Building a Comprehensive Mill-Level Database for the Industrial Sectors Integrated Solutions (ISIS) Model of the U.S. Pulp and Paper Sector

Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector.     

Friend or foe?: a plant's induced response to an omnivore

Omnivorous natural enemies of herbivores consume plant-based resources and may elicit induced resistance in their host plant. A greater induction threshold for damage produced by omnivorous predators than for strict herbivores might be expected if omnivore performance is enhanced on noninduced plants, allowing them to reduce future levels of herbivory. Currently, it is not known if a plant responds to feeding by omnivorous predators and by herbivores similarly. To examine this question, we chose herbivore and omnivore species that produce the same kind of quantifiable damage to cotton leaves, enabling us to control statistically for the intensity of plant damage, and ask whether plant responses differed depending on the identity of the damaging species. We first compared changes in plant peroxidase activity, gossypol gland number and density, and leaf area in response to feeding by the spider mite Tetranychus turkestani (Ugarov and Nikolski) (an herbivore) and by one of the mite's principal natural enemies, the western flower thrips Frankliniella occidentalis (Pergande) (an omnivore). Both species increased the activity of peroxidase, but when we controlled for the amount of damage, the peroxidase activity of mite-damaged plants was higher than that of thrips-damaged plants. We also found that thrips, but not spider mites, increased the density of gossypol glands in the second true leaf. In a second experiment we included an additional herbivore, the bean thrips Caliothrips fasciatus (Pergande), to see if the different responses of cotton to thrips and mite herbivory we first observed were attributable to differences in trophic function (herbivore versus omnivore) or to other differences in feeding generated by thrips versus mites. Cotton plants exhibited the same pattern of induced responses (elevated peroxidase, increased number of glands, reduced leaf area) to herbivory generated by the bean thrips (an herbivore) and western flower thrips (an omnivore), suggesting that trophic function was not a key determinant of plant response. Thrips-damaged plants again showed a significantly higher density of gossypol glands than did mite-damaged plants. Overall, our results suggest that (1) an omnivorous predator systemically induces resistance traits in cotton and (2) whereas there is evidence of taxonomic specificity (thrips versus mites), there is little support for trophic specificity (herbivorous thrips versus omnivorous thrips) in the elicitation of induced responses.     

Mesophyll conductance decreases in the wild type but not in an ABA‐deficient mutant (aba1) of Nicotiana plumbaginifolia under drought conditions

Under drought conditions, leaf photosynthesis is limited by the supply of CO₂. Drought induces production of abscisic acid (ABA), and ABA decreases stomatal conductance (g_s). Previous papers reported that the drought stress also causes the decrease in mesophyll conductance (g_m). However, the relationships between ABA content and g_m are unclear. We investigated the responses of g_m to the leaf ABA content [(ABA)_L] using an ABA‐deficient mutant, aba1, and the wild type (WT) of Nicotiana plumbaginifolia. We also measured leaf water potential (Ψ_L) because leaf hydraulics may be related to g_m. Under drought conditions, g_m decreased with the increase in (ABA)_L in WT, whereas both (ABA)_L and g_m were unchanged by the drought treatment in aba1. Exogenously applied ABA decreased g_m in both WT and aba1 in a dose‐dependent manner. Ψ_L in WT was decreased by the drought treatment to ?0.7 MPa, whereas Ψ_L in aba1 was around ?0.8 MPa even under the well‐watered conditions and unchanged by the drought treatment. From these results, we conclude that the increase in (ABA)_L is crucial for the decrease in g_m under drought conditions. We discuss possible relationships between the decrease in g_m and changes in the leaf hydraulics.     

A single muscle's multifunctional control potential of body dynamics for postural control and running

A neuromechanical approach to control requires understanding how mechanics alters the potential of neural feedback to control body dynamics. Here, we rewrite activation of individual motor units of a behaving animal to mimic the effects of neural feedback without concomitant changes in other muscles. We target a putative control muscle in the cockroach, Blaberus discoidalis (L.), and simultaneously capture limb and body dynamics through high-speed videography and a micro-accelerometer backpack. We test four neuromechanical control hypotheses. We supported the hypothesis that mechanics linearly translates neural feedback into accelerations and rotations during static postural control. However, during running, the same neural feedback produced a nonlinear acceleration control potential restricted to the vertical plane. Using this, we reject the hypothesis from previous work that this muscle acts primarily to absorb energy from the body. The conversion of the control potential is paralleled by nonlinear changes in limb kinematics, supporting the hypothesis that significant mechanical feedback filters the graded neural feedback for running control. Finally, we insert the same neural feedback signal but at different phases in the dynamics. In this context, mechanical feedback enables turning by changing the timing and direction of the accelerations produced by the graded neural feedback.     

