Pattern-oriented modeling of agent-based complex systems: lessons from ecology

Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.     

Host resistance to lung infection mediated by major vault protein in epithelial cells

The airway epithelium plays an essential role in innate immunity to lung pathogens. Ribonucleoprotein particles primarily composed of major vault protein (MVP) are highly expressed in cells that encounter xenobiotics. However, a clear biologic function for MVP is not established. We report here that MVP is rapidly recruited to lipid rafts when human lung epithelial cells are infected with Pseudomonas aeruginosa, and maximal recruitment is dependent on bacterial binding to the cystic fibrosis transmembrane conductance regulator. MVP was also essential for optimal epithelial cell internalization and clearance of P. aeruginosa. These results suggest that MVP makes a substantial contribution to epithelial cell-mediated resistance to infection.     

Endogenous enzymes, heat, and pH affect flavone profiles in parsley (Petroselinum crispum var. neapolitanum) and celery (Apium graveolens) during juice processing

Flavones are abundant in parsley and celery and possess unique anti-inflammatory properties in vitro and in animal models. However, their bioavailability and bioactivity depend in part on the conjugation of sugars and other functional groups to the flavone core. The effects of juice extraction, acidification, thermal processing, and endogenous enzymes on flavone glycoside profile and concentration in both parsley and celery were investigated. Parsley yielded 72% juice with 64% of the total flavones extracted, whereas celery yielded 79% juice with 56% of flavones extracted. Fresh parsley juice averaged 281 mg flavones/100 g and fresh celery juice, 28.5 mg/100 g. Flavones in steamed parsley and celery were predominantly malonyl apiosylglucoside conjugates, whereas those in fresh samples were primarily apiosylglucoside conjugates; this was apparently the result of endogenous malonyl esterases. Acidification and thermal processing of celery converted flavone apiosylglucosides to flavone glucosides, which may affect the intestinal absorption and metabolism of these compounds.     

Early growth and ecophysiological responses of Koa (Acacia koa A. Gray) seedlings to reduced water and phosphorus

Sites in need of restoration typically have one or more environmental factors that limit seedling establishment. Identifying ecophysiological responses to environmental stressors can provide important insights into mitigating measures that would allow seedlings to overcome such constraints to survival. Koa (Acacia koa A. Gray) is a nitrogen-fixing tree species endemic to Hawai?i that is highly valued in restoring degraded forest ecosystems, which are often limited in available water and phosphorus. This study examined how koa seedlings respond to conditions of reduced water (65 W) and no phosphorus (0P). After 17 weeks, seedlings subjected to 65 W or 0P accumulated less biomass, smaller root-collar diameters, and lower nitrogen and phosphorus contents. Combined reductions in water and P resulted in seedlings with increased root to shoot dry biomass and shorter shoots. Seedlings subjected to 65 W also had lower instantaneous rates of CO₂ assimilation, but higher instantaneous water-use efficiencies following irrigation, suggesting that koa responds to water deficits by decreasing water loss via reduced stomatal conductance. Seedlings subjected to 0P had similar rates of CO₂ assimilation relative to those grown with adequate P, suggesting that koa is able to employ strategies to avoid physiological impairment from conditions of inadequate P. Future research should assess whether subjecting koa seedlings to reduced water before planting on water-limited sites cues increased drought resistance and whether uptake and storage of P by seedlings in the nursery better supports growth following outplanting, particularly on sites with anticipated low plant-available water.

     

The ecological role of bivalve shellfish aquaculture in the estuarine environment: A review with application to oyster and clam culture in West Coast (USA) estuaries

Aquaculture is viewed as a potential mechanism to meet the growing demand for seafood around the world. The future of bivalve shellfish aquaculture in the U.S. hinges on sustainable practices on the part of industry and a more consistent regulatory regime. Bivalve shellfish aquaculture is a recent practice relative to its history in other countries, beginning in the late 1800s along the U.S. West Coast where it is now well established with farm raised product utilizing land-based hatcheries and grow-out directly in numerous estuaries. Bivalve shellfish aquaculture can be viewed as a disturbance which modifies the estuarine system in three ways: 1) changes in material processes — bivalves process food and produce wastes; 2) addition of physical structure — aquaculture introduces the cultured organisms and in some cases a physical anchoring structure; and 3) pulse disturbances like harvest and bed maintenance disturb sediments, remove species in addition to the cultured organisms themselves, and change resource or habitat availability. In U.S. West Coast estuaries, water column and sediment nutrient concentrations are relatively high and influenced by large tidal exchange and proximity to deeper nearshore ocean waters where upwelling controls production during summer months. Bivalves are unlikely to influence material processes except at local bed scales in these systems, although estuary-wide effects could appear as the fraction of cultured area rises or in poorly flushed bays. Bivalve culture clearly modifies estuarine habitat at local community and at landscape scales and effects are most often evaluated against existing structured habitat in the form of submerged aquatic vegetation. Individual activities act as pulse disturbances and the recovery of eelgrass (Zostera marina) to pre-disturbance levels is variable (< 2 to > 5 years). The extent of disturbance depends on the aquaculture practice and the distribution of eelgrass reflects a balance of space competition, pulse disturbance and recovery, and is therefore at dynamic equilibrium on aquaculture beds. Structure provided by aquaculture appears functionally similar to eelgrass for small benthic infauna and mobile epibenthic fauna while use of aquaculture as habitat by larger more mobile invertebrates and fish depends on mobility and varies with life-history stage and taxon being evaluated. Scale seems a very important management consideration and further research at estuarine landscape scales, especially for habitat use by important invertebrates and fish, may prove useful in designing and implementing best management practices. Though local and short term effects from aquaculture are clearly evident in U.S. West Coast estuaries, bivalve aquaculture does not remove area from the estuary or degrade water quality like other anthropogenic influences, and thus has not been implicated in shifts to alternate states or reduced adaptive capacity of the larger ecological system.