Les Houches Lectures on Community Ecology: From Niche Theory to Statistical Mechanics.

Ecosystems are among the most interesting and well-studied examples of self-organized complex systems. Community ecology, the study of how species interact with each other and the environment, has a rich tradition. Over the last few years, there has been a growing theoretical and experimental interest in these problems from the physics and quantitative biology communities. Here, we give an overview of community ecology, highlighting the deep connections between ecology and statistical physics. We start by introducing the two classes of mathematical models that have served as the workhorses of community ecology: Consumer Resource Models (CRM) and the generalized Lotka-Volterra models (GLV). We place a special emphasis on graphical methods and general principles. We then review recent works showing a deep and surprising connection between ecological dynamics and constrained optimization. We then shift our focus by analyzing these same models in "high-dimensions" (i.e. in the limit where the number of species and resources in the ecosystem becomes large) and discuss how such complex ecosystems can be analyzed using methods from the statistical physics of disordered systems such as the cavity method and Random Matrix Theory.

Anti-tumor activity of polysaccharides extracted from Pinus massoniana pollen in colorectal cancer- in vitro and in vivo studies.

The prevalence and mortality rate of colorectal cancer (CRC) have been increasing dramatically worldwide. Pinus massoniana pollen, a well-known natural food, is one of the most commonly consumed traditional medicines in China. P. massoniana pollen polysaccharides (PPPS) have antitumor effects, but it remains unclear whether they can inhibit CRC. Here, we have demonstrated that PPPS inhibited CRC cell proliferation effectively, induced morphology changes, triggered apoptosis by upregulating key apoptosis-related proteins, and arrested the cell cycle at the G0/G1 phase. Moreover, PPPS markedly inhibited CRC cell metastasis by downregulating MMP-9 and inhibiting epithelial-mesenchymal transition. In vivo, PPPS exhibited potent antitumor activity and no observable toxicity in BALB/c nude mice bearing HCT-116 tumors. Most strikingly, PPPS pre-treatment dramatically inhibited the growth of incipient tumors, although not as effectively as in the PPPS-Ther group. Thus, our results suggest that PPPS can be a potential anti-CRC agent, paving the way for developing complex carbohydrates for tumor prevention and treatment.

Pine pollen polysaccharides promote cell proliferation and accelerate wound healing by activating the JAK2-STAT3 signaling pathway.

Natural medicine can be used to develop wound healing agents due to its excellent characteristics of promoting rapid wound healing. Pine pollen polysaccharides (PPPS), a water-soluble polysaccharide with hydrophilicity and viscosity, which is suitable for the development of wound dressing. The purpose of this study is to explore the role and mechanism of PPPS in the process of wound healing. The results showed that PPPS could accelerate the wound healing, promote cell proliferation, transform the cell cycle from G1 phase to S and G2 phase, and increase the expression of Cyclin B1 in vitro. These effects of PPPS were achieved by activating JAK2-STAT3 signaling pathway. Similarly, PPPS could accelerate the healing of mouse cutaneous wounds, and could promote the growth of chicken embryo chorioallantoic vessels. In conclusion, this study indicates that PPPS is a new promising natural agent for promoting wound healing.

Diverse communities behave like typical random ecosystems.

In 1972, Robert May triggered a worldwide research program studying ecological communities using random matrix theory. Yet, it remains unclear if and when we can treat real communities as random ecosystems. Here, we draw on recent progress in random matrix theory and statistical physics to extend May's approach to generalized consumer-resource models. We show that in diverse ecosystems adding even modest amounts of noise to consumer preferences results in a transition to "typicality," where macroscopic ecological properties of communities are indistinguishable from those of random ecosystems, even when resource preferences have prominent designed structures. We test these ideas using numerical simulations on a wide variety of ecological models. Our work offers an explanation for the success of random consumer resource models in reproducing experimentally observed ecological patterns in microbial communities and highlights the difficulty of scaling up bottom-up approaches in synthetic ecology to diverse communities.

