Elastic behavior of cross-linked and bundled actin networks

Networks of cross-linked and bundled actin filaments are ubiquitous in the cellular cytoskeleton, but their elasticity remains poorly understood. We show that these networks exhibit exceptional elastic behavior that reflects the mechanical properties of individual filaments. There are two distinct regimes of elasticity, one reflecting bending of single filaments and a second reflecting stretching of entropic fluctuations of filament length. The mechanical stiffness can vary by several decades with small changes in cross-link concentration, and can increase markedly upon application of external stress. We parameterize the full range of behavior in a state diagram and elucidate its origin with a robust model.     

Noise propagation in gene networks

Accurately predicting noise propagation in gene networks is crucial for understanding signal fidelity in natural networks and designing noise-tolerant gene circuits. To quantify how noise propagates through gene networks, we measured expression correlations between genes in single cells. We found that noise in a gene was determined by its intrinsic fluctuations, transmitted noise from upstream genes, and global noise affecting all genes. A model was developed that explains the complex behavior exhibited by the correlations and reveals the dominant noise sources. The model successfully predicts the correlations as the network is systematically perturbed. This approach provides a step toward understanding and manipulating noise propagation in more complex gene networks.     

Transgenerational plasticity is adaptive in the wild

Plants exhibit adaptive responses to light, but it is not known whether parental plants transmit environmental cues that elicit adaptive responses in offspring. We show that offspring life history (annual versus biennial) is influenced by the maternal light environment (understory versus light gap). This transgenerational plasticity is adaptive when offspring are grown in their maternal light environment, where seeds typically disperse. Projections of population growth show that plants that are appropriately cued for their light environment through maternal effects have 3.4 times greater fitness than otherwise. Transgenerational plasticity has evolved in response to natural variation in light and provides a flexible mechanism by which sedentary organisms cope with heterogeneous environments.     

Phenotypic diversity, population growth, and information in fluctuating environments

Organisms in fluctuating environments must constantly adapt their behavior to survive. In clonal populations, this may be achieved through sensing followed by response or through the generation of diversity by stochastic phenotype switching. Here we show that stochastic switching can be favored over sensing when the environment changes infrequently. The optimal switching rates then mimic the statistics of environmental changes. We derive a relation between the long-term growth rate of the organism and the information available about its fluctuating environment.     

Evidence for network evolution in an Arabidopsis interactome map

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.     

Modeling effects of environmental change on wolf population dynamics, trait evolution, and life history

Environmental change has been observed to generate simultaneous responses in population dynamics, life history, gene frequencies, and morphology in a number of species. But how common are such eco-evolutionary responses to environmental change likely to be? Are they inevitable, or do they require a specific type of change? Can we accurately predict eco-evolutionary responses? We address these questions using theory and data from the study of Yellowstone wolves. We show that environmental change is expected to generate eco-evolutionary change, that changes in the average environment will affect wolves to a greater extent than changes in how variable it is, and that accurate prediction of the consequences of environmental change will probably prove elusive.     

Social networks in complex human and natural systems: the case of rotational grazing,weak ties,and eastern US dairy landscapes

Multifunctional agricultural systems seek to expand upon production-based benefits to enhance family wellbeing and animal health, reduce inputs, and improve environmental services such as biodiversity and water quality. However, in many countries a landscape-level conversion is uneven at best and stalled at worst. This is particularly true across the eastern rural landscape in the United States. We explore the role of social networks as drivers of system transformation within dairy production in the eastern United States, specifically rotational grazing as an alternative management option. We hypothesize the importance of weak ties within farmer social networks as drivers of change. In Wisconsin, Pennsylvania, and New York, we conducted 53 interviews with confinement, low-intensity, and rotational grazing dairy producers as well as 35 interviews with associated network actors. Though confinement and grazier networks had similar proportions of strong and weak ties, confinement producers had more market-based weak ties, while graziers had more weak-ties to government agencies and other graziers in the region. These agency weak ties supported rotational graziers through information exchange and cost sharing, both crucial to farmers’ transitions from confinement-based production to grazing systems. While weak ties were integral to initial innovation, farmers did not maintain these relationships beyond their transition to grazing. Of equal importance, grazier weak-tie networks did not include environmental organizations, suggesting unrealized potential for more diverse networks based on environmental services. By understanding the drivers, we can identify barriers to expanding weak tie networks and emergent properties in order to create institutions and policies necessary for change.     

