the auxin-related shoot branching regulation genes, MAX3 and MAX4, was down-regulated in igi1 mutants. Taken together, these results indicate that the overexpression of the IGI1 influenced MAX pathway in the shoot branching regulation