Interannual variation of reach specific migratory success for Sacramento River hatchery yearling late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss)

The release of hatchery reared salmonid smolts is a common management tool aimed at enhancing depleted wild stocks and maintaining fisheries throughout Northern California and the Pacific Northwest. In the Sacramento River watershed, smolts must migrate through the river, delta and estuary in order to successfully reach the Pacific Ocean. Migration success (success defined as apparent survival from one monitor location to another) may vary between species, year and habitat. We released 500 late-fall run Chinook salmon and 500 steelhead smolts in 2009 and 2010 in the Sacramento River (river kilometer 207). Each smolt was implanted with a coded ultrasonic tag, which was detected by an array of over 300 underwater receiver stations deployed throughout the system. Less than 25 % of fish migrated successfully to the Pacific Ocean in both years. We found that reach specific success was greater in the Delta in 2009 (>60 %) than in 2010 (<33 %), whereas this pattern was reversed in the Bay (<57 % in 2009, >75 % in 2010). Identifying the location, timing and causes of smolt mortality can lead to improved management of the resource.     

Computational structure characterisation tools in application to ordered and disordered porous materials

In this article, we present a set of computational tools for systematic characterisation of ordered and disordered porous materials. These tools include calculation of the accessible surface area and geometric pore size distribution, analysis of the structure connectivity and percolation analysis of the porous space. We briefly discuss the algorithms behind these calculations. To demonstrate the capabilities of the tools and the type of insights that can be gained from their application, we consider a series of case studies. These case studies include small molecular fragments, several crystalline metal-organic materials, and variants of these materials with induced defects and disorder in their structure. The simulation package is available upon request.     

Specificity, rank preference, and the colonization of a non-native host plant by the Melissa blue butterfly

Animals often express behavioral preferences for different types of food or other resources, and these preferences can evolve or shift following association with novel food types. Shifts in preference can involve at least two phenomena: a change in rank preference or a change in specificity. The former corresponds to a change in the order in which hosts are preferred, while a shift in specificity can be an increase in the tendency to utilize multiple hosts. These possibilities have been examined in relatively few systems that include extensive population-level replication. The Melissa blue butterfly, Lycaeides melissa, has colonized exotic alfalfa, Medicago sativa, throughout western North America. We assayed the host preferences of 229 females from ten populations associated with novel and native hosts. In four out of five native-associated populations, a native host was preferred over the exotic host, while preference for a native host characterized only two out of five of the alfalfa-associated populations. Across all individuals from alfalfa-associated populations, there appears to have been a decrease in specificity: females from these populations lay fewer eggs on the native host and more eggs on the exotic relative to females from native-host populations. However, females from alfalfa-associated populations did not lay more eggs on a third plant species, which suggests that preferences for specific hosts in this system can potentially be gained and lost independently. Geographic variation in oviposition preference in L. melissa highlights the value of surveying a large number of populations when studying the evolution of a complex behavioral trait.     

Observations of below-ground characteristics of young redwood trees (Sequoia sempervirens) from two sites in New Zealand – implications for erosion control

Aims

Radiata pine (Pinus radiata D. Don) plantations are widely used to control erosion in New Zealand. However, other species with similar growth but longer rotation lengths and ability to coppice may offer future alternatives to radiata pine. Comparing performance of alternative species to radiata thus becomes important if policy is to be developed to promote them.

Methods

The below-ground characteristics (roots) of young redwood (Sequoia sempervirens (D. Don) Endl.) trees from two established plantations in New Zealand were examined and compared with those of radiata pine, and selected poplar and New Zealand native species.

Results

Roots with diameters less than 10 mm comprised over 99 % of total root length in 3-yr-old trees and 98 % of total root length in 4-yr-old trees. For roots greater than 2 mm in diameter, total root length of young redwood trees was greater than that of young radiata pine, poplar and the best performing New Zealand native plant. Total root length at a given root collar diameter for young (1–4 year old) redwood trees was significantly greater than for radiata pine trees. Roots of redwoods were finer and more numerous than for radiata but the below-ground biomass for a given root collar diameter showed no statistical difference between the two species.