Ecological and biomechanical insights into the evolution of gliding in mammals

Gliding has evolved independently at least six times in mammals. Multiple hypotheses have been proposed to explain the evolution of gliding. These include the evasion of predators, economical locomotion or foraging, control of landing forces, and habitat structure. Here we use a combination of comparative methods and ecological and biomechanical data collected from free-ranging animals to evaluate these hypotheses. Our comparative data suggest that the origins of gliding are often associated with shifts to low-quality diets including leaves and plant exudates. Further, data from free-ranging colugos suggest that although gliding is not more energetically economical than moving through the canopy, it is much faster, allowing shorter times of transit between foraging patches and therefore more time available to forage in a given patch. In addition to moving quickly, gliding mammals spend only a small fraction of their overall time engaged in locomotion, likely offsetting its high cost. Kinetic data for both take-off and landing suggest that selection on these behaviors could also have shaped the evolution of gliding. Glides are initiated by high-velocity leaps that are potentially effective in evading arboreal predators. Further, upon landing, the ability to control aerodynamic forces and reduce velocity prior to impact is likely key to extending distances of leaps or glides while reducing the likelihood of injury. It is unlikely that any one of these hypotheses exclusively explains the evolution of gliding, but by examining gliding in multiple groups of extant animals in ecological and biomechanical contexts, new insights into the evolution of gliding can be gained.     

Wing-dimorphism and population expansion of Pterostichus melanarius (Illiger, 1798) at small and large scales in central Alberta, Canada (Coleoptera, Carabidae, Pterostichini)

A study spanning ten years revealed changes in wing-morph ratios corroborating the hypothesis that the wing-dimorphic introduced carabid, Pterostichus melanarius Ill.,is spreading through flight, from the city of Edmonton, Canada and establishing populations in natural aspen forest of more rural areas 45-50 km to the East. Comparison of wing-morph ratios between Pterostichus melanarius and the native wing dimorphic species Agonum retractum LeConte suggests that the spatial variation in ratios for Pterostichus melanarius does not reflect underlying environmental variation, but instead the action of selective forces on this wing-dimorphic species. About ten years after its earliest detection in some rural sites the frequency of macropterous individuals in Pterostichus melanarius has decreased c. five-fold, but it is still above the level seen in European populations in which the two wing-morphs are thought to exist in equilibrium. Pterostichus melanarius is expanding its range in native aspen forest much faster than three other introduced species Clivina fossor L.), Carabus granulatus O.F. Müllerand Clivina fossor L also encountered in this study. The two Carabus species are flightless, but Carabus fossor can be dimorphic. Although these four non-native ground beetle species comprise >85% of the carabids collected at sites in urban Edmonton, activity-density of native carabids was similar across the urban-rural gradient, suggesting little direct impact of introduced species on the local abundance of native species. In a second study conducted at a smaller scale near George Lake, Alberta, macropterous individuals of Pterostichus melanarius have penetrated furthest and most rapidly into native aspen forest. Furthermore, the percentage of micropterous individuals has increased markedly in areas first colonized a decade previously. Overall, these studies support the idea that macropterous beetles in wing-d dimorphic species are important vanguards for early colonization of unexploited territory, but that flightless individuals replace the flying morph relatively rapidly once populations are established.     

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.     

Loss of the SPHF homologue Slr1768 leads to a catastrophic failure in the maintenance of thylakoid membranes in Synechocystis sp. PCC 6803

Background

In cyanobacteria the photosystems are localised to, and maintained in, specialist membranes called the thylakoids. The mechanism driving the biogenesis of the thylakoid membranes is still an open question, with only two potential biogenesis factors, Vipp1 and Alb3 currently identified.

Methodology/Principal Findings

We generated a slr1768 knockout using the pGEM T-easy vector and REDIRECT. By comparing growth and pigment content (chlorophyll a fluoresence) of the Δslr1768 mutant with the wild-type, we found that Δslr1768 has a conditional phenotype; specifically under high light conditions (130 µmol m⁻² s⁻¹) thylakoid biogenesis is disrupted leading to cell death on a scale of days. The thylakoids show considerable disruption, with loss of both structure and density, while chlorophyll a density decreases with the loss of thylakoids, although photosynthetic efficiency is unaffected. Under low light (30 µmol m⁻² s⁻¹) the phenotype is significantly reduced, with a growth rate similar to the wild-type and only a low frequency of cells with evident thylakoid disruption.

Conclusions/Significance

This is the first example of a gene that affects the maintenance of the thylakoid membranes specifically under high light, and which displays a phenotype dependent on light intensity. Our results demonstrate that Slr1768 has a leading role in acclimatisation, linking light damage with maintenance of the thylakoids.