A general model for food web structure

A central problem in ecology is determining the processes that shape the complex networks known as food webs formed by species and their feeding relationships. The topology of these networks is a major determinant of ecosystems' dynamics and is ultimately responsible for their responses to human impacts. Several simple models have been proposed for the intricate food webs observed in nature. We show that the three main models proposed so far fail to fully replicate the empirical data, and we develop a likelihood-based approach for the direct comparison of alternative models based on the full structure of the network. Results drive a new model that is able to generate all the empirical data sets and to do so with the highest likelihood.     

Phototaxis and sensory transduction in Euglena

The accumulation of Euglena gracilis in an illuminated region is brought about by two main mechanisms: orientation and subsequent directed movement (positive phototaxis) toward light scattered from particles in the illuminated zone; and by the trapping of cells in this region because of shock reactions experienced upon the cells encountering a sudden decrease of light intensity at the light-dark boundary (inverse photophobic responses).Phototactic orientation is mediated by inverse photophobic reactions which occur when the shadow of the stigma periodically falls upon the photoreceptor proper. Euglena also exhibits shock reactions when an already high light intensity is increased further (direct photophobic responses). The expression of both types of phobic responses depends upon stimulus intensity and adaptation of the sensory system in a seemingly complex way. A definition of the minimum components of the stimulus transduction system and a systems analytical approach to the study of input-output relationships enables one to construct an electronic analog of the cell's signal processing system that converts the photoreceptor input to commands which activate or inhibit flagellar reorientation. Computer simulation studies show that this model has considerable predictive value. It is hoped that with the approach presented in this article, a generalized model has become available for dealing with the questions of sensory transduction in aneural systems. Certainly, at this point more questions have been raised than have been answered. Where is the processing device located? Are its kinetic properties determined by electrical processes or by the rates of chemical reactions? Is the processor, and thereby the behavior of the orgamism, modulated by natural environmental parameters, and can it be modified permanently through more drastic chemical treatment of the cell? Is the system capable of permanent or transitory modification through repeated response, that is, does it exhibit phenomena analogous to learning and memory in higher organisms? These are only a few of the problems that require study in the future.     

Arabidopsis Phytochrome D Is Involved in Red Light-Induced Negative Gravitropism of Hypocotyles

The phytochrome gene family, which is in Arabidopsis thaliana, consists of phytochromes A-E（phyA to phyE）, regulates plant responses to ambient light environments. PhyA and phyB have been characterized in detail, but studies on phyC to phyE have reported discrepant functions. In this study, we show that phyD regulates the Arabidopsis gravitropic response by inhibiting negative gravitropism of hypocotyls under red light condition. PhyD had only a limited effect on the gravitropic response of roots in red light condition. PhyD also enhanced phyB-regulated gravitropic responses in hypocotyls. Moreover, the regulation of hypocotyl gravitropic responses by phyD was dependent upon the red light fluence rate.     

不同培养环境对喜旱莲子草生长的影响

喜旱莲子草是中国首批9种重要的外来入侵植物之一,探究喜旱莲子草在5个不同环境下的生长势,进而为防治和利用喜旱莲子草提供参考。测定了5个不同小生境下喜旱莲子草生长的环境因子。结果表明:玻璃温室内喜旱莲子草的各生长指标均显著优于其它种植点。分析了环境温度、空气相对湿度和光照与喜旱莲子草的茎长、分枝数、节数和叶对数的相关性;并用逐步回归建立了这些生长指标与环境因子的模型。不同生长指标受环境因子的影响不一。茎长主要受晚上温度、中午湿度和早晨光照的影响,分枝数和节数受中午湿度和晚上温度的影响最大,中午、晚上温度和中午湿度是影响叶对数的主要因子。     

Phosphorylation networks regulating JNK activity in diverse genetic backgrounds

Cellular signaling networks have evolved to enable swift and accurate responses, even in the face of genetic or environmental perturbation. Thus, genetic screens may not identify all the genes that regulate different biological processes. Moreover, although classical screening approaches have succeeded in providing parts lists of the essential components of signaling networks, they typically do not provide much insight into the hierarchical and functional relations that exist among these components. We describe a high-throughput screen in which we used RNA interference to systematically inhibit two genes simultaneously in 17,724 combinations to identify regulators of Drosophila JUN NH(2)-terminal kinase (JNK). Using both genetic and phosphoproteomics data, we then implemented an integrative network algorithm to construct a JNK phosphorylation network, which provides structural and mechanistic insights into the systems architecture of JNK signaling.     