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice.

The stability of the intestinal microenvironment is the basis for maintaining the normal physiological activities of the intestine. On the contrary, disordered dynamic processes lead to chronic inflammation and disease pathology. Pinus massoniana pollen polysaccharide (PPPS), isolated from Taishan Pinus massoniana pollen, has been reported with extensive biological activities, including immune regulation. However, the role of PPPS in the intestinal microenvironment and intestinal diseases is still unknown. In this work, we initiated our investigation by using 16S rRNA high-throughput sequencing technology to assess the effect of PPPS on gut microbiota in mice. The result showed that PPPS regulated the composition of gut microbiota in mice and increased the proportion of probiotics. Subsequently, we established immunosuppressive mice using cyclophosphamide (CTX) and found that PPPS regulated the immunosuppressive state of lymphocytes in Peyer's patches (PPs). Moreover, PPPS also regulated systemic immunity by acting on intestinal PPs. PPPS alleviated lipopolysaccharide (LPS) -induced Caco2 cell damage, indicating that PPPS has the ability to reduce the damage and effectively improve the barrier dysfunction in Caco2 cells. In addition, PPPS alleviated colonic injury and relieved colitis symptoms in dextran sodium sulfate (DSS)-induced colitis mice. Overall, our findings indicate that PPPS shows a practical regulatory effect in the intestinal microenvironment, which provides an essential theoretical basis for us to develop the potential application value of PPPS further.

Screening active fractions from Pinus massoniana pollen for inhibiting ALV-J replication and their structure activity relationship investigation.

The objective was to identify the active fractions of polysaccharide against replication of ALV-J and elucidate their structure activity relationship. The optimal extraction conditions were extracting temperature 90℃, pH 9 and the ratio of liquid to solid 30:1. Under these conditions, extraction yield of total polysaccharide was 6.5 % ± 0.19 %. Total polysaccharide was then purified by DEAE-52 cellulose and Sephadex G-200 gel. Three fractions, PPP-1, PPP-2, and PPP-3, were identified with molecular weight of 463.70, 99.41, and 26.97 kDa, respectively. Three polysaccharide fractions were all composed of 10 monosaccharides in different proportions. Compared with PPP-1, which was mainly composed of glucose, PPP-2 and PPP-3 contained a higher proportion of galactose, glucuronic acid and galacturonic acid. The Congo red assay indicated that the PPP-2 may have a triple helical structure, while PPP-1 and PPP-3 were absent. In vitro assay showed that there was no significant cytotoxicity among the polysaccharide fractions under the concentration of 800 µg mL-1 (P > 0.05). The antiviral test showed that PPP-2 had the strongest activity, indicating PPP-2 was the major antiviral component. The structure-activity relationship showed that the antiviral activities of polysaccharide fractions were affected by their monosaccharide composition, molecular weight, and triple helical structure, which was a result of a combination of multiple molecular structural factors. These results showed that the PPP-2 could be exploited as a valued product for replacing synthetic antiviral drugs, and provided support for future applications of polysaccharide from Pinus massoniana pollen as a useful source for antiviral agent.

The Minimum Environmental Perturbation Principle: A New Perspective on Niche Theory.

AbstractFifty years ago, Robert MacArthur showed that stable equilibria optimize quadratic functions of the population sizes in several important ecological models. Here, we generalize this finding to a broader class of systems within the framework of contemporary niche theory and precisely state the conditions under which an optimization principle (not necessarily quadratic) can be obtained. We show that conducting the optimization in the space of environmental states instead of population sizes leads to a universal and transparent physical interpretation of the objective function. Specifically, the equilibrium state minimizes the perturbation of the environment induced by the presence of the competing species, subject to the constraint that no species has a positive net growth rate. We use this "minimum environmental perturbation principle" to make new predictions for evolution and community assembly, where the minimum perturbation increases monotonically under invasion by new species. We also describe a simple experimental setting where the conditions of validity for this optimization principle have been empirically tested.

