Social interactions dominate speed control in driving natural flocks toward criticality

Flocks of birds exhibit a remarkable degree of coordination and collective response. It is not just that thousands of individuals fly, on average, in the same direction and at the same speed, but that even the fluctuations around the mean velocity are correlated over long distances. Quantitative measurements on flocks of starlings, in particular, show that these fluctuations are scale-free, with effective correlation lengths proportional to the linear size of the flock. Here we construct models for the joint distribution of velocities in the flock that reproduce the observed local correlations between individuals and their neighbors, as well as the variance of flight speeds across individuals, but otherwise have as little structure as possible. These minimally structured, or maximum entropy models provide quantitative, parameter-free predictions for the spread of correlations throughout the flock, and these are in excellent agreement with the data. These models are mathematically equivalent to statistical physics models for ordering in magnets, and the correct prediction of scale-free correlations arises because the parameters - completely determined by the data - are in the critical regime. In biological terms, criticality allows the flock to achieve maximal correlation across long distances with limited speed fluctuations

Dynamical maximum entropy approach to flocking

Peer reviewedPublisher PD

A Renormalization Group Approach to Connect Discrete- and Continuous-Time Descriptions of Gaussian Processes

Discretization of continuous stochastic processes is needed to numerically simulate them or to infer models from experimental time series. However, depending on the nature of the process, the same discretization scheme, if not accurate enough, may perform very differently for the two tasks. Exact discretizations, which work equally well at any scale, are characterized by the property of invariance under coarse-graining. Motivated by this observation, we build an explicit Renormalization Group approach for Gaussian time series generated by auto-regressive models. We show that the RG fixed points correspond to discretizations of linear SDEs, and only come in the form of first order Markov processes or non-Markovian ones. This fact provides an alternative explanation of why standard delay-vector embedding procedures fail in reconstructing partially observed noise-driven systems. We also suggest a possible effective Markovian discretization for the inference of partially observed underdamped equilibrium processes based on the exploitation of the Einstein relation.Comment: 13 pages, 3 figures, 1 tabl

Building general Langevin models from discrete data sets

Many living and complex systems exhibit second order emergent dynamics. Limited experimental access to the configurational degrees of freedom results in data that appears to be generated by a non-Markovian process. This poses a challenge in the quantitative reconstruction of the model from experimental data, even in the simple case of equilibrium Langevin dynamics of Hamiltonian systems. We develop a novel Bayesian inference approach to learn the parameters of such stochastic effective models from discrete finite length trajectories. We first discuss the failure of naive inference approaches based on the estimation of derivatives through finite differences, regardless of the time resolution and the length of the sampled trajectories. We then derive, adopting higher order discretization schemes, maximum likelihood estimators for the model parameters that provide excellent results even with moderately long trajectories. We apply our method to second order models of collective motion and show that our results also hold in the presence of interactions.Comment: we correct previous inaccuracy about a reference; 29 pages, 9 figure

Flocking and turning: a new model for self-organized collective motion

Birds in a flock move in a correlated way, resulting in large polarization of velocities. A good understanding of this collective behavior exists for linear motion of the flock. Yet observing actual birds, the center of mass of the group often turns giving rise to more complicated dynamics, still keeping strong polarization of the flock. Here we propose novel dynamical equations for the collective motion of polarized animal groups that account for correlated turning including solely social forces. We exploit rotational symmetries and conservation laws of the problem to formulate a theory in terms of generalized coordinates of motion for the velocity directions akin to a Hamiltonian formulation for rotations. We explicitly derive the correspondence between this formulation and the dynamics of the individual velocities, thus obtaining a new model of collective motion. In the appropriate overdamped limit we recover the well-known Vicsek model, which dissipates rotational information and does not allow for polarized turns. Although the new model has its most vivid success in describing turning groups, its dynamics is intrinsically different from previous ones in a wide dynamical regime, while reducing to the hydrodynamic description of Toner and Tu at very large length-scales. The derived framework is therefore general and it may describe the collective motion of any strongly polarized active matter system.Comment: Accepted for the Special Issue of the Journal of Statistical Physics: Collective Behavior in Biological Systems, 17 pages, 4 figures, 3 video

GH10 xylanase D from Penicillium funiculosum: biochemical studies and xylooligosaccharide production