Gene regulatory networks and the evolution of animal body plans

Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early "Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the kernels" of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.     

Fish population and behavior revealed by instantaneous continental shelf-scale imaging

Until now, continental shelf environments have been monitored with highly localized line-transect methods from slow-moving research vessels. These methods significantly undersample fish populations in time and space, leaving an incomplete and ambiguous record of abundance and behavior. We show that fish populations in continental shelf environments can be instantaneously imaged over thousands of square kilometers and continuously monitored by a remote sensing technique in which the ocean acts as an acoustic waveguide. The technique has revealed the instantaneous horizontal structural characteristics and volatile short-term behavior of very large fish shoals, containing tens of millions of fish and stretching for many kilometers.     

Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins

Synthetic genetic devices that interface with native cellular pathways can be used to change natural networks to implement new forms of control and behavior. The engineering of gene networks has been limited by an inability to interface with native components. We describe a class of RNA control devices that overcome these limitations by coupling increased abundance of particular proteins to targeted gene expression events through the regulation of alternative RNA splicing. We engineered RNA devices that detect signaling through the nuclear factor κB and Wnt signaling pathways in human cells and rewire these pathways to produce new behaviors, thereby linking disease markers to noninvasive sensing and reprogrammed cellular fates. Our work provides a genetic platform that can build programmable sensing-actuation devices enabling autonomous control over cellular behavior.     

Integration of plant responses to environmentally activated phytohormonal signals

Plants live in fixed locations and survive adversity by integrating growth responses to diverse environmental signals. Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions. The growth restraint conferred by DELLA proteins is beneficial and promotes survival. We propose that DELLAs permit flexible and appropriate modulation of plant growth in response to changes in natural environments.     

The cell and molecular basis of mechanical, cold, and inflammatory pain

Peripheral pain pathways are activated by a range of stimuli. We used diphtheria toxin to kill all mouse postmitotic sensory neurons expressing the sodium channel Nav1.8. Mice showed normal motor activity and low-threshold mechanical and acute noxious heat responses but did not respond to noxious mechanical pressure or cold. They also showed a loss of enhanced pain responses and spontaneous pain behavior upon treatment with inflammatory insults. In contrast, nerve injury led to heightened pain sensitivity to thermal and mechanical stimuli indistinguishable from that seen with normal littermates. Pain behavior correlates well with central input from sensory neurons measured electrophysiologically in vivo. These data demonstrate that Na(v)1.8-expressing neurons are essential for mechanical, cold, and inflammatory pain but not for neuropathic pain or heat sensing.     

Microfluidic large-scale integration

We developed high-density microfluidic chips that contain plumbing networks with thousands of micromechanical valves and hundreds of individually addressable chambers. These fluidic devices are analogous to electronic integrated circuits fabricated using large-scale integration. A key component of these networks is the fluidic multiplexor, which is a combinatorial array of binary valve patterns that exponentially increases the processing power of a network by allowing complex fluid manipulations with a minimal number of inputs. We used these integrated microfluidic networks to construct the microfluidic analog of a comparator array and a microfluidic memory storage device whose behavior resembles random-access memory.     

Predicting human interactive learning by regret-driven neural networks

Much of human learning in a social context has an interactive nature: What an individual learns is affected by what other individuals are learning at the same time. Games represent a widely accepted paradigm for representing interactive decision-making. We explored the potential value of neural networks for modeling and predicting human interactive learning in repeated games. We found that even very simple learning networks, driven by regret-based feedback, accurately predict observed human behavior in different experiments on 21 games with unique equilibria in mixed strategies. Introducing regret in the feedback dramatically improved the performance of the neural network. We show that regret-based models provide better predictions of learning than established economic models.     

The genetic basis of singlet oxygen-induced stress responses of Arabidopsis thaliana

Plants under oxidative stress suffer from damages that have been interpreted as unavoidable consequences of injuries inflicted upon plants by toxic levels of reactive oxygen species (ROS). However, this paradigm needs to be modified. Inactivation of a single gene, EXECUTER1, is sufficient to abrogate stress responses of Arabidopsis thaliana caused by the release of singlet oxygen: External conditions under which these stress responses are observed and the amounts of ROS that accumulate in plants exposed to these environmental conditions do not directly cause damages. Instead, seedling lethality and growth inhibition of mature plants result from genetic programs that are activated after the release of singlet oxygen has been perceived by the plant.