Conclusions

Redwood, because of its comparable growth rate and the production of many fine lateral roots, has the potential to become a keystone erosion-control species in New Zealand, especially on steep lands where there is an increased risk of post-harvest landsliding associated with moderate to severe rainstorm events.     

Copper Supplementation at 8 mg Neither Affects Circulating Lipids nor Liver Function in Apparently Healthy Chilean Men

There is a close relationship between selenium deficiency and Kaschin–Beck disease (KBD). Although the etiology of KBD is not known and selenium deficiency is not its actual cause, it is an important environmental risk factor. In particular, in the Qing-Tibet Plateau, a selenium-deficient region, the prevalence of KBD is serious and still increasing and continues to damage public health. By providing selenium to the population in appropriate amounts, and especially to children, KBD can be effectively controlled and prevented.     

Analysis of the local organization and dynamics of cellular actin networks

A ctin filaments, with the aid of multiple accessory proteins, self-assemble into a variety of network patterns. We studied the organization and dynamics of the actin network in nonadhesive regions of cells bridging fibronectin-coated adhesive strips. The network was formed by actin nodes associated with and linked by myosin II and containing the formin disheveled-associated activator of morphogenesis 1 (DAAM1) and the cross-linker filamin A (FlnA). After Latrunculin A (LatA) addition, actin nodes appeared to be more prominent and demonstrated drift-diffusion motion. Superresolution microscopy revealed that, in untreated cells, DAAM1 formed patches with a similar spatial arrangement to the actin nodes. Node movement (diffusion coefficient and velocity) in LatA-treated cells was dependent on the level and activity of myosin IIA, DAAM1, and FlnA. Based on our results, we developed a computational model of the dynamic formin-filamin-actin asters that can self-organize into a contractile actomyosin network. We suggest that such networks are critical for connecting distant parts of the cell to maintain the mechanical coherence of the cytoplasm.     

Regulation of Phospholipase D Activity and Phosphatidic Acid Production after Purinergic (P2Y6) Receptor Stimulation

Phosphatidic acid (PA) is a lipid second messenger located at the intersection of several lipid metabolism and cell signaling events including membrane trafficking, survival, and proliferation. Generation of signaling PA has long been primarily attributed to the activation of phospholipase D (PLD). PLD catalyzes the hydrolysis of phosphatidylcholine into PA. A variety of both receptor-tyrosine kinase and G-protein-coupled receptor stimulations have been shown to lead to PLD activation and PA generation. This study focuses on profiling the PA pool upon P2Y₆ receptor signaling manipulation to determine the major PA producing enzymes. Here we show that PLD, although highly active, is not responsible for the majority of stable PA being produced upon UDP stimulation of the P2Y₆ receptor and that PA levels are tightly regulated. By following PA flux in the cell we show that PLD is involved in an initial increase in PA upon receptor stimulation; however, when PLD is blocked, the cell compensates by increasing PA production from other sources. We further delineate the P2Y₆ signaling pathway showing that phospholipase Cβ3 (PLCβ3), PLCδ1, DGKζ and PLD are all downstream of receptor activation. We also show that DGKζ is a novel negative regulator of PLD activity in this system that occurs through an inhibitory mechanism with PKCα. These results further define the downstream events resulting in PA production in the P2Y₆ receptor signaling pathway.     

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

The replication and life cycle of the influenza virus is governed by an intricate network of intracellular regulatory events during infection, including interactions with an even more complex system of biochemical interactions of the host cell. Computational modeling and systems biology have been successfully employed to further the understanding of various biological systems, however, computational studies of the complexity of intracellular interactions during influenza infection is lacking. In this work, we present the first large-scale dynamical model of the infection and replication cycle of influenza, as well as some of its interactions with the host’s signaling machinery. Specifically, we focus on and visualize the dynamics of the internalization and endocytosis of the virus, replication and translation of its genomic components, as well as the assembly of progeny virions. Simulations and analyses of the models dynamics qualitatively reproduced numerous biological phenomena discovered in the laboratory. Finally, comparisons of the dynamics of existing and proposed drugs, our results suggest that a drug targeting PB1:PA would be more efficient than existing Amantadin/Rimantaine or Zanamivir/Oseltamivir.