Effect of Resource Dynamics on Species Packing in Diverse Ecosystems.

The competitive exclusion principle asserts that coexisting species must occupy distinct ecological niches (i.e., the number of surviving species cannot exceed the number of resources). An open question is to understand if and how different resource dynamics affect this bound. Here, we analyze a generalized consumer resource model with externally supplied resources and show that-in contrast to self-renewing resources-species can occupy only half of all available environmental niches. This motivates us to construct a new schema for classifying ecosystems based on species packing properties.

The Community Simulator: A Python package for microbial ecology.

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns.

Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.

Taishan Pinus Massoniana pollen polysaccharide inhibits the replication of acute tumorigenic ALV-J and its associated tumor growth.

Avian leukosis virus subgroup J (ALV-J) has resulted in considerable economic losses in the poultry industry. In recent years, fibrosarcoma induced by ALV-J, which contains the v-fps oncogene, has gained momentum, and this has brought about new challenges to the poultry industry. To study the inhibitory effects of Taishan Pinus Massoniana pollen polysaccharide (TPPPS) on acute ALV-J infection and tumor development, antiviral and antitumor models of the Fu-J (SDAU1005) strain of ALV-J were established in vitro and in vivo. The results of in vitro experiments showed that TPPPS significantly inhibited viral replication in a dose-dependent manner during adsorption and pretreatment stages. The results of in vivo experiments have shown that TPPPS significantly reduced the viral load in the plasma and tumor tissues, as well as inhibited tumor growth. We further examined the difference in transcriptome expression by using RNA-Seq technology. A total of 560 differentially expressed genes were identified that included 329 up-regulated genes and 231 down-regulated genes. The up-regulated genes were mainly immune-related genes, whereas the down-regulated genes were mainly tumor-regulated genes. Gene Ontology (GO) term enrichment included immune system processes, positive regulation of immune system processes, regulation of immune system processes, leukocyte activation, cell activation, and protein binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the main immune and tumor-related pathways included T-cell receptor signaling pathway, cytokine-cytokine receptor interactions, natural killer cell-mediated cytotoxicity, PI3K-Akt signaling pathway, JAK-STAT signaling pathway, NF-κB signaling pathway, and Ras signaling pathway. In summary, our results preliminarily point to the antiviral and antitumor mechanism of TPPPS in vivo and in vitro.

Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions.

Quadratic programming (QP) is a common and important constrained optimization problem. Here, we derive a surprising duality between constrained optimization with inequality constraints, of which QP is a special case, and consumer resource models describing ecological dynamics. Combining this duality with a recent "cavity solution," we analyze high-dimensional, random QP where the optimization function and constraints are drawn randomly. Our theory shows remarkable agreement with numerics and points to a deep connection between optimization, dynamical systems, and ecology.

The thermodynamic uncertainty relation in biochemical oscillations.

Living systems regulate many aspects of their behaviour through periodic oscillations of molecular concentrations, which function as 'biochemical clocks.' The chemical reactions that drive these clocks are intrinsically stochastic at the molecular level, so that the duration of a full oscillation cycle is subject to random fluctuations. Their success in carrying out their biological function is thought to depend on the degree to which these fluctuations in the cycle period can be suppressed. Biochemical oscillators also require a constant supply of free energy in order to break detailed balance and maintain their cyclic dynamics. For a given free energy budget, the recently discovered 'thermodynamic uncertainty relation' yields the magnitude of period fluctuations in the most precise conceivable free-running clock. In this paper, we show that computational models of real biochemical clocks severely underperform this optimum, with fluctuations several orders of magnitude larger than the theoretical minimum. We argue that this suboptimal performance is due to the small number of internal states per molecule in these models, combined with the high level of thermodynamic force required to maintain the system in the oscillatory phase. We introduce a new model with a tunable number of internal states per molecule and confirm that it approaches the optimal precision as this number increases.