<p>Abstract</p> <p>Background</p> <p>The filamentous fungus <it>Penicillium funiculosum </it>produces a range of glycoside hydrolases (GH). The <it>XynD </it>gene, encoding the sole <it>P. funiculosum </it>GH10 xylanase described so far, was cloned into the pPICZαA vector and expressed in methylotrophe yeast <it>Pichia pastoris</it>, in order to compare the results obtained with the <it>P. funiculosum </it>GH11 xylanases data.</p> <p>Results</p> <p>High level expression of recombinant XynD was obtained with a secretion of around 60 mg.L^-1. The protein was purified to homogeneity using one purification step. The apparent size on SDS-PAGE was around 64 kDa and was 46 kDa by mass spectrometry thus higher than the expected molecular mass of 41 kDa. The recombinant protein was N- and O-glycosylated, as demonstrated using glycoprotein staining and deglycosylation reactions, which explained the discrepancy in molecular mass. Enzyme-catalysed hydrolysis of low viscosity arabinoxylan (LVAX) was maximal at pH 5.0 with <it>K</it>m_(app)and <it>k_cat</it>/<it>K</it>m_(app)of 3.7 ± 0.2 (mg.mL^-1) and 132 (s^-1mg^-1.mL), respectively. The activity of XynD was optimal at 80°C and the recombinant enzyme has shown an interesting high thermal stability at 70°C for at least 180 min without loss of activity. The enzyme had an endo-mode of action on xylan forming mainly xylobiose and short-chain xylooligosaccharides (XOS). The initial rate data from the hydrolysis of short XOS indicated that the catalytic efficiency increased slightly with increasing their chain length with a small difference of the XynD catalytic efficiency against the different XOS.</p> <p>Conclusion</p> <p>Because of its attractive properties XynD might be considered for biotechnological applications. Moreover, XOS hydrolysis suggested that XynD possess four catalytic subsites with a high energy of interaction with the substrate and a fifth subsite with a small energy of interaction, according to the GH10 xylanase literature data.</p

Reinforcing and broadening resistance against Fusarium diseases in durum wheat by an udp-glucosyltransferase transgene and its pyramiding with a pectin methyl esterase inhibitor transgene

Many species of the genus Fusarium are phytopathogenic fungi of a wide range of cereal crop plants, including wheat. F. graminearum is the main causal agent of Fusarium Head Blight (FHB), while F. culmorum and F. pseudograminearum are the main responsible species of Fusarium Crown Rot (FCR). Fusarium diseases represent major agricultural problems worldwide, causing reduction of grain yield, grain quality and food safety. The latter is associated with contamination of grains with mycotoxins, particularly deoxynivalenol (DON), which cause health problems in humans and animals. DON is a protein synthesis inhibitor, acting as a virulence factor during pathogenesis and resulting essential for fungal spread along the spike. Conversion of DON to deoxynivalenol-3-\u3b2-D-glucoside (D3G) by the activity of specific UDP-glucosyltransferases (UGTs), is one of the mechanisms involved in enhancing plant tolerance to DON. Previous studies demonstrated that the expression of the barley HvUGT13248 gene confers resistance to DON in Arabidopsis thaliana (Shin et al. 2012, J Exp Bot. 63:4731-40) and type II resistance to FHB (i.e. resistance to fungal spread within host tissues) in bread wheat (Li et al. 2015, MPMI 28:1237-46). Improvement of FHB resistance is a major target in both bread and durum wheat. The latter, however, is especially vulnerable, as effective sources of resistance are particularly limited. Therefore, we decided to verify whether the expression of the HvUGT13248 gene could enhance FHB resistance in durum wheat as well. To this aim, transgenic lines of Triticum durum cv. Svevo, constitutively expressing the HvUGT13248 gene, were produced. Transgenic plants in which presence of transcript and protein was confirmed, were infected with F. graminearum and evaluated for FHB severity, DON content and D3G conversion as compared to wild type plants. Our results showed that the HvUGT13248 gene determines in durum wheat a significant reduction of FHB symptoms (up to 30%) compared to control plants. This effect, however, was mainly evident at early infection stages, progressively decreasing at later stages. This outcome differs from what observed in transgenic bread wheat expressing the same UGT gene, in which FHB severity did not exceed 20% up to the last stages of infection (Li et al. 2015). To verify further the effectiveness of the DON-detoxifying approach, durum wheat lines with the same HvUGT13248 transgene were challenged with F. culmorum, also able to produce DON. A significant reduction of FCR symptoms compared to Svevo plants was observed. This represents the first report of improvement of FCR resistance associated with overexpression of an UGT involved in DON-detoxification. Recently, in order to combine in the same plant genes controlling two different mechanisms of type II resistance to FHB, we have crossed two types of durum wheat transgenic lines, one expressing the HvUGT13248 gene, the other AcPMEI, coding for a kiwi pectin methyl esterase inhibitor, known to increase resistance by strengthening the cell wall pectin fraction. On selected carriers of both transgenes, and in control lines with individual or no transgenes, the efficacy of the novel assembly will be verified against FHB and FCR

In vitro gastrointestinal digestion study of two wheat cultivars and evaluation of xylanase supplementation

International audienceBackground: The filamentous fungus Talaromyces versatilis is known to improve the metabolizable energy of wheat-based poultry diets thanks to its ability to produce a pool of CAZymes and particularly endo-beta(1,4)-xylanases. In order to appreciate their in vivo mode of action, the supplementation effect of two of its xylanases, XynD and XynB from families GH10 and GH11 respectively, have been evaluated on two different wheat cultivars Caphorn and Isengrain, which were chosen amongst 6 varieties for their difference in non starch polysaccharides content and arabinoxylan composition. Results: Polysaccharides digestion was followed during 6 h along the digestive tract using the TNO gastrointestinal model-1, to mimic monogastric metabolism. Polysaccharide degradation appeared to occur mainly at the jejunal level and was higher with Isengrain than with Caphorn. For both cultivars, XynD and XynB supplementation increased notably the amount of reducing end sugars into the jejuno-ileal dialysates, which has been confirmed by a valuable increase of the soluble glucose into the jejunal dialysates. Conclusions: The amounts of arabinose and xylose into the dialysates and ileal deliveries increased consequently mainly for Caphorn, suggesting that XynD and XynB supplementation in wheat-based diet could alleviate the anti-nutritional effects of arabinoxylans by limiting the physical entrapment of starch and could increase the available metabolizable energy

Signatures of irreversibility in microscopic models of flocking

Flocking in $d=2$ is a genuine non-equilibrium phenomenon for which irreversibility is an essential ingredient. We study a class of minimal flocking models whose only source of irreversibility is self-propulsion and use the entropy production rate (EPR) to quantify the departure from equilibrium across their phase diagrams. The EPR is maximal in the vicinity of the order-disorder transition, where reshuffling of the interaction network is fast. We show that signatures of irreversibility come in the form of asymmetries in the steady state distribution of the flock's microstates. They occur as consequences of the time reversal symmetry breaking in the considered self-propelled systems, independently of the interaction details. In the case of metric pairwise forces, they reduce to local asymmetries in the distribution of pairs of particles. This study suggests a possible use of pair asymmetries both to quantify the departure from equilibrium and to learn relevant information about aligning interaction potentials from data.Comment: 8 pages + Appendix; 6 figure

Wheat ati cm3, cm16 and 0.28 allergens produced in pichia pastoris display a different eliciting potential in food allergy to wheat

International audienceAlthough wheat is a staple food for most of the human population, some of its components trigger adverse reactions. Among wheat components, the alpha-amylase/trypsin inhibitors (ATI) are important triggers of several allergies and activators of innate immunity. ATI are a group of exogenous protease inhibitors and include several polypeptides. The three ATI polypeptides named CM3, CM16 and 0.28 are considered major allergens, and might also play a role in other common wheat-related pathologies, such as Non Celiac Wheat Sensitivity and even Celiac Disease. On this basis, we pointed to obtain high amounts of them in purity and to evaluate their allergenicity potential. We thus isolated the mRNA corresponding to the three ATI genes CM3, CM16 and 0.28 from 28 days post-anthesis wheat kernels and the corresponding cDNAs were used for heterologous expression in Pichia pastoris. The three purified proteins were tested in degranulation assay against human sera of patients with food allergy to wheat. A large range of degranulation values was observed for each protein according to the sera tested. All of the three purified proteins CM3, CM16 and 0.28 were active as allergens because they were able to induce basophils degranulation on wheat allergic patients' sera, with the highest values of beta-hexosaminidase release observed for CM3 protein