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

A polysaccharide found in Paulownia fortunei flowers can enhance cellular and humoral immunity in chickens.

A water-soluble polysaccharide known as Paulownia fortunei flower polysaccharide (PFFPS) was isolated from the flowers of Paulownia fortunei. Gel permeation chromatography (GPC) analysis showed that approximately 92.5% of PFFPS fractions had molecular weights under 500 kDa. High performance liquid chromatograph (HPLC) analysis revealed that PFFPS was composed of 10 monosaccharides, including galactose (28.61%), rhamnose (18.09%), glucose (15.21%), and arabinose (15.91%). Fourier transform infrared (FT-IR) spectra revealed the specific absorption peaks of the polysaccharide. Using in vivo tests in chickens, we found that even very low doses of PFFPS could significantly promote the development of the immune organs, increase the quantity of leukocytes and the ratio of lymphocytes, and improve antibody titers against Newcastle disease virus (NDV). In addition, PFFPS also increased the concentrations of IL-2 and IFN-γ, as well as the content of SIgA in the duodenum. Furthermore, PFFPS was found to be able to relieve immunosuppression caused by cyclophosphamide (CTX). This study therefore suggests that PFFPS may be a valuable component of new immunopotentiator and/or adjuvant for the livestock and poultry industries.

Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting.

In the immune system, T cells can quickly discriminate between foreign and self ligands with high accuracy. There is evidence that T-cells achieve this remarkable performance utilizing a network architecture based on a generalization of kinetic proofreading (KPR). KPR-based mechanisms actively consume energy to increase the specificity beyond what is possible in equilibrium. An important theoretical question that arises is to understand the trade-offs and fundamental limits on accuracy, speed, and dissipation (energy consumption) in KPR and its generalization. Here, we revisit this question through numerical simulations where we simultaneously measure the speed, accuracy, and energy consumption of the KPR and adaptive sorting networks for different parameter choices. Our simulations highlight the existence of a "feasible operating regime" in the speed-energy-accuracy plane where T-cells can quickly differentiate between foreign and self ligands at reasonable energy expenditure. We give general arguments for why we expect this feasible operating regime to be a generic property of all KPR-based biochemical networks and discuss implications for our understanding of the T cell receptor circuit.

Proximity-Driven Enhanced Magnetic Order at Ferromagnetic-Insulator-Magnetic-Topological-Insulator Interface.

Magnetic exchange driven proximity effect at a magnetic-insulator-topological-insulator (MI-TI) interface provides a rich playground for novel phenomena as well as a way to realize low energy dissipation quantum devices. Here we report a dramatic enhancement of proximity exchange coupling in the MI/magnetic-TI EuS/Sb(2-x)V(x)Te3 hybrid heterostructure, where V doping is used to drive the TI (Sb2Te3) magnetic. We observe an artificial antiferromagneticlike structure near the MI-TI interface, which may account for the enhanced proximity coupling. The interplay between the proximity effect and doping in a hybrid heterostructure provides insights into the engineering of magnetic ordering.

Near-field optical effect of a core-shell nanostructure in proximity to a flat surface.

We provide an analytical solution for studying the near-field optical effect of a core-shell nanostructure in proximity to a flat surface, within quasi-static approximation. The distribution of electrostatic potential and the field enhancement in this complex geometry are obtained by solving a set of linear equations. This analytical result can be applied to a wide range of systems associated with near-field optics and surface plasmon polaritons. To illustrate the power of this technique, we study the field-attenuation effect of an oxidized shell in a silver tip in a near-field scanning microscope. The thickness of oxidized layer can be monitored by measuring the intensity of light. We also find a linear relation between resonant frequency and temperature in an Ag-Au core-shell structure, which provides insight for local temperature detection with nm scale resolution. Our results also show good agreement with recent finite element method results.